Annotation of /FigKernelPackages/FIG.pm

Revision 1.292 - (view) (download) (as text)

1 :	efrank	1.1	package FIG;
2 :
3 :	olson	1.111	use strict;
4 :
5 :	overbeek	1.135	use Fcntl qw/:flock/; # import LOCK_* constants
6 :
7 :	olson	1.116	use POSIX;
8 :	olson	1.158	use IPC::Open2;
9 :	olson	1.116
10 :	efrank	1.1	use DBrtns;
11 :			use Sim;
12 :			use Blast;
13 :			use FIG_Config;
14 :	overbeek	1.36	use tree_utilities;
15 :	olson	1.93	use Subsystem;
16 :	olson	1.162	use SeedDas;
17 :	olson	1.183	use Construct;
18 :	parrello	1.200	use FIGRules;
19 :	parrello	1.210	use Tracer;
20 :	olson	1.260
21 :	olson	1.245	eval { require FigGFF; };
22 :	parrello	1.287	if ($@ and $ENV{USER} eq "olson") {
23 :	olson	1.260	warn $@;
24 :			}
25 :	olson	1.79
26 :			#
27 :			# Conditionally evaluate this in case its prerequisites are not available.
28 :			#
29 :
30 :			our $ClearinghouseOK = eval {
31 :			require Clearinghouse;
32 :			};
33 :	efrank	1.1
34 :	olson	1.10	use IO::Socket;
35 :
36 :	efrank	1.1	use FileHandle;
37 :
38 :			use Carp;
39 :			use Data::Dumper;
40 :	overbeek	1.25	use Time::Local;
41 :	olson	1.93	use File::Spec;
42 :	olson	1.123	use File::Copy;
43 :	olson	1.112	#
44 :			# Try to load the RPC stuff; it might fail on older versions of the software.
45 :			#
46 :			eval {
47 :			require FIGrpc;
48 :			};
49 :
50 :			my $xmlrpc_available = 1;
51 :	parrello	1.287	if ($@ ne "") {
52 :	olson	1.112	$xmlrpc_available = 0;
53 :			}
54 :
55 :	efrank	1.1
56 :	olson	1.111	use FIGAttributes;
57 :			use base 'FIGAttributes';
58 :
59 :			use vars qw(%_FunctionAttributes);
60 :
61 :			use Data::Dumper;
62 :
63 :	olson	1.124	#
64 :			# Force all new files to be all-writable.
65 :			#
66 :
67 :			umask 0;
68 :
69 :	parrello	1.210	=head1 FIG Genome Annotation System
70 :
71 :			=head2 Introduction
72 :
73 :			This is the main object for access to the SEED data store. The data store
74 :			itself is a combination of flat files and a database. The flat files can
75 :			be moved easily between systems and the database rebuilt as needed.
76 :
77 :			A reduced set of this object's functions are available via the B<SFXlate>
78 :			object. The SFXlate object uses a single database to represent all its
79 :			genomic information. It provides a much smaller capability for updating
80 :			the data, and eliminates all similarities except for bidirectional best
81 :			hits.
82 :
83 :			The key to making the FIG system work is proper configuration of the
84 :			C<FIG_Config.pm> file. This file contains names and URLs for the key
85 :			directories as well as the type and login information for the database.
86 :
87 :	parrello	1.287	FIG was designed to operate as a series of peer instances. Each instance is
88 :			updated independently by its owner, and the instances can be synchronized
89 :			using a process called a I<peer-to-peer update>. The terms
90 :			I<SEED instance> and I<peer> are used more-or-less interchangeably.
91 :
92 :			The POD documentation for this module is still in progress, and is provided
93 :			on an AS IS basis without warranty. If you have a correction and you're
94 :			not a developer, EMAIL the details to B<bruce@gigabarb.com> and I'll fold
95 :			it in.
96 :
97 :			B<NOTE>: The usage example for each method specifies whether it is static
98 :
99 :			FIG::something
100 :
101 :			or dynamic
102 :
103 :			$fig->something
104 :
105 :			If the method is static and has no parameters (C<FIG::something()>) it can
106 :			also be invoked dynamically. This is a general artifact of the
107 :			way PERL implements object-oriented programming.
108 :
109 :			=head2 Hiding/Caching in a FIG object
110 :
111 :			We save the DB handle, cache taxonomies, and put a few other odds and ends in the
112 :			FIG object. We expect users to invoke these services using the object $fig constructed
113 :			using:
114 :
115 :			use FIG;
116 :			my $fig = new FIG;
117 :
118 :			$fig is then used as the basic mechanism for accessing FIG services. It is, of course,
119 :			just a hash that is used to retain/cache data. The most commonly accessed item is the
120 :			DB filehandle, which is accessed via $self->db_handle.
121 :
122 :			We cache genus/species expansions, taxonomies, distances (very crudely estimated) estimated
123 :			between genomes, and a variety of other things.
124 :
125 :	parrello	1.210	=cut
126 :
127 :	parrello	1.287
128 :	parrello	1.210	#: Constructor FIG->new();
129 :
130 :			=head2 Public Methods
131 :
132 :			=head3 new
133 :
134 :			C<< my $fig = FIG->new(); >>
135 :
136 :			This is the constructor for a FIG object. It uses no parameters.
137 :
138 :			=cut
139 :
140 :	efrank	1.1	sub new {
141 :			my($class) = @_;
142 :
143 :	olson	1.102	#
144 :			# Check to see if we have a FIG_URL environment variable set.
145 :			# If we do, don't actually create a FIG object, but rather
146 :			# create a FIGrpc and return that as the return from this constructor.
147 :			#
148 :
149 :	parrello	1.210	if ($ENV{FIG_URL} ne "" && $xmlrpc_available) {
150 :			Trace("Creating figrpc for '$ENV{FIG_URL}'") if T(0);
151 :			my $figrpc = new FIGrpc($ENV{FIG_URL});
152 :			return $figrpc;
153 :	olson	1.102	}
154 :	parrello	1.292	# Here we have the normal case. Check for default tracing. We only do this if
155 :			# the proper parameters are present and nobody else has set up tracing yet.
156 :			if (defined($FIG_Config::trace_levels) && Tracer::Setups() == 0) {
157 :	parrello	1.287	# It's on, so we set it up. If the type is omitted, we default to WARN, which
158 :			# is the standard error output.
159 :			my $trace_type = (defined $FIG_Config::trace_type ? $FIG_Config::trace_type : "WARN");
160 :			TSetup($FIG_Config::trace_levels, $trace_type);
161 :			}
162 :			# Connect to the database, then return ourselves.
163 :	efrank	1.1	my $rdbH = new DBrtns;
164 :			bless {
165 :	parrello	1.210	_dbf => $rdbH,
166 :			}, $class;
167 :	efrank	1.1	}
168 :
169 :	parrello	1.287	=head3 db_handle
170 :
171 :			C<< my $dbh = $fig->db_handle; >>
172 :
173 :			Return the handle to the internal B<DBrtns> object. This allows direct access to
174 :			the database methods.
175 :
176 :			=cut
177 :
178 :			sub db_handle {
179 :			my($self) = @_;
180 :			return $self->{_dbf};
181 :			}
182 :
183 :	parrello	1.292
184 :			=head3 Open
185 :
186 :			C<< my $ok = FIG::Open($handle, $fileSpec, $message); >>
187 :
188 :			Open a file, translating invalid characters in the file name.
189 :
190 :			This is a general-purpose file open method that provides an easy way to deal with
191 :			invalid file name characters. It functions identically to C<Tracer::Open> with the
192 :			exception that the characters in the C<$FIG_Config::bad_chars> string will be
193 :			translated into underscores before the open takes place.
194 :
195 :			To find the file name, the method looks for a filemode character sequence and takes
196 :			everything after it, trimming spaces off either end. So, for example, in the
197 :			following strings the file name is C</usr/fig/myfile.txt>.
198 :
199 :			>>/usr/fig/myfile.txt
200 :			</usr/fig/myfile.txt
201 :			\| sort -u > /usr/fig/myfile.txt
202 :
203 :			Note that the file handle parameter has to be specified using glob syntax. To open
204 :			a file with the handle C<TMP>, you use
205 :
206 :			Open(\*TMP, "\| sort -u > /usr/fig/myfile.txt");
207 :
208 :			=over 4
209 :
210 :			=item handle
211 :
212 :			File handle. If this parameter is C<undef>, a file handle will be generated
213 :			and returned as the value of this method.
214 :
215 :			=item fileSpec
216 :
217 :			File name and mode, as per the PERL C<open> function.
218 :
219 :			=item message (optional)
220 :
221 :			Error message to use if the open fails. If omitted, a standard error message
222 :			will be generated. In either case, the error information from the file system
223 :			is appended to the message. To specify a conditional open that does not throw
224 :			an error if it fails, use C<0>.
225 :
226 :			=item RETURN
227 :
228 :			Returns the file handle assigned to the file, or C<undef> if the open failed.
229 :
230 :			=back
231 :
232 :			=cut
233 :			#: Return Type $;
234 :			sub Open {
235 :			# Get the parameters.
236 :			my ($handle, $fileSpec, $message) = @_;
237 :			# Check to see if we need to clean.
238 :			if ($FIG_Config::bad_chars) {
239 :			my ($fileName, $pos, $len) = Tracer::FindNamePart($fileSpec);
240 :			substr $fileSpec, $pos, $len, NameClean($fileName);
241 :			}
242 :			# Open the file.
243 :			my $retVal = Tracer::Open($handle, $fileSpec, $message);
244 :			# Return the result.
245 :			return $retVal;
246 :			}
247 :
248 :			=head3 OpenDir
249 :
250 :			C<< my @files = FIG::OpenDir($dirName, $filtered); >>
251 :
252 :			Open a directory and return all the file names. This function essentially performs
253 :			the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is
254 :			set to TRUE, all filenames beginning with a period (C<.>) will be filtered out of
255 :			the return list. If the directory does not open, an exception is thrown. So,
256 :			for example,
257 :
258 :			my @files = FIG::OpenDir("/Volumes/fig/contigs", 1);
259 :
260 :			is effectively the same as
261 :
262 :			opendir(TMP, "/Volumes/fig/contigs") \|\| Confess("Could not open /Volumes/fig/contigs.");
263 :			my @files = grep { $_ !~ /^\./ } readdir(TMP);
264 :
265 :			Similarly, the following code
266 :
267 :			my @files = grep { $_ =~ /^\d/ } FIG::OpenDir("/Volumes/fig/orgs");
268 :
269 :			Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and
270 :			automatically throws an error if the directory fails to open.
271 :
272 :			Unlike C<Tracer::OpenDir>, this version cleans bad characters out of the directory
273 :			name. See L</Open> for details about file name cleaning. Unlike L</Open>, however,
274 :			this method cleans the whole directory name. There is no need to scan for mode characters
275 :			or pipes.
276 :
277 :			=over 4
278 :
279 :			=item dirName
280 :
281 :			Name of the directory to open.
282 :
283 :			=item filtered
284 :
285 :			TRUE if files whose names begin with a period (C<.>) should be automatically removed
286 :			from the list, else FALSE.
287 :
288 :			=back
289 :
290 :			=cut
291 :			#: Return Type @;
292 :			sub OpenDir {
293 :			# Get the parameters.
294 :			my ($dirName, $filtered) = @_;
295 :			# Clean the directory name, if necessary.
296 :			if ($FIG_Config::bad_chars) {
297 :			$dirName = NameClean($dirName);
298 :			}
299 :			# Open and read the directory.
300 :			my @retVal = Tracer::OpenDir($dirName, $filtered);
301 :			return @retVal;
302 :			}
303 :
304 :			=head3 NameClean
305 :
306 :			C<< my $cleanName = FIG::NameClean($fileName); >>
307 :
308 :			Clean invalid characters from a file name. The characters cleaned are those found int
309 :			the C<$FIG_Config::bad_chars> configuration variable, and they will all be replaced by
310 :			underscores.
311 :
312 :			=over 4
313 :
314 :			=item fileName
315 :
316 :			File name to be cleaned.
317 :
318 :			=item RETURN
319 :
320 :			Returns the incoming file name with all of the designated characters converted to
321 :			underscores.
322 :
323 :			=back
324 :
325 :			=cut
326 :			#: Return Type $;
327 :			sub NameClean {
328 :			# Get the parameters.
329 :			my ($fileName) = @_;
330 :			# Clean the file name.
331 :			my $retVal = $fileName;
332 :			my $badChars = "[$FIG_Config::bad_chars]";
333 :			$retVal =~ s/$badChars/_/g;
334 :			# Return the result.
335 :			return $retVal;
336 :			}
337 :
338 :	parrello	1.287	=head3 cached
339 :
340 :			C<< my $x = $fig->cached($name); >>
341 :
342 :			Return a reference to a hash containing transient data. If no hash exists with the
343 :			specified name, create an empty one under that name and return it.
344 :
345 :			The idea behind this method is to allow clients to cache data in the FIG object for
346 :			later use. (For example, a method might cache feature data so that it can be
347 :			retrieved later without using the database.) This facility should be used sparingly,
348 :			since different clients may destroy each other's data if they use the same name.
349 :
350 :			=over 4
351 :
352 :			=item name
353 :
354 :			Name assigned to the cached data.
355 :
356 :			=item RETURN
357 :
358 :			Returns a reference to a hash that is permanently associated with the specified name.
359 :			If no such hash exists, an empty one will be created for the purpose.
360 :
361 :			=back
362 :
363 :			=cut
364 :
365 :			sub cached {
366 :			my($self,$what) = @_;
367 :
368 :			my $x = $self->{$what};
369 :			if (! $x) {
370 :			$x = $self->{$what} = {};
371 :			}
372 :			return $x;
373 :			}
374 :	parrello	1.210
375 :			=head3 get_system_name
376 :
377 :			C<< my $name = $fig->get_system_name; >>
378 :
379 :			Returns C<seed>, indicating that this is object is using the SEED
380 :			database. The same method on an SFXlate object will return C<sprout>.
381 :
382 :			=cut
383 :			#: Return Type $;
384 :			sub get_system_name {
385 :	olson	1.207	return "seed";
386 :	olson	1.205	}
387 :	parrello	1.210
388 :	parrello	1.287	=head3 DESTROY
389 :
390 :			The destructor releases the database handle.
391 :
392 :			=cut
393 :	olson	1.205
394 :	parrello	1.287	sub DESTROY {
395 :	efrank	1.1	my($self) = @_;
396 :			my($rdbH);
397 :
398 :	parrello	1.210	if ($rdbH = $self->db_handle) {
399 :			$rdbH->DESTROY;
400 :	efrank	1.1	}
401 :			}
402 :
403 :	parrello	1.210	=head3 delete_genomes
404 :
405 :			C<< $fig->delete_genomes(\@genomes); >>
406 :
407 :			Delete the specified genomes from the data store. This requires making
408 :			system calls to move and delete files.
409 :
410 :			=cut
411 :			#: Return Type ;
412 :	overbeek	1.7	sub delete_genomes {
413 :			my($self,$genomes) = @_;
414 :			my $tmpD = "$FIG_Config::temp/tmp.deleted.$$";
415 :			my $tmp_Data = "$FIG_Config::temp/Data.$$";
416 :
417 :			my %to_del = map { $_ => 1 } @$genomes;
418 :			open(TMP,">$tmpD") \|\| die "could not open $tmpD";
419 :
420 :			my $genome;
421 :	parrello	1.287	foreach $genome ($self->genomes) {
422 :			if (! $to_del{$genome}) {
423 :			print TMP "$genome\n";
424 :			}
425 :	overbeek	1.7	}
426 :			close(TMP);
427 :
428 :			&run("extract_genomes $tmpD $FIG_Config::data $tmp_Data");
429 :	parrello	1.200
430 :	overbeek	1.47	# &run("mv $FIG_Config::data $FIG_Config::data.deleted; mv $tmp_Data $FIG_Config::data; fig load_all; rm -rf $FIG_Config::data.deleted");
431 :	parrello	1.200
432 :			&run("mv $FIG_Config::data $FIG_Config::data.deleted");
433 :	overbeek	1.47	&run("mv $tmp_Data $FIG_Config::data");
434 :			&run("fig load_all");
435 :			&run("rm -rf $FIG_Config::data.deleted");
436 :	overbeek	1.7	}
437 :	parrello	1.200
438 :	parrello	1.210	=head3 add_genome
439 :
440 :			C<< my $ok = $fig->add_genome($genomeF); >>
441 :
442 :			Add a new genome to the data store. A genome's data is kept in a directory
443 :	parrello	1.287	by itself, underneath the main organism directory. This method essentially
444 :			moves genome data from an external directory to the main directory and
445 :			performs some indexing tasks to integrate it.
446 :	parrello	1.210
447 :			=over 4
448 :
449 :			=item genomeF
450 :
451 :	parrello	1.287	Name of the directory containing the genome files. This should be a
452 :			fully-qualified directory name. The last segment of the directory
453 :			name should be the genome ID.
454 :	parrello	1.210
455 :			=item RETURN
456 :
457 :			Returns TRUE if successful, else FALSE.
458 :
459 :			=back
460 :
461 :			=cut
462 :			#: Return Type $;
463 :	efrank	1.1	sub add_genome {
464 :			my($self,$genomeF) = @_;
465 :
466 :			my $rc = 0;
467 :	olson	1.93
468 :			my(undef, $path, $genome) = File::Spec->splitpath($genomeF);
469 :
470 :	parrello	1.287	if ($genome !~ /^\d+\.\d+$/) {
471 :			warn "Invalid genome filename $genomeF\n";
472 :			return $rc;
473 :	olson	1.93	}
474 :
475 :	parrello	1.287	if (-d $FIG_Config::organisms/$genome) {
476 :			warn "Organism already exists for $genome\n";
477 :			return $rc;
478 :	olson	1.93	}
479 :	parrello	1.200
480 :	olson	1.93
481 :			#
482 :			# We're okay, it doesn't exist.
483 :			#
484 :
485 :			my @errors = `$FIG_Config::bin/verify_genome_directory $genomeF`;
486 :
487 :	parrello	1.287	if (@errors) {
488 :			warn "Errors found while verifying genome directory $genomeF:\n";
489 :			print join("", @errors);
490 :			return $rc;
491 :	olson	1.93	}
492 :	parrello	1.200
493 :	olson	1.93	&run("cp -r $genomeF $FIG_Config::organisms");
494 :			&run("chmod -R 777 $FIG_Config::organisms/$genome");
495 :
496 :			&run("index_contigs $genome");
497 :			&run("compute_genome_counts $genome");
498 :			&run("load_features $genome");
499 :
500 :			$rc = 1;
501 :	parrello	1.287	if (-s "$FIG_Config::organisms/$genome/Features/peg/fasta") {
502 :			&run("index_translations $genome");
503 :			my @tmp = `cut -f1 $FIG_Config::organisms/$genome/Features/peg/tbl`;
504 :			chomp @tmp;
505 :			&run("cat $FIG_Config::organisms/$genome/Features/peg/fasta >> $FIG_Config::data/Global/nr");
506 :			&enqueue_similarities(\@tmp);
507 :	olson	1.93	}
508 :			if ((-s "$FIG_Config::organisms/$genome/assigned_functions") \|\|
509 :	parrello	1.287	(-d "$FIG_Config::organisms/$genome/UserModels")) {
510 :			&run("add_assertions_of_function $genome");
511 :	efrank	1.1	}
512 :	parrello	1.200
513 :	efrank	1.1	return $rc;
514 :			}
515 :
516 :	parrello	1.287	=head3 parse_genome_args
517 :
518 :			C<< my ($mode, @genomes) = FIG::parse_genome_args(@args); >>
519 :
520 :			Extract a list of genome IDs from an argument list. If the argument list is empty,
521 :			return all the genomes in the data store.
522 :
523 :			This is a function that is performed by many of the FIG command-line utilities. The
524 :			user has the option of specifying a list of specific genome IDs or specifying none
525 :			in order to get all of them. If your command requires additional arguments in the
526 :			command line, you can still use this method if you shift them out of the argument list
527 :			before calling. The $mode return value will be C<all> if the user asked for all of
528 :			the genomes or C<some> if he specified a list of IDs. This is useful to know if,
529 :			for example, we are loading a table. If we're loading everything, we can delete the
530 :			entire table; if we're only loading some genomes, we must delete them individually.
531 :
532 :			This method uses the genome directory rather than the database because it may be used
533 :			before the database is ready.
534 :
535 :			=over 4
536 :
537 :			=item args1, args2, ... argsN
538 :
539 :			List of genome IDs. If all genome IDs are to be processed, then this list should be
540 :			empty.
541 :
542 :			=item RETURN
543 :
544 :			Returns a list. The first element of the list is C<all> if the user is asking for all
545 :			the genome IDs and C<some> otherwise. The remaining elements of the list are the
546 :			desired genome IDs.
547 :
548 :			=back
549 :
550 :			=cut
551 :
552 :			sub parse_genome_args {
553 :			# Get the parameters.
554 :			my @args = @_;
555 :			# Check the mode.
556 :			my $mode = (@args > 0 ? 'some' : 'all');
557 :			# Build the return list.
558 :			my @retVal = ($mode);
559 :			# Process according to the mode.
560 :			if ($mode eq 'all') {
561 :			# We want all the genomes, so we get them from the organism directory.
562 :			my $orgdir = "$FIG_Config::organisms";
563 :			opendir( GENOMES, $orgdir ) \|\| Confess("Could not open directory $orgdir");
564 :			push @retVal, grep { $_ =~ /^\d/ } readdir( GENOMES );
565 :			closedir( GENOMES );
566 :			} else {
567 :			# We want only the genomes specified by the user.
568 :			push @retVal, @args;
569 :			}
570 :			# Return the result.
571 :			return @retVal;
572 :			}
573 :
574 :			=head3 reload_table
575 :
576 :			C<< $fig->reload_table($mode, $table, $flds, $xflds, $fileName, $keyList, $keyName); >>
577 :
578 :			Reload a database table from a sequential file. If I<$mode> is C<all>, the table
579 :			will be dropped and re-created. If I<$mode> is C<some>, the data for the individual
580 :			items in I<$keyList> will be deleted before the table is loaded. Thus, the load
581 :			process is optimized for the type of reload.
582 :
583 :			=over 4
584 :
585 :			=item mode
586 :
587 :			C<all> if we are reloading the entire table, C<some> if we are only reloading
588 :			specific entries.
589 :
590 :			=item table
591 :
592 :			Name of the table to reload.
593 :
594 :			=item flds
595 :
596 :			String defining the table columns, in SQL format. In general, this is a
597 :			comma-delimited set of field specifiers, each specifier consisting of the
598 :			field name followed by the field type and any optional qualifiers (such as
599 :			C<NOT NULL> or C<DEFAULT>); however, it can be anything that would appear
600 :			between the parentheses in a C<CREATE TABLE> statement. The order in which
601 :			the fields are specified is important, since it is presumed that is the
602 :			order in which they are appearing in the load file.
603 :
604 :			=item xflds
605 :
606 :			Reference to a hash that describes the indexes. The hash is keyed by index name.
607 :			The value is the index's field list. This is a comma-delimited list of field names
608 :			in order from most significant to least significant. If a field is to be indexed
609 :			in descending order, its name should be followed by the qualifier C<DESC>. For
610 :			example, the following I<$xflds> value will create two indexes, one for name followed
611 :			by creation date in reverse chronological order, and one for ID.
612 :
613 :			{ name_index => "name, createDate DESC", id_index => "id" }
614 :
615 :			=item fileName
616 :
617 :			Fully-qualified name of the file containing the data to load. Each line of the
618 :			file must correspond to a record, and the fields must be arranged in order and
619 :			tab-delimited.
620 :
621 :			=item keyList
622 :
623 :			Reference to a list of the IDs for the objects being reloaded. This parameter is
624 :			only used if I<$mode> is C<some>.
625 :
626 :			=item keyName (optional)
627 :
628 :			Name of the key field containing the IDs in the keylist. If omitted, C<genome> is
629 :			assumed.
630 :
631 :			=back
632 :
633 :			=cut
634 :
635 :			sub reload_table {
636 :			# Get the parameters.
637 :			my ($self, $mode, $table, $flds, $xflds, $fileName, $keyList, $keyName) = @_;
638 :			if (!defined $keyName) {
639 :			$keyName = 'genome';
640 :			}
641 :			# Get the database handler.
642 :			my $dbf = $self->{_dbf};
643 :			# If we're in ALL mode, we drop and re-create the table. Otherwise,
644 :			# we delete the obsolete genomes.
645 :			if ( $mode eq 'all') {
646 :			Trace("Recreating $table.") if T(2);
647 :			$dbf->drop_table( tbl => $table );
648 :			$dbf->create_table( tbl => $table, flds => $flds );
649 :			} else {
650 :			Trace("Clearing obsolete data from $table.") if T(2);
651 :			foreach my $key ( @{$keyList} ) {
652 :			$dbf->SQL("DELETE FROM $table WHERE ( $keyName = \'$key\' )");
653 :			}
654 :			}
655 :			# The table is now reading for loading.
656 :			Trace("Loading $table from $fileName.") if T(2);
657 :			$dbf->load_table( tbl => $table, file => $fileName );
658 :			# If we're in ALL mode, we need to build the indexes.
659 :			if ( $mode eq 'all' ) {
660 :			Trace("Creating indexes for $table.") if T(2);
661 :			# Loop through the indexes in the index hash.
662 :			for my $idxName (keys %{$xflds}) {
663 :			Trace("Creating index $idxName.") if T(3);
664 :			$dbf->create_index( idx => $idxName,
665 :			tbl => $table,
666 :			type => "btree",
667 :			flds => $xflds->{$idxName}
668 :			);
669 :			}
670 :			$dbf->vacuum_it( "$table" );
671 :			}
672 :			}
673 :
674 :	parrello	1.210	=head3 enqueue_similarities
675 :	olson	1.93
676 :	parrello	1.287	C<< FIG::enqueue_similarities(\@fids); >>
677 :
678 :			Queue the passed Feature IDs for similarity computation. The actual
679 :			computation is performed by L</create_sim_askfor_pool>. The queue is a
680 :			persistent text file in the global data directory, and this method
681 :			essentially writes new IDs on the end of it.
682 :
683 :			=over 4
684 :
685 :			=item fids
686 :
687 :			Reference to a list of feature IDs.
688 :	olson	1.93
689 :	parrello	1.287	=back
690 :	olson	1.93
691 :			=cut
692 :	parrello	1.210	#: Return Type ;
693 :	olson	1.93	sub enqueue_similarities {
694 :	efrank	1.1	my($fids) = @_;
695 :			my $fid;
696 :
697 :	olson	1.93	my $sim_q = "$FIG_Config::global/queued_similarities";
698 :
699 :			open(TMP,">>$sim_q")
700 :	parrello	1.287	\|\| die "could not open $sim_q";
701 :	olson	1.93
702 :			#
703 :			# We need to lock here so that if a computation is creating a snapshot of the
704 :			# queue, we block until it's done.
705 :			#
706 :
707 :			flock(TMP, LOCK_EX) or die "Cannot lock $sim_q\n";
708 :
709 :	parrello	1.287	foreach $fid (@$fids) {
710 :			print TMP "$fid\n";
711 :	efrank	1.1	}
712 :			close(TMP);
713 :	olson	1.10	}
714 :
715 :	olson	1.281	=head3 export_similarity_request
716 :
717 :			Creates a similarity computation request from the queued similarities and
718 :	parrello	1.287	the current NR.
719 :	olson	1.281
720 :			We keep track of the exported requests in case one gets lost.
721 :
722 :			=cut
723 :
724 :	parrello	1.287	sub export_similarity_request {
725 :	olson	1.281	my($self, $nr_file, $fasta_file) = @_;
726 :
727 :			my $req_dir = "$FIG_Config::fig/var/sim_requests";
728 :			&verify_dir("$FIG_Config::fig/var");
729 :			&verify_dir($req_dir);
730 :
731 :			$req_dir = "$req_dir/" . time;
732 :			&verify_dir($req_dir);
733 :
734 :			#
735 :			# Open all of our output files before zeroing out the sim queue, in case
736 :			# there is a problem.
737 :			#
738 :
739 :			open(my $user_fasta_fh, ">$fasta_file") or confess "Cannot open $fasta_file for writing: $!";
740 :			open(my $fasta_fh, ">$req_dir/fasta.in");
741 :
742 :			open(my $user_nr_fh, ">$nr_file") or confess "Cannot open $nr_file for writing: $!";
743 :			open(my $nr_fh, ">$req_dir/nr") or confess "Cannot open $req_dir/nr for writing: $!";
744 :
745 :			open(my $nr_read_fh, "<$FIG_Config::data/Global/nr") or die "Cannot open $FIG_Config::data/Global/nr for reading: $!";
746 :	parrello	1.287
747 :	olson	1.281	my $sim_q = "$FIG_Config::global/queued_similarities";
748 :
749 :			#
750 :			# We need to lock here so that if a computation is creating a snapshot of the
751 :			# queue, we block until it's done.
752 :			#
753 :
754 :			open(my $sim_q_lock, ">>$sim_q") or confess "could not open $sim_q";
755 :			flock($sim_q_lock, LOCK_EX) or confess "Cannot lock $sim_q\n";
756 :
757 :			#
758 :			# Everything open & locked, start copying.
759 :			#
760 :	parrello	1.287
761 :	olson	1.281	copy("$sim_q", "$req_dir/q") or confess "Copy $sim_q $req_dir/q failed: $!";
762 :	parrello	1.287
763 :	olson	1.281	my($buf);
764 :	parrello	1.287	while (1) {
765 :			my $n = read($nr_read_fh, $buf, 4096);
766 :			defined($n) or confess "Error reading nr: $!";
767 :			last unless $n;
768 :			syswrite($user_nr_fh, $buf) or confess "Error writing $nr_file: $!";
769 :			syswrite($nr_fh, $buf) or confess "Error writing $req_dir/nr: $!";
770 :	olson	1.281	}
771 :
772 :			close($nr_read_fh);
773 :			close($nr_fh);
774 :			close($user_nr_fh);
775 :
776 :			#
777 :			# We can zero out the queue and unlock now.
778 :			#
779 :
780 :			open(F, ">$sim_q") or die "Cannot open $sim_q to truncate it: $!\n";
781 :			close(F);
782 :	parrello	1.287
783 :	olson	1.281	close($sim_q_lock);
784 :
785 :			#
786 :			# Generate the fasta input from the queued ids.
787 :			#
788 :
789 :			open(my $q_fh, "<$req_dir/q");
790 :	parrello	1.287	while (my $id = <$q_fh>) {
791 :			chomp $id;
792 :	olson	1.281
793 :	parrello	1.287	my $seq = $self->get_translation($id);
794 :	olson	1.281
795 :	parrello	1.287	display_id_and_seq($id, \$seq, $user_fasta_fh);
796 :			display_id_and_seq($id, \$seq, $fasta_fh);
797 :	olson	1.281	}
798 :			close($q_fh);
799 :
800 :			close($user_fasta_fh);
801 :			close($fasta_fh);
802 :			}
803 :
804 :	parrello	1.210	=head3 create_sim_askfor_pool
805 :	olson	1.93
806 :	parrello	1.287	C<< $fig->create_sim_askfor_pool($chunk_size); >>
807 :	olson	1.93
808 :	parrello	1.287	Creates an askfor pool, which a snapshot of the current NR and similarity
809 :			queue. This process clears the old queue.
810 :	olson	1.123
811 :			The askfor pool needs to keep track of which sequences need to be
812 :			calculated, which have been handed out, etc. To simplify this task we
813 :	olson	1.279	chunk the sequences into fairly small numbers (20k characters) and
814 :	olson	1.123	allocate work on a per-chunk basis. We make use of the relational
815 :			database to keep track of chunk status as well as the seek locations
816 :			into the file of sequence data. The initial creation of the pool
817 :			involves indexing the sequence data with seek offsets and lengths and
818 :			populating the sim_askfor_index table with this information and with
819 :			initial status information.
820 :	olson	1.93
821 :	parrello	1.287	=over 4
822 :
823 :			=item chunk_size
824 :
825 :			Number of features to put into a processing chunk. The default is 15.
826 :
827 :			=back
828 :
829 :	parrello	1.200	=cut
830 :	parrello	1.210	#: Return Type $;
831 :	parrello	1.287	sub create_sim_askfor_pool {
832 :	olson	1.123	my($self, $chunk_size) = @_;
833 :
834 :	olson	1.279	$chunk_size = 20000 unless $chunk_size =~ /^\d+$/;
835 :	olson	1.93
836 :	olson	1.279	my $pool_dir = "$FIG_Config::fig/var/sim_pools";
837 :	olson	1.93	&verify_dir($pool_dir);
838 :
839 :			#
840 :			# Lock the pool directory.
841 :			#
842 :			open(my $lock, ">$pool_dir/lockfile");
843 :
844 :			flock($lock, LOCK_EX);
845 :
846 :			my $num = 0;
847 :	parrello	1.287	if (open(my $toc, "<$pool_dir/TOC")) {
848 :			while (<$toc>) {
849 :			chomp;
850 :			# print STDERR "Have toc entry $_\n";
851 :			my ($idx, $time, $str) = split(/\s+/, $_, 3);
852 :	olson	1.93
853 :	parrello	1.287	$num = max($num, $idx);
854 :			}
855 :			close($toc);
856 :	olson	1.93	}
857 :			$num++;
858 :			open(my $toc, ">>$pool_dir/TOC") or die "Cannot write $pool_dir/TOC: $!\n";
859 :
860 :			print $toc "$num ", time(), " New toc entry\n";
861 :			close($toc);
862 :
863 :	olson	1.123	my $cpool_id = sprintf "%04d", $num;
864 :			my $cpool_dir = "$pool_dir/$cpool_id";
865 :	olson	1.93
866 :			#
867 :			# All set, create the directory for this pool.
868 :			#
869 :
870 :			&verify_dir($cpool_dir);
871 :
872 :			#
873 :			# Now we can copy the nr and sim queue here.
874 :			# Do this stuff inside an eval so we can clean up
875 :			# the lockfile.
876 :			#
877 :
878 :			eval {
879 :	parrello	1.287	my $sim_q = "$FIG_Config::global/queued_similarities";
880 :	olson	1.93
881 :	parrello	1.287	copy("$sim_q", "$cpool_dir/q");
882 :			copy("$FIG_Config::data/Global/nr", "$cpool_dir/nr");
883 :	olson	1.93
884 :	parrello	1.287	open(F, ">$sim_q") or die "Cannot open $sim_q to truncate it: $!\n";
885 :			close(F);
886 :	olson	1.93	};
887 :	parrello	1.200
888 :	olson	1.93	unlink("$pool_dir/lockfile");
889 :			close($lock);
890 :	olson	1.123
891 :			#
892 :			# We've created our pool; we can now run the formatdb and
893 :			# extract the sequences for the blast run.
894 :			#
895 :	parrello	1.287	my $child_pid = $self->run_in_background(
896 :			sub {
897 :			#
898 :			# Need to close db or there's all sorts of trouble.
899 :			#
900 :
901 :			my $cmd = "$FIG_Config::ext_bin/formatdb -i $cpool_dir/nr -p T -l $cpool_dir/formatdb.log";
902 :			print "Will run '$cmd'\n";
903 :			&run($cmd);
904 :			print "finished. Logfile:\n";
905 :			print &FIG::file_read("$cpool_dir/formatdb.log");
906 :			unlink("$cpool_dir/formatdb.pid");
907 :			});
908 :	olson	1.279	warn "Running formatdb in background job $child_pid\n";
909 :	olson	1.123	open(FPID, ">$cpool_dir/formatdb.pid");
910 :			print FPID "$child_pid\n";
911 :			close(FPID);
912 :
913 :			my $db = $self->db_handle();
914 :	parrello	1.287	if (!$db->table_exists("sim_queue")) {
915 :			$db->create_table(tbl => "sim_queue",
916 :			flds => "qid varchar(32), chunk_id INTEGER, seek INTEGER, len INTEGER, " .
917 :			"assigned BOOL, finished BOOL, output_file varchar(255), " .
918 :			"assignment_expires INTEGER, worker_info varchar(255)"
919 :			);
920 :	olson	1.123	}
921 :
922 :			#
923 :			# Write the fasta input file. Keep track of how many have been written,
924 :			# and write seek info into the database as appropriate.
925 :			#
926 :
927 :			open(my $seq_fh, ">$cpool_dir/fasta.in");
928 :
929 :			my($chunk_idx, $chunk_begin, $seq_idx);
930 :
931 :	olson	1.279	my $cur_size = 0;
932 :
933 :	olson	1.123	$chunk_idx = 0;
934 :			$chunk_begin = 0;
935 :			$seq_idx = 0;
936 :
937 :			my(@seeks);
938 :
939 :	olson	1.279	my $tmpfile = "$FIG_Config::temp/simseek.$$";
940 :			open(my $tmpfh, ">$tmpfile") or confess "Cannot open tmpfile $tmpfile: $!";
941 :
942 :	olson	1.123	open(my $q_fh, "<$cpool_dir/q");
943 :	parrello	1.287	while (my $id = <$q_fh>) {
944 :			chomp $id;
945 :	olson	1.123
946 :	parrello	1.287	my $seq = $self->get_translation($id);
947 :	olson	1.123
948 :	parrello	1.287	#
949 :			# check if we're at the beginning of a chunk
950 :			#
951 :
952 :			print $seq_fh ">$id\n$seq\n";
953 :
954 :			#
955 :			# Check if we're at the end of a chunk
956 :			#
957 :
958 :			$cur_size += length($seq);
959 :			if ($cur_size >= $chunk_size) {
960 :			my $chunk_end = tell($seq_fh);
961 :			my $chunk_len = $chunk_end - $chunk_begin;
962 :
963 :			push(@seeks, [$cpool_id, $chunk_idx, $chunk_begin, $chunk_len]);
964 :			print $tmpfh join("\t", $cpool_id, $chunk_idx, $chunk_begin, $chunk_len, 'FALSE', 'FALSE'), "\n";
965 :			$chunk_idx++;
966 :			$chunk_begin = $chunk_end;
967 :			$cur_size = 0;
968 :			}
969 :			$seq_idx++;
970 :	olson	1.123	}
971 :
972 :	parrello	1.287	if ($cur_size > 0) {
973 :			my $chunk_end = tell($seq_fh);
974 :			my $chunk_len = $chunk_end - $chunk_begin;
975 :	olson	1.123
976 :	parrello	1.287	print $tmpfh join("\t", $cpool_id, $chunk_idx, $chunk_begin, $chunk_len, 'FALSE', 'FALSE'), "\n";
977 :			push(@seeks, [$cpool_id, $chunk_idx, $chunk_begin, $chunk_len]);
978 :	olson	1.123	}
979 :
980 :			close($q_fh);
981 :			close($seq_fh);
982 :	olson	1.279	close($tmpfh);
983 :	olson	1.123
984 :	olson	1.279	warn "Write seqs from $tmpfile\n";
985 :	olson	1.123
986 :	olson	1.279	$self->db_handle->load_table(tbl => 'sim_queue',
987 :			file => $tmpfile);
988 :	parrello	1.200
989 :	olson	1.279	unlink($tmpfile);
990 :	parrello	1.287
991 :	olson	1.279	# for my $seek (@seeks)
992 :			# {
993 :			# my($cpool_id, $chunk_idx, $chunk_begin, $chunk_len) = @$seek;
994 :
995 :			# $db->SQL("insert into sim_queue (qid, chunk_id, seek, len, assigned, finished) " .
996 :			# "values('$cpool_id', $chunk_idx, $chunk_begin, $chunk_len, FALSE, FALSE)");
997 :			# }
998 :	parrello	1.200
999 :	olson	1.123	return $cpool_id;
1000 :			}
1001 :
1002 :	parrello	1.210	#=head3 get_sim_queue
1003 :			#
1004 :			#usage: get_sim_queue($pool_id, $all_sims)
1005 :			#
1006 :			#Returns the sims in the given pool. If $all_sims is true, return the entire queue. Otherwise,
1007 :			#just return the sims awaiting processing.
1008 :			#
1009 :			#=cut
1010 :	olson	1.123
1011 :	parrello	1.287	sub get_sim_queue {
1012 :	olson	1.123	my($self, $pool_id, $all_sims) = @_;
1013 :	olson	1.279	}
1014 :
1015 :	parrello	1.287	=head3 get_sim_work
1016 :	olson	1.279
1017 :	parrello	1.287	C<< my ($nrPath, $fasta) = $fig->get_sim_work(); >>
1018 :	olson	1.279
1019 :			Get the next piece of sim computation work to be performed. Returned are
1020 :			the path to the NR and a string containing the fasta data.
1021 :
1022 :			=cut
1023 :
1024 :	parrello	1.287	sub get_sim_work {
1025 :
1026 :			my ($self) = @_;
1027 :	olson	1.279
1028 :			#
1029 :			# For now, just don't care about order of data that we get back.
1030 :			#
1031 :
1032 :			my $db = $self->db_handle();
1033 :			my $lock = FIG::SimLock->new;
1034 :
1035 :			my $work = $db->SQL(qq(SELECT qid, chunk_id, seek, len
1036 :			FROM sim_queue
1037 :			WHERE not finished
1038 :			LIMIT 1));
1039 :			print "Got work ", Dumper($work), "\n";
1040 :
1041 :	parrello	1.287	if (not $work or @$work == 0) {
1042 :			return undef;
1043 :	olson	1.279	}
1044 :
1045 :			my($cpool_id, $chunk_id, $seek, $len) = @{$work->[0]};
1046 :	parrello	1.287
1047 :	olson	1.279	my $pool_dir = "$FIG_Config::fig/var/sim_pools";
1048 :			my $cpool_dir = "$pool_dir/$cpool_id";
1049 :
1050 :			my $nr = "$cpool_dir/nr";
1051 :			open(my $fh, "<$cpool_dir/fasta.in");
1052 :			seek($fh, $seek, 0);
1053 :			my $fasta;
1054 :			read($fh, $fasta, $len);
1055 :
1056 :			return($cpool_id, $chunk_id, $nr, $fasta, "$cpool_dir/out.$chunk_id");
1057 :			}
1058 :
1059 :			=head3 sim_work_done
1060 :
1061 :	parrello	1.287	C<< $fig->sim_work_done($pool_id, $chunk_id, $out_file); >>
1062 :
1063 :	olson	1.279	Declare that the work in pool_id/chunk_id has been completed, and output written
1064 :			to the pool directory (get_sim_work gave it the path).
1065 :
1066 :	parrello	1.287	=over 4
1067 :
1068 :			=item pool_id
1069 :
1070 :			The ID number of the pool containing the work that just completed.
1071 :
1072 :			=item chunk_id
1073 :
1074 :			The ID number of the chunk completed.
1075 :
1076 :			=item out_file
1077 :
1078 :			The file into which the work was placed.
1079 :
1080 :			=back
1081 :
1082 :	olson	1.279	=cut
1083 :
1084 :	parrello	1.287	sub sim_work_done {
1085 :			my ($self, $pool_id, $chunk_id, $out_file) = @_;
1086 :	olson	1.279
1087 :	parrello	1.287	if (! -f $out_file) {
1088 :			Confess("sim_work_done: output file $out_file does not exist");
1089 :	olson	1.279	}
1090 :
1091 :			my $db = $self->db_handle();
1092 :			my $lock = FIG::SimLock->new;
1093 :
1094 :			my $dbh = $db->{_dbh};
1095 :
1096 :			my $rows = $dbh->do(qq(UPDATE sim_queue
1097 :			SET finished = TRUE, output_file = ?
1098 :			WHERE qid = ? and chunk_id = ?), undef, $out_file, $pool_id, $chunk_id);
1099 :	parrello	1.287	if ($rows != 1) {
1100 :			if ($dbh->errstr) {
1101 :			Confess("Update not able to set finished=TRUE: ", $dbh->errstr);
1102 :			} else {
1103 :			Confess("Update not able to set finished=TRUE");
1104 :			}
1105 :	olson	1.279	}
1106 :			#
1107 :			# Determine if this was the last piece of work for this pool. If so, we can
1108 :	parrello	1.287	# schedule the postprocessing work.
1109 :	olson	1.279	#
1110 :			# Note we're still holding the lock.
1111 :			#
1112 :
1113 :			my $out = $db->SQL(qq(SELECT chunk_id
1114 :			FROM sim_queue
1115 :			WHERE qid = ? AND not finished), undef, $pool_id);
1116 :	parrello	1.287	if (@$out == 0) {
1117 :			#
1118 :			# Pool is done.
1119 :			#
1120 :			$self->schedule_sim_pool_postprocessing($pool_id);
1121 :	olson	1.279	}
1122 :	olson	1.123	}
1123 :
1124 :	olson	1.279	=head3 schedule_sim_pool_postprocessing
1125 :
1126 :	parrello	1.287	C<< $fig->schedule_sim_pool_postprocessing($pool_id); >>
1127 :
1128 :			Schedule a job to do the similarity postprocessing for the specified pool.
1129 :
1130 :			=over 4
1131 :
1132 :			=item pool_id
1133 :
1134 :			ID of the pool whose similarity postprocessing needs to be scheduled.
1135 :	olson	1.279
1136 :	parrello	1.287	=back
1137 :	olson	1.279
1138 :			=cut
1139 :
1140 :	parrello	1.287	sub schedule_sim_pool_postprocessing {
1141 :
1142 :	olson	1.279	my($self, $pool_id) = @_;
1143 :
1144 :			my $pool_dir = "$FIG_Config::fig/var/sim_pools";
1145 :			my $cpool_dir = "$pool_dir/$pool_id";
1146 :
1147 :			my $js = JobScheduler->new();
1148 :			my $job = $js->job_create();
1149 :
1150 :			my $spath = $job->get_script_path();
1151 :			open(my $sfh, ">$spath");
1152 :			print $sfh <<END;
1153 :			#!/bin/sh
1154 :			. $FIG_Config::fig_disk/config/fig-user-env.sh
1155 :			$FIG_Config::bin/postprocess_computed_sims $pool_id
1156 :			END
1157 :
1158 :			close($sfh);
1159 :			chmod(0775, $spath);
1160 :
1161 :			#
1162 :			# Write the job ID to the subsystem queue dir.
1163 :			#
1164 :
1165 :			open(J, ">$cpool_dir/postprocess_jobid");
1166 :			print J $job->get_id(), "\n";
1167 :			close(J);
1168 :
1169 :			$job->enqueue();
1170 :			}
1171 :
1172 :			=head3 postprocess_computed_sims
1173 :
1174 :	parrello	1.287	C<< $fig->postprocess_computed_sims($pool_id); >>
1175 :
1176 :			Set up to reduce, reformat, and split the similarities in a given pool. We build
1177 :			a pipe to this pipeline:
1178 :	olson	1.279
1179 :			reduce_sims peg.synonyms 300 \| reformat_sims nr \| split_sims dest prefix
1180 :
1181 :	parrello	1.287	Then we put the new sims in the pool directory, and then copy to NewSims.
1182 :
1183 :			=over 4
1184 :
1185 :			=item pool_id
1186 :
1187 :			ID of the pool whose similarities are to be post-processed.
1188 :
1189 :			=back
1190 :	olson	1.279
1191 :			=cut
1192 :
1193 :	parrello	1.287	sub postprocess_computed_sims {
1194 :	olson	1.279	my($self, $pool_id) = @_;
1195 :
1196 :			#
1197 :			# We don't lock here because the job is already done, and we
1198 :			# shouldn't (ha, ha) ever postprocess twice.
1199 :			#
1200 :
1201 :			my $pool_dir = "$FIG_Config::fig/var/sim_pools";
1202 :			my $cpool_dir = "$pool_dir/$pool_id";
1203 :
1204 :			my $sim_dir = "$cpool_dir/NewSims";
1205 :			&verify_dir($sim_dir);
1206 :
1207 :			#
1208 :			# Open the processing pipeline.
1209 :			#
1210 :
1211 :			my $reduce = "$FIG_Config::bin/reduce_sims $FIG_Config::global/peg.synonyms 300";
1212 :			my $reformat = "$FIG_Config::bin/reformat_sims $cpool_dir/nr";
1213 :			my $split = "$FIG_Config::bin/split_sims $sim_dir sims.$pool_id";
1214 :			open(my $process, "\| $reduce \| $reformat \| $split");
1215 :
1216 :			#
1217 :			# Iterate over all the sims files, taken from the database.
1218 :			#
1219 :
1220 :			my $dbh = $self->db_handle()->{_dbh};
1221 :			my $files = $dbh->selectcol_arrayref(qq(SELECT output_file
1222 :			FROM sim_queue
1223 :			WHERE qid = ? and output_file IS NOT NULL
1224 :			ORDER BY chunk_id), undef, $pool_id);
1225 :	parrello	1.287	for my $file (@$files) {
1226 :			my $buf;
1227 :			open(my $fh, "<$file") or confess "Cannot sim input file $file: $!";
1228 :			while (read($fh, $buf, 4096)) {
1229 :			print $process $buf;
1230 :			}
1231 :			close($fh);
1232 :	olson	1.279	}
1233 :			my $res = close($process);
1234 :	parrello	1.287	if (!$res) {
1235 :			if ($!) {
1236 :			confess "Error closing process pipeline: $!";
1237 :			} else {
1238 :			confess "Process pipeline exited with status $?";
1239 :			}
1240 :	olson	1.279	}
1241 :
1242 :			#
1243 :			# If we got here, it worked. Copy the new sims files over to NewSims.
1244 :			#
1245 :
1246 :			opendir(my $simdh, $sim_dir) or confess "Cannot open $sim_dir: $!";
1247 :			my @new_sims = grep { $_ !~ /^\./ } readdir($simdh);
1248 :			closedir($simdh);
1249 :
1250 :			&verify_dir("$FIG_Config::data/NewSims");
1251 :
1252 :	parrello	1.287	for my $sim_file (@new_sims) {
1253 :			my $target = "$FIG_Config::data/NewSims/$sim_file";
1254 :			if (-s $target) {
1255 :			Confess("$target already exists");
1256 :			}
1257 :			print "copying sim file $sim_file\n";
1258 :			&FIG::run("cp $sim_dir/$sim_file $target");
1259 :			&FIG::run("$FIG_Config::bin/index_sims $target");
1260 :	olson	1.279	}
1261 :			}
1262 :
1263 :	parrello	1.210	=head3 get_active_sim_pools
1264 :	olson	1.123
1265 :	parrello	1.287	C<< @pools = $fig->get_active_sim_pools(); >>
1266 :	olson	1.123
1267 :	parrello	1.287	Return a list of the pool IDs for the sim processing queues that have
1268 :			entries awaiting computation.
1269 :	olson	1.123
1270 :			=cut
1271 :	parrello	1.210	#: Return Type @;
1272 :	parrello	1.287	sub get_active_sim_pools {
1273 :	olson	1.123	my($self) = @_;
1274 :
1275 :			my $dbh = $self->db_handle();
1276 :
1277 :			my $res = $dbh->SQL("select distinct qid from sim_queue where not finished");
1278 :			return undef unless $res;
1279 :
1280 :			return map { $_->[0] } @$res;
1281 :			}
1282 :
1283 :	parrello	1.210	=head3 get_sim_pool_info
1284 :	olson	1.123
1285 :	parrello	1.287	C<< my ($total_entries, $n_finished, $n_assigned, $n_unassigned) = $fig->get_sim_pool_info($pool_id); >>
1286 :
1287 :			Return information about the given sim pool.
1288 :
1289 :			=over 4
1290 :
1291 :			=item pool_id
1292 :
1293 :			Pool ID of the similarity processing queue whose information is desired.
1294 :
1295 :			=item RETURN
1296 :
1297 :			Returns a four-element list. The first is the number of features in the
1298 :			queue; the second is the number of features that have been processed; the
1299 :			third is the number of features that have been assigned to a
1300 :			processor, and the fourth is the number of features left over.
1301 :	olson	1.123
1302 :	parrello	1.287	=back
1303 :	olson	1.123
1304 :			=cut
1305 :	parrello	1.210	#: Return Type @;
1306 :	parrello	1.287	sub get_sim_pool_info {
1307 :
1308 :	olson	1.123	my($self, $pool_id) = @_;
1309 :			my($dbh, $res, $total_entries, $n_finished, $n_assigned, $n_unassigned);
1310 :
1311 :			$dbh = $self->db_handle();
1312 :
1313 :			$res = $dbh->SQL("select count(chunk_id) from sim_queue where qid = '$pool_id'");
1314 :	parrello	1.200	$total_entries = $res->[0]->[0];
1315 :	olson	1.123
1316 :			$res = $dbh->SQL("select count(chunk_id) from sim_queue where qid = '$pool_id' and finished");
1317 :			$n_finished = $res->[0]->[0];
1318 :
1319 :			$res = $dbh->SQL("select count(chunk_id) from sim_queue where qid = '$pool_id' and assigned and not finished");
1320 :			$n_assigned = $res->[0]->[0];
1321 :
1322 :			$res = $dbh->SQL("select count(chunk_id) from sim_queue where qid = '$pool_id' and not finished and not assigned");
1323 :			$n_unassigned = $res->[0]->[0];
1324 :
1325 :			return ($total_entries, $n_finished, $n_assigned, $n_unassigned);
1326 :	olson	1.93	}
1327 :
1328 :	parrello	1.210	#=head3 get_sim_chunk
1329 :			#
1330 :			#usage: get_sim_chunk($n_seqs, $worker_id)
1331 :			#
1332 :			#Returns a chunk of $n_seqs of work.
1333 :			#
1334 :			#From Ross, about how sims are processed:
1335 :			#
1336 :			#Here is how I process them:
1337 :			#
1338 :			#
1339 :			# bash$ cd /Volumes/seed/olson/Sims/June22.out
1340 :			# bash$ for i in really*
1341 :			# > do
1342 :			# > cat < $i >> /Volumes/laptop/new.sims
1343 :			# > done
1344 :			#
1345 :			#
1346 :			#Then, I need to "reformat" them by adding to columns to each one
1347 :			# and split the result into files of about 3M each This I do using
1348 :			#
1349 :			#reduce_sims /Volumes/laptop/NR/NewNR/peg.synonyms.june21 300 < /Volumes/laptop/new.sims \|
1350 :			# reformat_sims /Volumes/laptop/NR/NewNR/checked.nr.june21 > /Volumes/laptop/reformated.sims
1351 :			#rm /Volumes/laptop/new.sims
1352 :			#split_sims /Volumes/laptop/NewSims sims.june24 reformated.sims
1353 :			#rm reformatted.sims
1354 :			#
1355 :			#=cut
1356 :	olson	1.93
1357 :	parrello	1.287	sub get_sim_chunk {
1358 :	parrello	1.210	my($self, $n_seqs, $worker_id) = @_;
1359 :			}
1360 :	olson	1.123
1361 :	parrello	1.210	=head3 get_local_hostname
1362 :	parrello	1.200
1363 :	parrello	1.287	C<< my $result = FIG::get_local_hostname(); >>
1364 :
1365 :			Return the local host name for the current processor. The name may be
1366 :			stored in a configuration file, or we may have to get it from the
1367 :			operating system.
1368 :	olson	1.123
1369 :	olson	1.93	=cut
1370 :	parrello	1.213	#: Return Type $;
1371 :	olson	1.10	sub get_local_hostname {
1372 :	olson	1.52
1373 :			#
1374 :			# See if there is a FIGdisk/config/hostname file. If there
1375 :			# is, force the hostname to be that.
1376 :			#
1377 :
1378 :			my $hostfile = "$FIG_Config::fig_disk/config/hostname";
1379 :	parrello	1.287	if (-f $hostfile) {
1380 :			my $fh;
1381 :			if (open($fh, $hostfile)) {
1382 :			my $hostname = <$fh>;
1383 :			chomp($hostname);
1384 :			return $hostname;
1385 :			}
1386 :	olson	1.52	}
1387 :	parrello	1.200
1388 :	olson	1.10	#
1389 :			# First check to see if we our hostname is correct.
1390 :			#
1391 :			# Map it to an IP address, and try to bind to that ip.
1392 :			#
1393 :
1394 :			my $tcp = getprotobyname('tcp');
1395 :	parrello	1.200
1396 :	olson	1.10	my $hostname = `hostname`;
1397 :	golsen	1.44	chomp($hostname);
1398 :	olson	1.10
1399 :			my @hostent = gethostbyname($hostname);
1400 :
1401 :	parrello	1.287	if (@hostent > 0) {
1402 :			my $sock;
1403 :			my $ip = $hostent[4];
1404 :
1405 :			socket($sock, PF_INET, SOCK_STREAM, $tcp);
1406 :			if (bind($sock, sockaddr_in(0, $ip))) {
1407 :			#
1408 :			# It worked. Reverse-map back to a hopefully fqdn.
1409 :			#
1410 :
1411 :			my @rev = gethostbyaddr($ip, AF_INET);
1412 :			if (@rev > 0) {
1413 :			my $host = $rev[0];
1414 :			#
1415 :			# Check to see if we have a FQDN.
1416 :			#
1417 :
1418 :			if ($host =~ /\./) {
1419 :			#
1420 :			# Good.
1421 :			#
1422 :			return $host;
1423 :			} else {
1424 :			#
1425 :			# We didn't get a fqdn; bail and return the IP address.
1426 :			#
1427 :			return get_hostname_by_adapter()
1428 :			}
1429 :			} else {
1430 :			return inet_ntoa($ip);
1431 :			}
1432 :			} else {
1433 :			#
1434 :			# Our hostname must be wrong; we can't bind to the IP
1435 :			# address it maps to.
1436 :			# Return the name associated with the adapter.
1437 :			#
1438 :			return get_hostname_by_adapter()
1439 :			}
1440 :			} else {
1441 :			#
1442 :			# Our hostname isn't known to DNS. This isn't good.
1443 :			# Return the name associated with the adapter.
1444 :			#
1445 :			return get_hostname_by_adapter()
1446 :			}
1447 :			}
1448 :
1449 :			=head3 get_hostname_by_adapter
1450 :	parrello	1.200
1451 :	parrello	1.287	C<< my $name = FIG::get_hostname_by_adapter(); >>
1452 :	olson	1.10
1453 :	parrello	1.287	Return the local host name for the current network environment.
1454 :	parrello	1.213
1455 :			=cut
1456 :			#: Return Type $;
1457 :	olson	1.10	sub get_hostname_by_adapter {
1458 :			#
1459 :			# Attempt to determine our local hostname based on the
1460 :			# network environment.
1461 :			#
1462 :			# This implementation reads the routing table for the default route.
1463 :			# We then look at the interface config for the interface that holds the default.
1464 :			#
1465 :			#
1466 :			# Linux routing table:
1467 :			# [olson@yips 0.0.0]$ netstat -rn
1468 :			# Kernel IP routing table
1469 :			# Destination Gateway Genmask Flags MSS Window irtt Iface
1470 :			# 140.221.34.32 0.0.0.0 255.255.255.224 U 0 0 0 eth0
1471 :			# 169.254.0.0 0.0.0.0 255.255.0.0 U 0 0 0 eth0
1472 :			# 127.0.0.0 0.0.0.0 255.0.0.0 U 0 0 0 lo
1473 :			# 0.0.0.0 140.221.34.61 0.0.0.0 UG 0 0 0 eth0
1474 :	parrello	1.200	#
1475 :	olson	1.10	# Mac routing table:
1476 :	parrello	1.200	#
1477 :	olson	1.10	# bash-2.05a$ netstat -rn
1478 :			# Routing tables
1479 :	parrello	1.200	#
1480 :	olson	1.10	# Internet:
1481 :			# Destination Gateway Flags Refs Use Netif Expire
1482 :			# default 140.221.11.253 UGSc 12 120 en0
1483 :			# 127.0.0.1 127.0.0.1 UH 16 8415486 lo0
1484 :			# 140.221.8/22 link#4 UCS 12 0 en0
1485 :			# 140.221.8.78 0:6:5b:f:51:c4 UHLW 0 183 en0 408
1486 :			# 140.221.8.191 0:3:93:84:ab:e8 UHLW 0 92 en0 622
1487 :			# 140.221.8.198 0:e0:98:8e:36:e2 UHLW 0 5 en0 691
1488 :			# 140.221.9.6 0:6:5b:f:51:d6 UHLW 1 63 en0 1197
1489 :			# 140.221.10.135 0:d0:59:34:26:34 UHLW 2 2134 en0 1199
1490 :			# 140.221.10.152 0:30:1b:b0:ec:dd UHLW 1 137 en0 1122
1491 :			# 140.221.10.153 127.0.0.1 UHS 0 0 lo0
1492 :			# 140.221.11.37 0:9:6b:53:4e:4b UHLW 1 624 en0 1136
1493 :			# 140.221.11.103 0:30:48:22:59:e6 UHLW 3 973 en0 1016
1494 :			# 140.221.11.224 0:a:95:6f:7:10 UHLW 1 1 en0 605
1495 :			# 140.221.11.237 0:1:30:b8:80:c0 UHLW 0 0 en0 1158
1496 :			# 140.221.11.250 0:1:30:3:1:0 UHLW 0 0 en0 1141
1497 :			# 140.221.11.253 0:d0:3:e:70:a UHLW 13 0 en0 1199
1498 :			# 169.254 link#4 UCS 0 0 en0
1499 :	parrello	1.200	#
1500 :	olson	1.10	# Internet6:
1501 :			# Destination Gateway Flags Netif Expire
1502 :			# UH lo0
1503 :			# fe80::%lo0/64 Uc lo0
1504 :			# link#1 UHL lo0
1505 :			# fe80::%en0/64 link#4 UC en0
1506 :			# 0:a:95:a8:26:68 UHL lo0
1507 :			# ff01::/32 U lo0
1508 :			# ff02::%lo0/32 UC lo0
1509 :			# ff02::%en0/32 link#4 UC en0
1510 :
1511 :			my($fh);
1512 :
1513 :	parrello	1.287	if (!open($fh, "netstat -rn \|")) {
1514 :			warn "Cannot run netstat to determine local IP address\n";
1515 :			return "localhost";
1516 :	olson	1.10	}
1517 :
1518 :			my $interface_name;
1519 :	parrello	1.200
1520 :	parrello	1.287	while (<$fh>) {
1521 :			my @cols = split();
1522 :	olson	1.10
1523 :	parrello	1.287	if ($cols[0] eq "default" \|\| $cols[0] eq "0.0.0.0") {
1524 :			$interface_name = $cols[$#cols];
1525 :			}
1526 :	olson	1.10	}
1527 :			close($fh);
1528 :	parrello	1.200
1529 :	olson	1.11	# print "Default route on $interface_name\n";
1530 :	olson	1.10
1531 :			#
1532 :			# Find ifconfig.
1533 :			#
1534 :
1535 :			my $ifconfig;
1536 :
1537 :	parrello	1.287	for my $dir ((split(":", $ENV{PATH}), "/sbin", "/usr/sbin")) {
1538 :			if (-x "$dir/ifconfig") {
1539 :			$ifconfig = "$dir/ifconfig";
1540 :			last;
1541 :			}
1542 :	olson	1.10	}
1543 :
1544 :	parrello	1.287	if ($ifconfig eq "") {
1545 :			warn "Ifconfig not found\n";
1546 :			return "localhost";
1547 :	olson	1.10	}
1548 :	olson	1.11	# print "Foudn $ifconfig\n";
1549 :	olson	1.10
1550 :	parrello	1.287	if (!open($fh, "$ifconfig $interface_name \|")) {
1551 :			warn "Could not run $ifconfig: $!\n";
1552 :			return "localhost";
1553 :	olson	1.10	}
1554 :
1555 :			my $ip;
1556 :	parrello	1.287	while (<$fh>) {
1557 :			#
1558 :			# Mac:
1559 :			# inet 140.221.10.153 netmask 0xfffffc00 broadcast 140.221.11.255
1560 :			# Linux:
1561 :			# inet addr:140.221.34.37 Bcast:140.221.34.63 Mask:255.255.255.224
1562 :			#
1563 :
1564 :			chomp;
1565 :			s/^\s*//;
1566 :
1567 :			# print "Have '$_'\n";
1568 :			if (/inet\s+addr:(\d+\.\d+\.\d+\.\d+)\s+/) {
1569 :			#
1570 :			# Linux hit.
1571 :			#
1572 :			$ip = $1;
1573 :			# print "Got linux $ip\n";
1574 :			last;
1575 :			} elsif (/inet\s+(\d+\.\d+\.\d+\.\d+)\s+/) {
1576 :			#
1577 :			# Mac hit.
1578 :			#
1579 :			$ip = $1;
1580 :			# print "Got mac $ip\n";
1581 :			last;
1582 :			}
1583 :	olson	1.10	}
1584 :			close($fh);
1585 :
1586 :	parrello	1.287	if ($ip eq "") {
1587 :			warn "Didn't find an IP\n";
1588 :			return "localhost";
1589 :	olson	1.10	}
1590 :
1591 :			return $ip;
1592 :	efrank	1.1	}
1593 :
1594 :	parrello	1.213	=head3 get_seed_id
1595 :
1596 :	parrello	1.287	C<< my $id = FIG::get_seed_id(); >>
1597 :
1598 :			Return the Universally Unique ID for this SEED instance. If one
1599 :			does not exist, it will be created.
1600 :	parrello	1.213
1601 :			=cut
1602 :			#: Return type $;
1603 :	olson	1.38	sub get_seed_id {
1604 :			#
1605 :			# Retrieve the seed identifer from FIGdisk/config/seed_id.
1606 :			#
1607 :			# If it's not there, create one, and make it readonly.
1608 :			#
1609 :			my $id;
1610 :			my $id_file = "$FIG_Config::fig_disk/config/seed_id";
1611 :	parrello	1.287	if (! -f $id_file) {
1612 :			my $newid = `uuidgen`;
1613 :			if (!$newid) {
1614 :			die "Cannot run uuidgen: $!";
1615 :			}
1616 :	olson	1.38
1617 :	parrello	1.287	chomp($newid);
1618 :			my $fh = new FileHandle(">$id_file");
1619 :			if (!$fh) {
1620 :			die "error creating $id_file: $!";
1621 :			}
1622 :			print $fh "$newid\n";
1623 :			$fh->close();
1624 :			chmod(0444, $id_file);
1625 :	olson	1.38	}
1626 :			my $fh = new FileHandle("<$id_file");
1627 :			$id = <$fh>;
1628 :			chomp($id);
1629 :			return $id;
1630 :			}
1631 :
1632 :	parrello	1.287	=head3 get_release_info
1633 :	olson	1.155
1634 :	parrello	1.287	C<< my ($name, $id, $inst, $email, $parent_id, $description) = FIG::get_release_info(); >>
1635 :	olson	1.155
1636 :	parrello	1.287	Return the current data release information..
1637 :	olson	1.195
1638 :			The release info comes from the file FIG/Data/RELEASE. It is formatted as:
1639 :
1640 :	parrello	1.287	<release-name>
1641 :			<unique id>
1642 :			<institution>
1643 :			<contact email>
1644 :			<unique id of data release this release derived from>
1645 :			<description>
1646 :	olson	1.195
1647 :			For instance:
1648 :
1649 :	parrello	1.287	-----
1650 :			SEED Data Release, 09/15/2004.
1651 :			4148208C-1DF2-11D9-8417-000A95D52EF6
1652 :			ANL/FIG
1653 :			olson@mcs.anl.gov
1654 :
1655 :			Test release.
1656 :			-----
1657 :	olson	1.195
1658 :			If no RELEASE file exists, this routine will create one with a new unique ID. This
1659 :			lets a peer optimize the data transfer by being able to cache ID translations
1660 :			from this instance.
1661 :	olson	1.155
1662 :			=cut
1663 :	parrello	1.213	#: Return Type @;
1664 :	parrello	1.287	sub get_release_info {
1665 :	olson	1.196	my($fig, $no_create) = @_;
1666 :	olson	1.195
1667 :			my $rel_file = "$FIG_Config::data/RELEASE";
1668 :
1669 :	parrello	1.287	if (! -f $rel_file and !$no_create) {
1670 :	olson	1.195	#
1671 :			# Create a new one.
1672 :			#
1673 :
1674 :	parrello	1.287	my $newid = `uuidgen`;
1675 :			if (!$newid) {
1676 :			die "Cannot run uuidgen: $!";
1677 :			}
1678 :	olson	1.195
1679 :	parrello	1.287	chomp($newid);
1680 :	olson	1.195
1681 :	parrello	1.287	my $relinfo = "Automatically generated release info " . localtime();
1682 :			my $inst = "Unknown";
1683 :			my $contact = "Unknown";
1684 :			my $parent = "";
1685 :			my( $a, $b, $e, $v, $env ) = $fig->genome_counts;
1686 :			my $description = "Automatically generated release info\n";
1687 :			$description .= "Contains $a archaeal, $b bacterial, $e eukaryal, $v viral and $env environmental genomes.\n";
1688 :
1689 :			my $fh = new FileHandle(">$rel_file");
1690 :			if (!$fh) {
1691 :			warn "error creating $rel_file: $!";
1692 :			return undef;
1693 :			}
1694 :			print $fh "$relinfo\n";
1695 :			print $fh "$newid\n";
1696 :			print $fh "$inst\n";
1697 :			print $fh "$contact\n";
1698 :			print $fh "$parent\n";
1699 :			print $fh $description;
1700 :			$fh->close();
1701 :			chmod(0444, $rel_file);
1702 :	olson	1.195	}
1703 :
1704 :	parrello	1.287	if (open(my $fh, $rel_file)) {
1705 :			my(@lines) = <$fh>;
1706 :			close($fh);
1707 :	parrello	1.200
1708 :	parrello	1.287	chomp(@lines);
1709 :	parrello	1.200
1710 :	parrello	1.287	my($info, $id, $inst, $contact, $parent, @desc) = @lines;
1711 :	olson	1.195
1712 :	parrello	1.287	return ($info, $id, $inst, $contact, $parent, join("\n", @desc));
1713 :	olson	1.195	}
1714 :	olson	1.155
1715 :			return undef;
1716 :			}
1717 :
1718 :	parrello	1.287	=head3 get_peer_last_update
1719 :	olson	1.155
1720 :	parrello	1.287	C<< my $date = $fig->get_peer_last_update($peer_id); >>
1721 :	parrello	1.213
1722 :	olson	1.155	Return the timestamp from the last successful peer-to-peer update with
1723 :	parrello	1.287	the given peer. If the specified peer has made updates, comparing this
1724 :			timestamp to the timestamp of the updates can tell you whether or not
1725 :			the updates have been integrated into your SEED data store.
1726 :	olson	1.155
1727 :			We store this information in FIG/Data/Global/Peers/<peer-id>.
1728 :
1729 :	parrello	1.287	=over 4
1730 :
1731 :			=item peer_id
1732 :
1733 :			Universally Unique ID for the desired peer.
1734 :
1735 :			=item RETURN
1736 :
1737 :			Returns the date/time stamp for the last peer-to-peer updated performed
1738 :			with the identified SEED instance.
1739 :
1740 :			=back
1741 :
1742 :	olson	1.155	=cut
1743 :	parrello	1.213	#: Return Type $;
1744 :	parrello	1.287	sub get_peer_last_update {
1745 :	olson	1.155	my($self, $peer_id) = @_;
1746 :
1747 :			my $dir = "$FIG_Config::data/Global/Peers";
1748 :			&verify_dir($dir);
1749 :			$dir .= "/$peer_id";
1750 :			&verify_dir($dir);
1751 :
1752 :			my $update_file = "$dir/last_update";
1753 :	parrello	1.287	if (-f $update_file) {
1754 :			my $time = file_head($update_file, 1);
1755 :			chomp $time;
1756 :			return $time;
1757 :			} else {
1758 :			return undef;
1759 :	olson	1.155	}
1760 :			}
1761 :
1762 :	parrello	1.287	=head3 set_peer_last_update
1763 :	parrello	1.213
1764 :	parrello	1.287	C<< $fig->set_peer_last_update($peer_id, $time); >>
1765 :	parrello	1.213
1766 :	parrello	1.287	Manually set the update timestamp for a specified peer. This informs
1767 :			the SEED that you have all of the assignments and updates from a
1768 :			particular SEED instance as of a certain date.
1769 :	parrello	1.213
1770 :			=cut
1771 :			#: Return Type ;
1772 :
1773 :	parrello	1.287	sub set_peer_last_update {
1774 :	olson	1.155	my($self, $peer_id, $time) = @_;
1775 :
1776 :			my $dir = "$FIG_Config::data/Global/Peers";
1777 :			&verify_dir($dir);
1778 :			$dir .= "/$peer_id";
1779 :			&verify_dir($dir);
1780 :
1781 :			my $update_file = "$dir/last_update";
1782 :			open(F, ">$update_file");
1783 :			print F "$time\n";
1784 :			close(F);
1785 :			}
1786 :
1787 :	parrello	1.213	=head3 cgi_url
1788 :
1789 :	parrello	1.287	C<< my $url = FIG::$fig->cgi_url(); >>
1790 :
1791 :			Return the URL for the CGI script directory.
1792 :	parrello	1.213
1793 :			=cut
1794 :			#: Return Type $;
1795 :	efrank	1.1	sub cgi_url {
1796 :			return &plug_url($FIG_Config::cgi_url);
1797 :			}
1798 :	parrello	1.200
1799 :	parrello	1.213	=head3 temp_url
1800 :
1801 :	parrello	1.287	C<< my $url = FIG::temp_url(); >>
1802 :
1803 :			Return the URL of the temporary file directory.
1804 :	parrello	1.213
1805 :			=cut
1806 :			#: Return Type $;
1807 :	efrank	1.1	sub temp_url {
1808 :			return &plug_url($FIG_Config::temp_url);
1809 :			}
1810 :	parrello	1.200
1811 :	parrello	1.213	=head3 plug_url
1812 :
1813 :	parrello	1.287	C<< my $url2 = $fig->plug_url($url); >>
1814 :
1815 :			or
1816 :
1817 :			C<< my $url2 = $fig->plug_url($url); >>
1818 :
1819 :			Change the domain portion of a URL to point to the current domain. This essentially
1820 :			relocates URLs into the current environment.
1821 :
1822 :			=over 4
1823 :
1824 :			=item url
1825 :
1826 :			URL to relocate.
1827 :
1828 :			=item RETURN
1829 :
1830 :			Returns a new URL with the base portion converted to the current operating host.
1831 :			If the URL does not begin with C<http://>, the URL will be returned unmodified.
1832 :
1833 :			=back
1834 :	parrello	1.213
1835 :			=cut
1836 :			#: Return Type $;
1837 :	efrank	1.1	sub plug_url {
1838 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1839 :	efrank	1.1	my($url) = @_;
1840 :
1841 :	golsen	1.44	my $name;
1842 :
1843 :			# Revised by GJO
1844 :			# First try to get url from the current http request
1845 :
1846 :			if ( defined( $ENV{ 'HTTP_HOST' } ) # This is where $cgi->url gets its value
1847 :			&& ( $name = $ENV{ 'HTTP_HOST' } )
1848 :			&& ( $url =~ s~^http://[^/]*~http://$name~ ) # ~ is delimiter
1849 :			) {}
1850 :
1851 :			# Otherwise resort to alternative sources
1852 :
1853 :			elsif ( ( $name = &get_local_hostname )
1854 :			&& ( $url =~ s~^http://[^/]*~http://$name~ ) # ~ is delimiter
1855 :			) {}
1856 :
1857 :	efrank	1.1	return $url;
1858 :			}
1859 :
1860 :	parrello	1.213	=head3 file_read
1861 :
1862 :	parrello	1.287	C<< my $text = $fig->file_read($fileName); >>
1863 :
1864 :			or
1865 :
1866 :			C<< my @lines = $fig->file_read($fileName); >>
1867 :
1868 :			or
1869 :
1870 :			C<< my $text = FIG::file_read($fileName); >>
1871 :
1872 :			or
1873 :
1874 :			C<< my @lines = FIG::file_read($fileName); >>
1875 :
1876 :			Read an entire file into memory. In a scalar context, the file is returned
1877 :			as a single text string with line delimiters included. In a list context, the
1878 :			file is returned as a list of lines, each line terminated by a line
1879 :			delimiter. (For a method that automatically strips the line delimiters,
1880 :			use C<Tracer::GetFile>.)
1881 :
1882 :			=over 4
1883 :
1884 :			=item fileName
1885 :
1886 :			Fully-qualified name of the file to read.
1887 :
1888 :			=item RETURN
1889 :
1890 :			In a list context, returns a list of the file lines. In a scalar context, returns
1891 :			a string containing all the lines of the file with delimiters included.
1892 :	parrello	1.213
1893 :	parrello	1.287	=back
1894 :	parrello	1.213
1895 :			=cut
1896 :			#: Return Type $;
1897 :			#: Return Type @;
1898 :	parrello	1.287	sub file_read {
1899 :
1900 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1901 :	parrello	1.287	my($fileName) = @_;
1902 :			return file_head($fileName, '*');
1903 :	olson	1.90
1904 :			}
1905 :
1906 :
1907 :	parrello	1.213	=head3 file_head
1908 :
1909 :	parrello	1.287	C<< my $text = $fig->file_head($fileName, $count); >>
1910 :
1911 :			or
1912 :
1913 :			C<< my @lines = $fig->file_head($fileName, $count); >>
1914 :	parrello	1.213
1915 :	parrello	1.287	or
1916 :	parrello	1.213
1917 :	parrello	1.287	C<< my $text = FIG::file_head($fileName, $count); >>
1918 :	olson	1.90
1919 :	parrello	1.287	or
1920 :	olson	1.90
1921 :	parrello	1.287	C<< my @lines = FIG::file_head($fileName, $count); >>
1922 :	olson	1.90
1923 :	parrello	1.287	Read a portion of a file into memory. In a scalar context, the file portion is
1924 :			returned as a single text string with line delimiters included. In a list
1925 :			context, the file portion is returned as a list of lines, each line terminated
1926 :			by a line delimiter.
1927 :	olson	1.155
1928 :	parrello	1.287	=over 4
1929 :	olson	1.90
1930 :	parrello	1.287	=item fileName
1931 :	olson	1.90
1932 :	parrello	1.287	Fully-qualified name of the file to read.
1933 :	efrank	1.1
1934 :	parrello	1.287	=item count (optional)
1935 :	efrank	1.1
1936 :	parrello	1.287	Number of lines to read from the file. If omitted, C<1> is assumed. If the
1937 :			non-numeric string C<*> is specified, the entire file will be read.
1938 :	efrank	1.1
1939 :	parrello	1.287	=item RETURN
1940 :	efrank	1.1
1941 :	parrello	1.287	In a list context, returns a list of the desired file lines. In a scalar context, returns
1942 :			a string containing the desired lines of the file with delimiters included.
1943 :	efrank	1.1
1944 :	parrello	1.287	=back
1945 :	efrank	1.1
1946 :			=cut
1947 :	parrello	1.287	#: Return Type $;
1948 :			#: Return Type @;
1949 :			sub file_head {
1950 :	efrank	1.1
1951 :	parrello	1.287	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1952 :			my($file, $count) = @_;
1953 :	efrank	1.1
1954 :	parrello	1.287	my ($n, $allFlag);
1955 :			if ($count eq '*') {
1956 :			Trace("Full file read for \"$file\".") if T(2);
1957 :			$allFlag = 1;
1958 :			$n = 0;
1959 :			} else {
1960 :			$allFlag = 0;
1961 :			$n = (!$count ? 1 : $count);
1962 :			Trace("Reading $n record(s) from \"$file\".") if T(2);
1963 :			}
1964 :	efrank	1.1
1965 :	parrello	1.287	if (open(my $fh, "<$file")) {
1966 :			my(@ret, $i);
1967 :			$i = 0;
1968 :			while (<$fh>) {
1969 :			push(@ret, $_);
1970 :			$i++;
1971 :			last if !$allFlag && $i >= $n;
1972 :			}
1973 :			close($fh);
1974 :			if (wantarray) {
1975 :			return @ret;
1976 :			} else {
1977 :			return join("", @ret);
1978 :			}
1979 :	efrank	1.1	}
1980 :			}
1981 :
1982 :			################ Basic Routines [ existed since WIT ] ##########################
1983 :
1984 :	parrello	1.287	=head3 min
1985 :
1986 :			C<< my $min = FIG::min(@x); >>
1987 :
1988 :			or
1989 :
1990 :			C<< my $min = $fig->min(@x); >>
1991 :
1992 :			Return the minimum numeric value from a list.
1993 :
1994 :			=over 4
1995 :
1996 :			=item x1, x2, ... xN
1997 :	efrank	1.1
1998 :	parrello	1.287	List of numbers to process.
1999 :	efrank	1.1
2000 :	parrello	1.287	=item RETURN
2001 :	efrank	1.1
2002 :	parrello	1.287	Returns the numeric value of the list entry possessing the lowest value. Returns
2003 :			C<undef> if the list is empty.
2004 :	efrank	1.1
2005 :	parrello	1.287	=back
2006 :	efrank	1.1
2007 :			=cut
2008 :	parrello	1.213	#: Return Type $;
2009 :	efrank	1.1	sub min {
2010 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
2011 :	efrank	1.1	my(@x) = @_;
2012 :			my($min,$i);
2013 :
2014 :			(@x > 0) \|\| return undef;
2015 :			$min = $x[0];
2016 :	parrello	1.287	for ($i=1; ($i < @x); $i++) {
2017 :			$min = ($min > $x[$i]) ? $x[$i] : $min;
2018 :	efrank	1.1	}
2019 :			return $min;
2020 :			}
2021 :
2022 :	parrello	1.287	=head3 max
2023 :
2024 :			C<< my $max = FIG::max(@x); >>
2025 :
2026 :			or
2027 :
2028 :			C<< my $max = $fig->max(@x); >>
2029 :	efrank	1.1
2030 :	parrello	1.287	Return the maximum numeric value from a list.
2031 :	efrank	1.1
2032 :	parrello	1.287	=over 4
2033 :
2034 :			=item x1, x2, ... xN
2035 :
2036 :			List of numbers to process.
2037 :
2038 :			=item RETURN
2039 :
2040 :			Returns the numeric value of t/he list entry possessing the highest value. Returns
2041 :			C<undef> if the list is empty.
2042 :	efrank	1.1
2043 :	parrello	1.287	=back
2044 :	efrank	1.1
2045 :			=cut
2046 :	parrello	1.213	#: Return Type $;
2047 :	efrank	1.1	sub max {
2048 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
2049 :	efrank	1.1	my(@x) = @_;
2050 :			my($max,$i);
2051 :
2052 :			(@x > 0) \|\| return undef;
2053 :			$max = $x[0];
2054 :	parrello	1.287	for ($i=1; ($i < @x); $i++) {
2055 :			$max = ($max < $x[$i]) ? $x[$i] : $max;
2056 :	efrank	1.1	}
2057 :			return $max;
2058 :			}
2059 :
2060 :	parrello	1.287	=head3 between
2061 :	efrank	1.1
2062 :	parrello	1.287	C<< my $flag = FIG::between($x, $y, $z); >>
2063 :	efrank	1.1
2064 :	parrello	1.287	or
2065 :
2066 :			C<< my $flag = $fig->between($x, $y, $z); >>
2067 :
2068 :			Determine whether or not $y is between $x and $z.
2069 :
2070 :			=over 4
2071 :
2072 :			=item x
2073 :
2074 :			First edge number.
2075 :
2076 :			=item y
2077 :	efrank	1.1
2078 :	parrello	1.287	Number to examine.
2079 :
2080 :			=item z
2081 :
2082 :			Second edge number.
2083 :
2084 :			=item RETURN
2085 :
2086 :			Return TRUE if the number I<$y> is between the numbers I<$x> and I<$z>. The check
2087 :			is inclusive (that is, if I<$y> is equal to I<$x> or I<$z> the function returns
2088 :			TRUE), and the order of I<$x> and I<$z> does not matter. If I<$x> is lower than
2089 :			I<$z>, then the return is TRUE if I<$x> <= I<$y> <= I<$z>. If I<$z> is lower,
2090 :			then the return is TRUE if I<$x> >= I$<$y> >= I<$z>.
2091 :
2092 :			=back
2093 :	efrank	1.1
2094 :			=cut
2095 :	parrello	1.213	#: Return Type $;
2096 :	efrank	1.1	sub between {
2097 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
2098 :	efrank	1.1	my($x,$y,$z) = @_;
2099 :
2100 :	parrello	1.287	if ($x < $z) {
2101 :			return (($x <= $y) && ($y <= $z));
2102 :			} else {
2103 :			return (($x >= $y) && ($y >= $z));
2104 :	efrank	1.1	}
2105 :			}
2106 :
2107 :	parrello	1.287	=head3 standard_genetic_code
2108 :	efrank	1.1
2109 :	parrello	1.287	C<< my $code = FIG::standard_genetic_code(); >>
2110 :	efrank	1.1
2111 :	parrello	1.287	Return a hash containing the standard translation of nucleotide triples to proteins.
2112 :			Methods such as L</translate> can take a translation scheme as a parameter. This method
2113 :			returns the default translation scheme. The scheme is implemented as a reference to a
2114 :			hash that contains nucleotide triplets as keys and has protein letters as values.
2115 :	efrank	1.1
2116 :			=cut
2117 :	parrello	1.213	#: Return Type $;
2118 :	efrank	1.1	sub standard_genetic_code {
2119 :	parrello	1.200
2120 :	efrank	1.1	my $code = {};
2121 :
2122 :			$code->{"AAA"} = "K";
2123 :			$code->{"AAC"} = "N";
2124 :			$code->{"AAG"} = "K";
2125 :			$code->{"AAT"} = "N";
2126 :			$code->{"ACA"} = "T";
2127 :			$code->{"ACC"} = "T";
2128 :			$code->{"ACG"} = "T";
2129 :			$code->{"ACT"} = "T";
2130 :			$code->{"AGA"} = "R";
2131 :			$code->{"AGC"} = "S";
2132 :			$code->{"AGG"} = "R";
2133 :			$code->{"AGT"} = "S";
2134 :			$code->{"ATA"} = "I";
2135 :			$code->{"ATC"} = "I";
2136 :			$code->{"ATG"} = "M";
2137 :			$code->{"ATT"} = "I";
2138 :			$code->{"CAA"} = "Q";
2139 :			$code->{"CAC"} = "H";
2140 :			$code->{"CAG"} = "Q";
2141 :			$code->{"CAT"} = "H";
2142 :			$code->{"CCA"} = "P";
2143 :			$code->{"CCC"} = "P";
2144 :			$code->{"CCG"} = "P";
2145 :			$code->{"CCT"} = "P";
2146 :			$code->{"CGA"} = "R";
2147 :			$code->{"CGC"} = "R";
2148 :			$code->{"CGG"} = "R";
2149 :			$code->{"CGT"} = "R";
2150 :			$code->{"CTA"} = "L";
2151 :			$code->{"CTC"} = "L";
2152 :			$code->{"CTG"} = "L";
2153 :			$code->{"CTT"} = "L";
2154 :			$code->{"GAA"} = "E";
2155 :			$code->{"GAC"} = "D";
2156 :			$code->{"GAG"} = "E";
2157 :			$code->{"GAT"} = "D";
2158 :			$code->{"GCA"} = "A";
2159 :			$code->{"GCC"} = "A";
2160 :			$code->{"GCG"} = "A";
2161 :			$code->{"GCT"} = "A";
2162 :			$code->{"GGA"} = "G";
2163 :			$code->{"GGC"} = "G";
2164 :			$code->{"GGG"} = "G";
2165 :			$code->{"GGT"} = "G";
2166 :			$code->{"GTA"} = "V";
2167 :			$code->{"GTC"} = "V";
2168 :			$code->{"GTG"} = "V";
2169 :			$code->{"GTT"} = "V";
2170 :			$code->{"TAA"} = "*";
2171 :			$code->{"TAC"} = "Y";
2172 :			$code->{"TAG"} = "*";
2173 :			$code->{"TAT"} = "Y";
2174 :			$code->{"TCA"} = "S";
2175 :			$code->{"TCC"} = "S";
2176 :			$code->{"TCG"} = "S";
2177 :			$code->{"TCT"} = "S";
2178 :			$code->{"TGA"} = "*";
2179 :			$code->{"TGC"} = "C";
2180 :			$code->{"TGG"} = "W";
2181 :			$code->{"TGT"} = "C";
2182 :			$code->{"TTA"} = "L";
2183 :			$code->{"TTC"} = "F";
2184 :			$code->{"TTG"} = "L";
2185 :			$code->{"TTT"} = "F";
2186 :	parrello	1.200
2187 :	efrank	1.1	return $code;
2188 :			}
2189 :
2190 :	parrello	1.287	=head3 translate
2191 :
2192 :			C<< my $aa_seq = &FIG::translate($dna_seq, $code, $fix_start); >>
2193 :
2194 :			Translate a DNA sequence to a protein sequence using the specified genetic code.
2195 :			If I<$fix_start> is TRUE, will translate an initial C<TTG> or C<GTG> code to
2196 :			C<M>. (In the standard genetic code, these two combinations normally translate
2197 :			to C<V> and C<L>, respectively.)
2198 :
2199 :			=over 4
2200 :	efrank	1.1
2201 :	parrello	1.287	=item dna_seq
2202 :	efrank	1.1
2203 :	parrello	1.287	DNA sequence to translate. Note that the DNA sequence can only contain
2204 :			known nucleotides.
2205 :	efrank	1.1
2206 :	parrello	1.287	=item code
2207 :	efrank	1.1
2208 :	parrello	1.287	Reference to a hash specifying the translation code. The hash is keyed by
2209 :			nucleotide triples, and the value for each key is the corresponding protein
2210 :			letter. If this parameter is omitted, the L</standard_genetic_code> will be
2211 :			used.
2212 :	efrank	1.1
2213 :	parrello	1.287	=item fix_start
2214 :
2215 :			TRUE if the first triple is to get special treatment, else FALSE. If TRUE,
2216 :			then a value of C<TTG> or C<GTG> in the first position will be translated to
2217 :			C<M> instead of the value specified in the translation code.
2218 :
2219 :			=item RETURN
2220 :
2221 :			Returns a string resulting from translating each nucleotide triple into a
2222 :			protein letter.
2223 :
2224 :			=back
2225 :
2226 :			=cut
2227 :			#: Return Type $;
2228 :			sub translate {
2229 :			shift if UNIVERSAL::isa($_[0],__PACKAGE__);
2230 :
2231 :			my( $dna,$code,$start ) = @_;
2232 :			my( $i,$j,$ln );
2233 :			my( $x,$y );
2234 :			my( $prot );
2235 :
2236 :			if (! defined($code)) {
2237 :			$code = &FIG::standard_genetic_code;
2238 :	efrank	1.1	}
2239 :			$ln = length($dna);
2240 :			$prot = "X" x ($ln/3);
2241 :			$dna =~ tr/a-z/A-Z/;
2242 :
2243 :	parrello	1.287	for ($i=0,$j=0; ($i < ($ln-2)); $i += 3,$j++) {
2244 :			$x = substr($dna,$i,3);
2245 :			if ($y = $code->{$x}) {
2246 :			substr($prot,$j,1) = $y;
2247 :	efrank	1.1	}
2248 :			}
2249 :	parrello	1.200
2250 :	parrello	1.287	if (($start) && ($ln >= 3) && (substr($dna,0,3) =~ /^[GT]TG$/)) {
2251 :			substr($prot,0,1) = 'M';
2252 :	efrank	1.1	}
2253 :			return $prot;
2254 :			}
2255 :
2256 :	parrello	1.287	=head3 reverse_comp
2257 :
2258 :			C<< my $dnaR = FIG::reverse_comp($dna); >>
2259 :
2260 :			or
2261 :
2262 :			C<< my $dnaR = $fig->reverse_comp($dna); >>
2263 :
2264 :			Return the reverse complement os the specified DNA sequence.
2265 :	efrank	1.1
2266 :	parrello	1.287	NOTE: for extremely long DNA strings, use L</rev_comp>, which allows you to
2267 :			pass the strings around in the form of pointers.
2268 :	efrank	1.1
2269 :	parrello	1.287	=over 4
2270 :
2271 :			=item dna
2272 :	efrank	1.1
2273 :	parrello	1.287	DNA sequence whose reverse complement is desired.
2274 :
2275 :			=item RETURN
2276 :
2277 :			Returns the reverse complement of the incoming DNA sequence.
2278 :
2279 :			=back
2280 :	efrank	1.1
2281 :			=cut
2282 :	parrello	1.213	#: Return Type $;
2283 :	efrank	1.1	sub reverse_comp {
2284 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
2285 :	efrank	1.1	my($seq) = @_;
2286 :
2287 :			return ${&rev_comp(\$seq)};
2288 :			}
2289 :
2290 :	parrello	1.287	=head3 rev_comp
2291 :
2292 :			C<< my $dnaRP = FIG::rev_comp(\$dna); >>
2293 :
2294 :			or
2295 :
2296 :			C<< my $dnaRP = $fig->rev_comp(\$dna); >>
2297 :
2298 :			Return the reverse complement of the specified DNA sequence. The DNA sequence
2299 :			is passed in as a string reference rather than a raw string for performance
2300 :			reasons. If this is unnecessary, use L</reverse_comp>, which processes strings
2301 :			instead of references to strings.
2302 :
2303 :			=over 4
2304 :
2305 :			=item dna
2306 :
2307 :			Reference to the DNA sequence whose reverse complement is desired.
2308 :
2309 :			=item RETURN
2310 :
2311 :			Returns a reference to the reverse complement of the incoming DNA sequence.
2312 :
2313 :			=back
2314 :	parrello	1.213
2315 :			=cut
2316 :			#: Return Type $;
2317 :	efrank	1.1	sub rev_comp {
2318 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
2319 :	efrank	1.1	my( $seqP ) = @_;
2320 :			my( $rev );
2321 :
2322 :			$rev = reverse( $$seqP );
2323 :			$rev =~ tr/a-z/A-Z/;
2324 :			$rev =~ tr/ACGTUMRWSYKBDHV/TGCAAKYWSRMVHDB/;
2325 :			return \$rev;
2326 :			}
2327 :
2328 :	parrello	1.287	=head3 verify_dir
2329 :
2330 :			C<< FIG::verify_dir($dir); >>
2331 :	efrank	1.1
2332 :	parrello	1.287	or
2333 :	efrank	1.1
2334 :	parrello	1.287	C<< $fig->verify_dir($dir); >>
2335 :	efrank	1.1
2336 :	parrello	1.287	Insure that the specified directory exists. If it must be created, the permissions will
2337 :			be set to C<0777>.
2338 :	efrank	1.1
2339 :			=cut
2340 :
2341 :			sub verify_dir {
2342 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
2343 :	efrank	1.1	my($dir) = @_;
2344 :
2345 :	parrello	1.287	if (-d $dir) {
2346 :			return
2347 :			}
2348 :			if ($dir =~ /^(.*)\/[^\/]+$/) {
2349 :			&verify_dir($1);
2350 :	efrank	1.1	}
2351 :	parrello	1.287	mkdir($dir,0777) \|\| Confess("Could not make directory $dir: $!");
2352 :	efrank	1.1	}
2353 :
2354 :	parrello	1.287	=head3 run
2355 :	efrank	1.1
2356 :	parrello	1.287	C<< FIG::run($cmd); >>
2357 :	overbeek	1.283
2358 :	parrello	1.287	or
2359 :
2360 :			C<< $fig->run($cmd); >>
2361 :	overbeek	1.283
2362 :	parrello	1.287	Run a command. If the command fails, the error will be traced.
2363 :	overbeek	1.283
2364 :			=cut
2365 :
2366 :	parrello	1.287	sub run {
2367 :			shift if UNIVERSAL::isa($_[0],__PACKAGE__);
2368 :			my($cmd) = @_;
2369 :
2370 :			if ($ENV{VERBOSE}) {
2371 :			my @tmp = `date`;
2372 :			chomp @tmp;
2373 :			print STDERR "$tmp[0]: running $cmd\n";
2374 :			}
2375 :			Trace("Running command: $cmd") if T(3);
2376 :			(system($cmd) == 0) \|\| Confess("FAILED: $cmd");
2377 :			}
2378 :
2379 :			=head3 augment_path
2380 :
2381 :			C<< FIG::augment_path($dirName); >>
2382 :	overbeek	1.283
2383 :	parrello	1.287	Add a directory to the system path.
2384 :	overbeek	1.283
2385 :	parrello	1.287	This method adds a new directory to the front of the system path. It looks in the
2386 :			configuration file to determine whether this is Windows or Unix, and uses the
2387 :			appropriate separator.
2388 :	efrank	1.1
2389 :	parrello	1.287	=over 4
2390 :	efrank	1.1
2391 :	parrello	1.287	=item dirName
2392 :
2393 :			Name of the directory to add to the path.
2394 :
2395 :			=back
2396 :	efrank	1.1
2397 :			=cut
2398 :
2399 :	parrello	1.287	sub augment_path {
2400 :			my ($dirName) = @_;
2401 :			if ($FIG_Config::win_mode) {
2402 :			$ENV{PATH} = "$dirName;$ENV{PATH}";
2403 :			} else {
2404 :			$ENV{PATH} = "$dirName:$ENV{PATH}";
2405 :	overbeek	1.278	}
2406 :	efrank	1.1	}
2407 :
2408 :	parrello	1.287	=head3 read_fasta_record
2409 :	gdpusch	1.45
2410 :	parrello	1.287	C<< my ($seq_id, $seq_pointer, $comment) = FIG::read_fasta_record(\*FILEHANDLE); >>
2411 :	gdpusch	1.45
2412 :	parrello	1.287	or
2413 :	gdpusch	1.45
2414 :	parrello	1.287	C<< my ($seq_id, $seq_pointer, $comment) = $fig->read_fasta_record(\*FILEHANDLE); >>
2415 :	gdpusch	1.45
2416 :	parrello	1.287	Read and parse the next logical record of a FASTA file. A FASTA logical record
2417 :			consists of multiple lines of text. The first line begins with a C<< > >> symbol
2418 :			and contains the sequence ID followed by an optional comment. (NOTE: comments
2419 :			are currently deprecated, because not all tools handle them properly.) The
2420 :			remaining lines contain the sequence data.
2421 :
2422 :			This method uses a trick to smooth its operation: the line terminator character
2423 :			is temporarily changed to C<< \n> >> so that a single read operation brings in
2424 :			the entire logical record.
2425 :	gdpusch	1.45
2426 :	parrello	1.287	=over 4
2427 :	gdpusch	1.45
2428 :	parrello	1.287	=item FILEHANDLE
2429 :	gdpusch	1.45
2430 :	parrello	1.287	Open handle of the FASTA file. If not specified, C<STDIN> is assumed.
2431 :
2432 :			=item RETURN
2433 :
2434 :			If we are at the end of the file, returns C<undef>. Otherwise, returns a
2435 :			three-element list. The first element is the sequence ID, the second is
2436 :			a pointer to the sequence data (that is, a string reference as opposed to
2437 :			as string), and the third is the comment.
2438 :
2439 :			=back
2440 :	gdpusch	1.45
2441 :			=cut
2442 :	parrello	1.213	#: Return Type @;
2443 :	parrello	1.287	sub read_fasta_record {
2444 :
2445 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
2446 :	gdpusch	1.45	my ($file_handle) = @_;
2447 :	parrello	1.287	my ($old_end_of_record, $fasta_record, @lines, $head, $sequence, $seq_id, $comment, @parsed_fasta_record);
2448 :	parrello	1.200
2449 :	gdpusch	1.45	if (not defined($file_handle)) { $file_handle = \*STDIN; }
2450 :	parrello	1.200
2451 :	gdpusch	1.45	$old_end_of_record = $/;
2452 :			$/ = "\n>";
2453 :	parrello	1.200
2454 :	parrello	1.287	if (defined($fasta_record = <$file_handle>)) {
2455 :			chomp $fasta_record;
2456 :			@lines = split( /\n/, $fasta_record );
2457 :			$head = shift @lines;
2458 :			$head =~ s/^>?//;
2459 :			$head =~ m/^(\S+)/;
2460 :			$seq_id = $1;
2461 :			if ($head =~ m/^\S+\s+(.*)$/) { $comment = $1; } else { $comment = ""; }
2462 :			$sequence = join( "", @lines );
2463 :			@parsed_fasta_record = ( $seq_id, \$sequence, $comment );
2464 :			} else {
2465 :			@parsed_fasta_record = ();
2466 :	gdpusch	1.45	}
2467 :	parrello	1.200
2468 :	gdpusch	1.45	$/ = $old_end_of_record;
2469 :	parrello	1.200
2470 :	gdpusch	1.45	return @parsed_fasta_record;
2471 :			}
2472 :
2473 :	parrello	1.287	=head3 display_id_and_seq
2474 :
2475 :			C<< FIG::display_id_and_seq($id_and_comment, $seqP, $fh); >>
2476 :
2477 :			or
2478 :
2479 :			C<< $fig->display_id_and_seq($id_and_comment, $seqP, $fh); >>
2480 :
2481 :			Display a fasta ID and sequence to the specified open file. This method is designed
2482 :			to work well with L</read_fasta_sequence> and L</rev_comp>, because it takes as
2483 :			input a string pointer rather than a string. If the file handle is omitted it
2484 :			defaults to STDOUT.
2485 :
2486 :			The output is formatted into a FASTA record. The first line of the output is
2487 :			preceded by a C<< > >> symbol, and the sequence is split into 60-character
2488 :			chunks displayed one per line. Thus, this method can be used to produce
2489 :			FASTA files from data gathered by the rest of the system.
2490 :
2491 :			=over 4
2492 :
2493 :			=item id_and_comment
2494 :
2495 :			The sequence ID and (optionally) the comment from the sequence's FASTA record.
2496 :			The ID
2497 :	gdpusch	1.45
2498 :	parrello	1.287	=item seqP
2499 :	efrank	1.1
2500 :	parrello	1.287	Reference to a string containing the sequence. The sequence is automatically
2501 :			formatted into 60-character chunks displayed one per line.
2502 :	efrank	1.1
2503 :	parrello	1.287	=item fh
2504 :	efrank	1.1
2505 :	parrello	1.287	Open file handle to which the ID and sequence should be output. If omitted,
2506 :			C<STDOUT> is assumed.
2507 :
2508 :			=back
2509 :	efrank	1.1
2510 :			=cut
2511 :
2512 :	parrello	1.287	sub display_id_and_seq {
2513 :	mkubal	1.53
2514 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
2515 :	parrello	1.287
2516 :	efrank	1.1	my( $id, $seq, $fh ) = @_;
2517 :	parrello	1.200
2518 :	efrank	1.1	if (! defined($fh) ) { $fh = \*STDOUT; }
2519 :	parrello	1.200
2520 :	efrank	1.1	print $fh ">$id\n";
2521 :			&display_seq($seq, $fh);
2522 :			}
2523 :
2524 :	parrello	1.287	=head3 display_id_and_seq
2525 :
2526 :			C<< FIG::display_seq($seqP, $fh); >>
2527 :
2528 :			or
2529 :
2530 :			C<< $fig->display_seq($seqP, $fh); >>
2531 :
2532 :			Display a fasta sequence to the specified open file. This method is designed
2533 :			to work well with L</read_fasta_sequence> and L</rev_comp>, because it takes as
2534 :			input a string pointer rather than a string. If the file handle is omitted it
2535 :			defaults to STDOUT.
2536 :
2537 :			The sequence is split into 60-character chunks displayed one per line for
2538 :			readability.
2539 :
2540 :			=over 4
2541 :
2542 :			=item seqP
2543 :
2544 :			Reference to a string containing the sequence.
2545 :
2546 :			=item fh
2547 :
2548 :			Open file handle to which the sequence should be output. If omitted,
2549 :			C<STDOUT> is assumed.
2550 :
2551 :			=back
2552 :
2553 :			=cut
2554 :
2555 :	efrank	1.1	sub display_seq {
2556 :	parrello	1.287
2557 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
2558 :	parrello	1.287
2559 :	efrank	1.1	my ( $seq, $fh ) = @_;
2560 :			my ( $i, $n, $ln );
2561 :	parrello	1.200
2562 :	efrank	1.1	if (! defined($fh) ) { $fh = \*STDOUT; }
2563 :
2564 :			$n = length($$seq);
2565 :			# confess "zero-length sequence ???" if ( (! defined($n)) \|\| ($n == 0) );
2566 :	parrello	1.287	for ($i=0; ($i < $n); $i += 60) {
2567 :			if (($i + 60) <= $n) {
2568 :			$ln = substr($$seq,$i,60);
2569 :			} else {
2570 :			$ln = substr($$seq,$i,($n-$i));
2571 :			}
2572 :			print $fh "$ln\n";
2573 :	efrank	1.1	}
2574 :			}
2575 :
2576 :			########## I commented the pods on the following routines out, since they should not
2577 :			########## be part of the SOAP/WSTL interface
2578 :			#=pod
2579 :			#
2580 :	parrello	1.287	#=head3 file2N
2581 :	efrank	1.1	#
2582 :			#usage: $n = $fig->file2N($file)
2583 :			#
2584 :			#In some of the databases I need to store filenames, which can waste a lot of
2585 :			#space. Hence, I maintain a database for converting filenames to/from integers.
2586 :			#
2587 :			#=cut
2588 :			#
2589 :	olson	1.111	sub file2N :scalar {
2590 :	efrank	1.1	my($self,$file) = @_;
2591 :			my($relational_db_response);
2592 :
2593 :			my $rdbH = $self->db_handle;
2594 :
2595 :			if (($relational_db_response = $rdbH->SQL("SELECT fileno FROM file_table WHERE ( file = \'$file\')")) &&
2596 :	parrello	1.287	(@$relational_db_response == 1)) {
2597 :			return $relational_db_response->[0]->[0];
2598 :			} elsif (($relational_db_response = $rdbH->SQL("SELECT MAX(fileno) FROM file_table ")) && (@$relational_db_response == 1) && ($relational_db_response->[0]->[0])) {
2599 :			my $fileno = $relational_db_response->[0]->[0] + 1;
2600 :			if ($rdbH->SQL("INSERT INTO file_table ( file, fileno ) VALUES ( \'$file\', $fileno )")) {
2601 :			return $fileno;
2602 :			}
2603 :			} elsif ($rdbH->SQL("INSERT INTO file_table ( file, fileno ) VALUES ( \'$file\', 1 )")) {
2604 :			return 1;
2605 :	efrank	1.1	}
2606 :			return undef;
2607 :			}
2608 :
2609 :			#=pod
2610 :			#
2611 :	parrello	1.287	#=head3 N2file
2612 :	efrank	1.1	#
2613 :			#usage: $filename = $fig->N2file($n)
2614 :			#
2615 :			#In some of the databases I need to store filenames, which can waste a lot of
2616 :			#space. Hence, I maintain a database for converting filenames to/from integers.
2617 :			#
2618 :			#=cut
2619 :			#
2620 :	olson	1.111	sub N2file :scalar {
2621 :	efrank	1.1	my($self,$fileno) = @_;
2622 :			my($relational_db_response);
2623 :
2624 :			my $rdbH = $self->db_handle;
2625 :
2626 :			if (($relational_db_response = $rdbH->SQL("SELECT file FROM file_table WHERE ( fileno = $fileno )")) &&
2627 :	parrello	1.287	(@$relational_db_response == 1)) {
2628 :			return $relational_db_response->[0]->[0];
2629 :	efrank	1.1	}
2630 :			return undef;
2631 :			}
2632 :
2633 :
2634 :			#=pod
2635 :			#
2636 :	parrello	1.287	#=head3 openF
2637 :	efrank	1.1	#
2638 :			#usage: $fig->openF($filename)
2639 :			#
2640 :			#Parts of the system rely on accessing numerous different files. The most obvious case is
2641 :			#the situation with similarities. It is important that the system be able to run in cases in
2642 :			#which an arbitrary number of files cannot be open simultaneously. This routine (with closeF) is
2643 :			#a hack to handle this. I should probably just pitch them and insist that the OS handle several
2644 :			#hundred open filehandles.
2645 :			#
2646 :			#=cut
2647 :			#
2648 :			sub openF {
2649 :			my($self,$file) = @_;
2650 :			my($fxs,$x,@fxs,$fh);
2651 :
2652 :			$fxs = $self->cached('_openF');
2653 :	parrello	1.287	if ($x = $fxs->{$file}) {
2654 :			$x->[1] = time();
2655 :			return $x->[0];
2656 :	efrank	1.1	}
2657 :	parrello	1.200
2658 :	efrank	1.1	@fxs = keys(%$fxs);
2659 :	parrello	1.287	if (defined($fh = new FileHandle "<$file")) {
2660 :			if (@fxs >= 50) {
2661 :			@fxs = sort { $fxs->{$a}->[1] <=> $fxs->{$b}->[1] } @fxs;
2662 :			$x = $fxs->{$fxs[0]};
2663 :			undef $x->[0];
2664 :			delete $fxs->{$fxs[0]};
2665 :			}
2666 :			$fxs->{$file} = [$fh,time()];
2667 :			return $fh;
2668 :	efrank	1.1	}
2669 :			return undef;
2670 :			}
2671 :
2672 :			#=pod
2673 :			#
2674 :	parrello	1.287	#=head3 closeF
2675 :	efrank	1.1	#
2676 :			#usage: $fig->closeF($filename)
2677 :			#
2678 :			#Parts of the system rely on accessing numerous different files. The most obvious case is
2679 :			#the situation with similarities. It is important that the system be able to run in cases in
2680 :			#which an arbitrary number of files cannot be open simultaneously. This routine (with openF) is
2681 :			#a hack to handle this. I should probably just pitch them and insist that the OS handle several
2682 :			#hundred open filehandles.
2683 :			#
2684 :			#=cut
2685 :			#
2686 :			sub closeF {
2687 :			my($self,$file) = @_;
2688 :			my($fxs,$x);
2689 :
2690 :	parrello	1.287	if (($fxs = $self->{_openF}) && ($x = $fxs->{$file})) {
2691 :			undef $x->[0];
2692 :			delete $fxs->{$file};
2693 :	efrank	1.1	}
2694 :			}
2695 :
2696 :	parrello	1.287	=head3 ec_name
2697 :
2698 :			C<< my $enzymatic_function = $fig->ec_name($ec); >>
2699 :	efrank	1.1
2700 :	parrello	1.287	Returns the enzymatic name corresponding to the specified enzyme code.
2701 :	efrank	1.1
2702 :	parrello	1.287	=over 4
2703 :
2704 :			=item ec
2705 :	efrank	1.1
2706 :	parrello	1.287	Code number for the enzyme whose name is desired. The code number is actually
2707 :			a string of digits and periods (e.g. C<1.2.50.6>).
2708 :
2709 :			=item RETURN
2710 :
2711 :			Returns the name of the enzyme specified by the indicated code, or a null string
2712 :			if the code is not found in the database.
2713 :
2714 :			=back
2715 :	efrank	1.1
2716 :			=cut
2717 :
2718 :			sub ec_name {
2719 :			my($self,$ec) = @_;
2720 :
2721 :			($ec =~ /^\d+\.\d+\.\d+\.\d+$/) \|\| return "";
2722 :			my $rdbH = $self->db_handle;
2723 :			my $relational_db_response = $rdbH->SQL("SELECT name FROM ec_names WHERE ( ec = \'$ec\' )");
2724 :
2725 :			return (@$relational_db_response == 1) ? $relational_db_response->[0]->[0] : "";
2726 :			return "";
2727 :			}
2728 :
2729 :	parrello	1.287	=head3 all_roles
2730 :	efrank	1.1
2731 :	parrello	1.287	C<< my @roles = $fig->all_roles; >>
2732 :	efrank	1.1
2733 :	parrello	1.287	Return a list of the known roles. Currently, this is a list of the enzyme codes and names.
2734 :	efrank	1.1
2735 :	parrello	1.287	The return value is a list of list references. Each element of the big list contains an
2736 :			enzyme code (EC) followed by the enzymatic name.
2737 :	efrank	1.1
2738 :			=cut
2739 :
2740 :			sub all_roles {
2741 :			my($self) = @_;
2742 :
2743 :			my $rdbH = $self->db_handle;
2744 :			my $relational_db_response = $rdbH->SQL("SELECT ec,name FROM ec_names");
2745 :
2746 :			return @$relational_db_response;
2747 :			}
2748 :
2749 :	parrello	1.287	=head3 expand_ec
2750 :	efrank	1.1
2751 :	parrello	1.287	C<< my $expanded_ec = $fig->expand_ec($ec); >>
2752 :	efrank	1.1
2753 :			Expands "1.1.1.1" to "1.1.1.1 - alcohol dehydrogenase" or something like that.
2754 :
2755 :			=cut
2756 :
2757 :			sub expand_ec {
2758 :			my($self,$ec) = @_;
2759 :			my($name);
2760 :
2761 :			return ($name = $self->ec_name($ec)) ? "$ec - $name" : $ec;
2762 :			}
2763 :
2764 :	parrello	1.287	=head3 clean_tmp
2765 :	efrank	1.1
2766 :	parrello	1.287	C<< FIG::clean_tmp(); >>
2767 :	efrank	1.1
2768 :	parrello	1.287	Delete temporary files more than two days old.
2769 :	efrank	1.1
2770 :			We store temporary files in $FIG_Config::temp. There are specific classes of files
2771 :			that are created and should be saved for at least a few days. This routine can be
2772 :			invoked to clean out those that are over two days old.
2773 :
2774 :			=cut
2775 :
2776 :			sub clean_tmp {
2777 :
2778 :			my($file);
2779 :	parrello	1.287	if (opendir(TMP,"$FIG_Config::temp")) {
2780 :			# change the pattern to pick up other files that need to be cleaned up
2781 :			my @temp = grep { $_ =~ /^(Geno\|tmp)/ } readdir(TMP);
2782 :			foreach $file (@temp) {
2783 :			if (-M "$FIG_Config::temp/$file" > 2) {
2784 :			unlink("$FIG_Config::temp/$file");
2785 :			}
2786 :			}
2787 :	efrank	1.1	}
2788 :			}
2789 :
2790 :			################ Routines to process genomes and genome IDs ##########################
2791 :
2792 :
2793 :	parrello	1.287	=head3 genomes
2794 :	efrank	1.1
2795 :	parrello	1.287	C<< my @genome_ids = $fig->genomes($complete, $restrictions, $domain); >>
2796 :	efrank	1.1
2797 :	parrello	1.287	Return a list of genome IDs. If called with no parameters, all genome IDs
2798 :			in the database will be returned.
2799 :	efrank	1.1
2800 :			Genomes are assigned ids of the form X.Y where X is the taxonomic id maintained by
2801 :			NCBI for the species (not the specific strain), and Y is a sequence digit assigned to
2802 :			this particular genome (as one of a set with the same genus/species). Genomes also
2803 :			have versions, but that is a separate issue.
2804 :
2805 :	parrello	1.287	=over 4
2806 :
2807 :			=item complete
2808 :
2809 :			TRUE if only complete genomes should be returned, else FALSE.
2810 :
2811 :			=item restrictions
2812 :
2813 :			TRUE if only restriction genomes should be returned, else FALSE.
2814 :
2815 :			=item domain
2816 :
2817 :			Name of the domain from which the genomes should be returned. Possible values are
2818 :			C<Bacteria>, C<Virus>, C<Eukaryota>, C<unknown>, C<Archaea>, and
2819 :			C<Environmental Sample>. If no domain is specified, all domains will be
2820 :			eligible.
2821 :
2822 :			=item RETURN
2823 :
2824 :			Returns a list of all the genome IDs with the specified characteristics.
2825 :
2826 :			=back
2827 :
2828 :	efrank	1.1	=cut
2829 :
2830 :	olson	1.111	sub genomes :remote :list {
2831 :	golsen	1.150	my( $self, $complete, $restrictions, $domain ) = @_;
2832 :	overbeek	1.13
2833 :			my $rdbH = $self->db_handle;
2834 :
2835 :			my @where = ();
2836 :	parrello	1.287	if ($complete) {
2837 :			push(@where, "( complete = \'1\' )")
2838 :	overbeek	1.13	}
2839 :
2840 :	parrello	1.287	if ($restrictions) {
2841 :			push(@where, "( restrictions = \'1\' )")
2842 :	overbeek	1.13	}
2843 :	golsen	1.150
2844 :	parrello	1.287	if ($domain) {
2845 :			push( @where, "( maindomain = '$domain' )" )
2846 :	golsen	1.150	}
2847 :
2848 :	overbeek	1.13	my $relational_db_response;
2849 :	parrello	1.287	if (@where > 0) {
2850 :			my $where = join(" AND ",@where);
2851 :			$relational_db_response = $rdbH->SQL("SELECT genome FROM genome where $where");
2852 :			} else {
2853 :			$relational_db_response = $rdbH->SQL("SELECT genome FROM genome");
2854 :	overbeek	1.13	}
2855 :			my @genomes = sort { $a <=> $b } map { $_->[0] } @$relational_db_response;
2856 :	efrank	1.1	return @genomes;
2857 :			}
2858 :
2859 :	parrello	1.287	=head3 is_complete
2860 :
2861 :			C<< my $flag = $fig->is_complete($genome); >>
2862 :
2863 :			Return TRUE if the genome with the specified ID is complete, else FALSE.
2864 :
2865 :			=over 4
2866 :
2867 :			=item genome
2868 :
2869 :			ID of the relevant genome.
2870 :
2871 :			=item RETURN
2872 :
2873 :			Returns TRUE if there is a complete genome in the database with the specified ID,
2874 :			else FALSE.
2875 :
2876 :			=back
2877 :
2878 :			=cut
2879 :
2880 :	overbeek	1.180	sub is_complete {
2881 :			my($self,$genome) = @_;
2882 :
2883 :			my $rdbH = $self->db_handle;
2884 :			my $relational_db_response = $rdbH->SQL("SELECT genome FROM genome where (genome = '$genome') AND (complete = '1')");
2885 :			return (@$relational_db_response == 1)
2886 :	parrello	1.287	}
2887 :
2888 :			=head3 genome_counts
2889 :
2890 :			C<< my ($arch, $bact, $euk, $vir, $env, $unk) = $fig->genome_counts($complete); >>
2891 :
2892 :			Count the number of genomes in each domain. If I<$complete> is TRUE, only complete
2893 :			genomes will be included in the counts.
2894 :
2895 :			=over 4
2896 :
2897 :			=item complete
2898 :
2899 :			TRUE if only complete genomes are to be counted, FALSE if all genomes are to be
2900 :			counted
2901 :
2902 :			=item RETURN
2903 :
2904 :			A six-element list containing the number of genomes in each of six categories--
2905 :			Archaea, Bacteria, Eukaryota, Viral, Environmental, and Unknown, respectively.
2906 :
2907 :			=back
2908 :
2909 :			=cut
2910 :	golsen	1.150
2911 :	efrank	1.2	sub genome_counts {
2912 :	overbeek	1.13	my($self,$complete) = @_;
2913 :			my($x,$relational_db_response);
2914 :	efrank	1.2
2915 :	overbeek	1.13	my $rdbH = $self->db_handle;
2916 :
2917 :	parrello	1.287	if ($complete) {
2918 :			$relational_db_response = $rdbH->SQL("SELECT genome, maindomain FROM genome where complete = '1'");
2919 :			} else {
2920 :			$relational_db_response = $rdbH->SQL("SELECT genome,maindomain FROM genome");
2921 :	overbeek	1.13	}
2922 :
2923 :	gdpusch	1.107	my ($arch, $bact, $euk, $vir, $env, $unk) = (0, 0, 0, 0, 0, 0);
2924 :	parrello	1.287	if (@$relational_db_response > 0) {
2925 :			foreach $x (@$relational_db_response) {
2926 :			if ($x->[1] =~ /^archaea/i) { ++$arch }
2927 :			elsif ($x->[1] =~ /^bacter/i) { ++$bact }
2928 :			elsif ($x->[1] =~ /^eukar/i) { ++$euk }
2929 :			elsif ($x->[1] =~ /^vir/i) { ++$vir }
2930 :			elsif ($x->[1] =~ /^env/i) { ++$env }
2931 :			else { ++$unk }
2932 :			}
2933 :	efrank	1.2	}
2934 :	parrello	1.200
2935 :	gdpusch	1.107	return ($arch, $bact, $euk, $vir, $env, $unk);
2936 :			}
2937 :
2938 :
2939 :	parrello	1.287	=head3 genome_domain
2940 :
2941 :			C<< my $domain = $fig->genome_domain($genome_id); >>
2942 :
2943 :			Find the domain of a genome.
2944 :	gdpusch	1.107
2945 :	parrello	1.287	=over 4
2946 :
2947 :			=item genome_id
2948 :	gdpusch	1.107
2949 :	parrello	1.287	ID of the genome whose domain is desired.
2950 :	gdpusch	1.107
2951 :	parrello	1.287	=item RETURN
2952 :
2953 :			Returns the name of the genome's domain (archaea, bacteria, etc.), or C<undef> if
2954 :			the genome is not in the database.
2955 :	gdpusch	1.107
2956 :	parrello	1.292	=back
2957 :
2958 :	gdpusch	1.107	=cut
2959 :
2960 :			sub genome_domain {
2961 :			my($self,$genome) = @_;
2962 :			my $relational_db_response;
2963 :			my $rdbH = $self->db_handle;
2964 :	parrello	1.200
2965 :	parrello	1.287	if ($genome) {
2966 :			if (($relational_db_response = $rdbH->SQL("SELECT genome,maindomain FROM genome WHERE ( genome = \'$genome\' )"))
2967 :			&& (@$relational_db_response == 1)) {
2968 :			# die Dumper($relational_db_response);
2969 :			return $relational_db_response->[0]->[1];
2970 :			}
2971 :	gdpusch	1.107	}
2972 :			return undef;
2973 :	efrank	1.2	}
2974 :
2975 :	gdpusch	1.92
2976 :	parrello	1.287	=head3 genome_pegs
2977 :	gdpusch	1.92
2978 :	parrello	1.287	C<< my $num_pegs = $fig->genome_pegs($genome_id); >>
2979 :	gdpusch	1.92
2980 :	parrello	1.287	Return the number of protein-encoding genes (PEGs) for a specified
2981 :			genome.
2982 :	gdpusch	1.92
2983 :	parrello	1.287	=over 4
2984 :
2985 :			=item genome_id
2986 :
2987 :			ID of the genome whose PEG count is desired.
2988 :
2989 :			=item RETURN
2990 :
2991 :			Returns the number of PEGs for the specified genome, or C<undef> if the genome
2992 :			is not indexed in the database.
2993 :
2994 :			=back
2995 :	gdpusch	1.92
2996 :			=cut
2997 :
2998 :			sub genome_pegs {
2999 :			my($self,$genome) = @_;
3000 :			my $relational_db_response;
3001 :			my $rdbH = $self->db_handle;
3002 :	parrello	1.200
3003 :	parrello	1.287	if ($genome) {
3004 :			if (($relational_db_response = $rdbH->SQL("SELECT pegs FROM genome WHERE ( genome = \'$genome\' )"))
3005 :			&& (@$relational_db_response == 1)) {
3006 :			return $relational_db_response->[0]->[0];
3007 :			}
3008 :	gdpusch	1.92	}
3009 :			return undef;
3010 :			}
3011 :
3012 :
3013 :	parrello	1.287	=head3 genome_rnas
3014 :
3015 :			C<< my $num_rnas = $fig->genome_rnas($genome_id); >>
3016 :
3017 :			Return the number of RNA-encoding genes for a genome.
3018 :			"$genome_id" is indexed in the "genome" database, and 'undef' otherwise.
3019 :	efrank	1.1
3020 :	parrello	1.287	=over 4
3021 :
3022 :			=item genome_id
3023 :
3024 :			ID of the genome whose RNA count is desired.
3025 :
3026 :			=item RETURN
3027 :	gdpusch	1.92
3028 :	parrello	1.287	Returns the number of RNAs for the specified genome, or C<undef> if the genome
3029 :			is not indexed in the database.
3030 :	gdpusch	1.92
3031 :	parrello	1.287	=back
3032 :	gdpusch	1.92
3033 :			=cut
3034 :
3035 :			sub genome_rnas {
3036 :			my($self,$genome) = @_;
3037 :			my $relational_db_response;
3038 :			my $rdbH = $self->db_handle;
3039 :	parrello	1.200
3040 :	parrello	1.287	if ($genome) {
3041 :			if (($relational_db_response = $rdbH->SQL("SELECT rnas FROM genome WHERE ( genome = \'$genome\' )"))
3042 :			&& (@$relational_db_response == 1)) {
3043 :			return $relational_db_response->[0]->[0];
3044 :			}
3045 :	gdpusch	1.92	}
3046 :			return undef;
3047 :			}
3048 :
3049 :
3050 :	parrello	1.287	=head3 genome_szdna
3051 :
3052 :			usage: $szdna = $fig->genome_szdna($genome_id);
3053 :
3054 :			Return the number of DNA base-pairs in a genome's contigs.
3055 :
3056 :			=over 4
3057 :
3058 :			=item genome_id
3059 :
3060 :			ID of the genome whose base-pair count is desired.
3061 :	gdpusch	1.92
3062 :	parrello	1.287	=item RETURN
3063 :	efrank	1.1
3064 :	parrello	1.287	Returns the number of base pairs in the specified genome's contigs, or C<undef>
3065 :			if the genome is not indexed in the database.
3066 :	gdpusch	1.91
3067 :	parrello	1.287	=back
3068 :	gdpusch	1.91
3069 :			=cut
3070 :
3071 :	gdpusch	1.92	sub genome_szdna {
3072 :	gdpusch	1.91	my($self,$genome) = @_;
3073 :			my $relational_db_response;
3074 :			my $rdbH = $self->db_handle;
3075 :	parrello	1.200
3076 :	parrello	1.287	if ($genome) {
3077 :			if (($relational_db_response =
3078 :			$rdbH->SQL("SELECT szdna FROM genome WHERE ( genome = \'$genome\' )"))
3079 :			&& (@$relational_db_response == 1)) {
3080 :
3081 :			return $relational_db_response->[0]->[0];
3082 :
3083 :			}
3084 :	gdpusch	1.91	}
3085 :			return undef;
3086 :			}
3087 :
3088 :	parrello	1.287	=head3 genome_version
3089 :	gdpusch	1.91
3090 :	parrello	1.287	C<< my $version = $fig->genome_version($genome_id); >>
3091 :	gdpusch	1.91
3092 :	parrello	1.287	Return the version number of the specified genome.
3093 :	efrank	1.1
3094 :			Versions are incremented for major updates. They are put in as major
3095 :			updates of the form 1.0, 2.0, ...
3096 :
3097 :			Users may do local "editing" of the DNA for a genome, but when they do,
3098 :			they increment the digits to the right of the decimal. Two genomes remain
3099 :	parrello	1.200	comparable only if the versions match identically. Hence, minor updating should be
3100 :	efrank	1.1	committed only by the person/group responsible for updating that genome.
3101 :
3102 :			We can, of course, identify which genes are identical between any two genomes (by matching
3103 :			the DNA or amino acid sequences). However, the basic intent of the system is to
3104 :			support editing by the main group issuing periodic major updates.
3105 :
3106 :	parrello	1.287	=over 4
3107 :
3108 :			=item genome_id
3109 :
3110 :			ID of the genome whose version is desired.
3111 :
3112 :			=item RETURN
3113 :
3114 :			Returns the version number of the specified genome, or C<undef> if the genome is not in
3115 :			the data store or no version number has been assigned.
3116 :
3117 :			=back
3118 :
3119 :	efrank	1.1	=cut
3120 :
3121 :	olson	1.113	sub genome_version :scalar {
3122 :	efrank	1.1	my($self,$genome) = @_;
3123 :
3124 :			my(@tmp);
3125 :			if ((-s "$FIG_Config::organisms/$genome/VERSION") &&
3126 :	parrello	1.287	(@tmp = `cat $FIG_Config::organisms/$genome/VERSION`) &&
3127 :			($tmp[0] =~ /^(\S+)$/)) {
3128 :			return $1;
3129 :	efrank	1.1	}
3130 :			return undef;
3131 :			}
3132 :
3133 :	parrello	1.287	=head3 genome_md5sum
3134 :	olson	1.236
3135 :	parrello	1.287	C<< my $md5sum = $fig->genome_md5sum($genome_id); >>
3136 :	olson	1.236
3137 :	parrello	1.287	Returns the MD5 checksum of the specified genome.
3138 :	olson	1.236
3139 :			The checksum of a genome is defined as the checksum of its signature file. The signature
3140 :			file consists of tab-separated lines, one for each contig, ordered by the contig id.
3141 :	parrello	1.287	Each line contains the contig ID, the length of the contig in nucleotides, and the
3142 :	olson	1.236	MD5 checksum of the nucleotide data, with uppercase letters forced to lower case.
3143 :
3144 :	parrello	1.287	The checksum is indexed in the database. If you know a genome's checksum, you can use
3145 :			the L</genome_with_md5sum> method to find its ID in the database.
3146 :
3147 :			=over 4
3148 :
3149 :			=item genome
3150 :
3151 :			ID of the genome whose checksum is desired.
3152 :
3153 :			=item RETURN
3154 :
3155 :			Returns the specified genome's checksum, or C<undef> if the genome is not in the
3156 :			database.
3157 :
3158 :			=back
3159 :	olson	1.236
3160 :			=cut
3161 :
3162 :	olson	1.237	sub genome_md5sum :scalar {
3163 :	olson	1.236	my($self,$genome) = @_;
3164 :			my $relational_db_response;
3165 :			my $rdbH = $self->db_handle;
3166 :
3167 :	parrello	1.287	if ($genome) {
3168 :			if (($relational_db_response =
3169 :			$rdbH->SQL("SELECT md5sum FROM genome_md5sum WHERE ( genome = \'$genome\' )"))
3170 :			&& (@$relational_db_response == 1)) {
3171 :			return $relational_db_response->[0]->[0];
3172 :			}
3173 :	olson	1.236	}
3174 :			return undef;
3175 :			}
3176 :
3177 :	parrello	1.287	=head3 genome_with_md5sum
3178 :
3179 :			C<< my $genome = $fig->genome_with_md5sum($cksum); >>
3180 :
3181 :			Find a genome with the specified checksum.
3182 :
3183 :			The MD5 checksum is computed from the content of the genome (see L</genome_md5sum>). This method
3184 :			can be used to determine if a genome already exists for a specified content.
3185 :
3186 :			=over 4
3187 :
3188 :			=item cksum
3189 :
3190 :			Checksum to use for searching the genome table.
3191 :	olson	1.260
3192 :	parrello	1.287	=item RETURN
3193 :
3194 :			The ID of a genome with the specified checksum, or C<undef> if no such genome exists.
3195 :	olson	1.260
3196 :	parrello	1.287	=back
3197 :	olson	1.260
3198 :			=cut
3199 :
3200 :			sub genome_with_md5sum :scalar {
3201 :			my($self,$cksum) = @_;
3202 :			my $relational_db_response;
3203 :			my $rdbH = $self->db_handle;
3204 :
3205 :	parrello	1.287	if (($relational_db_response =
3206 :			$rdbH->SQL("SELECT genome FROM genome_md5sum WHERE ( md5sum = \'$cksum\' )"))
3207 :			&& (@$relational_db_response == 1)) {
3208 :			return $relational_db_response->[0]->[0];
3209 :	olson	1.260	}
3210 :
3211 :			return undef;
3212 :			}
3213 :
3214 :	parrello	1.287	=head3 contig_md5sum
3215 :
3216 :			C<< my $cksum = $fig->contig_md5sum($genome, $contig); >>
3217 :
3218 :			Return the MD5 checksum for a contig. The MD5 checksum is computed from the content
3219 :			of the contig. This method retrieves the checksum stored in the database. The checksum
3220 :			can be compared to the checksum of an external contig as a cheap way of seeing if they
3221 :			match.
3222 :
3223 :			=over 4
3224 :
3225 :			=item genome
3226 :
3227 :			ID of the genome containing the contig.
3228 :
3229 :			=item contig
3230 :
3231 :			ID of the relevant contig.
3232 :
3233 :			=item RETURN
3234 :
3235 :			Returns the checksum of the specified contig, or C<undef> if the contig is not in the
3236 :			database.
3237 :
3238 :			=back
3239 :
3240 :			=cut
3241 :
3242 :	olson	1.237	sub contig_md5sum :scalar {
3243 :			my($self, $genome, $contig) = @_;
3244 :			my $relational_db_response;
3245 :			my $rdbH = $self->db_handle;
3246 :
3247 :	parrello	1.287	if ($genome) {
3248 :			if (($relational_db_response =
3249 :			$rdbH->SQL(qq(SELECT md5 FROM contig_md5sums WHERE (genome = ? AND contig = ?)), undef, $genome, $contig))
3250 :			&& (@$relational_db_response == 1)) {
3251 :			return $relational_db_response->[0]->[0];
3252 :			}
3253 :	olson	1.237	}
3254 :			return undef;
3255 :			}
3256 :
3257 :	parrello	1.287	=head3 genus_species
3258 :
3259 :			C<< my $gs = $fig->genus_species($genome_id); >>
3260 :
3261 :			Return the genus, species, and possibly also the strain of a specified genome.
3262 :
3263 :			This method converts a genome ID into a more recognizble species name. The species name
3264 :			is stored directly in the genome table of the database. Essentially, if the strain is
3265 :			present in the database, it will be returned by this method, and if it's not present,
3266 :			it won't.
3267 :	efrank	1.1
3268 :	parrello	1.287	=over 4
3269 :
3270 :			=item genome_id
3271 :
3272 :			ID of the genome whose name is desired.
3273 :	efrank	1.1
3274 :	parrello	1.287	=item RETURN
3275 :
3276 :			Returns the scientific species name associated with the specified ID, or C<undef> if the
3277 :			ID is not in the database.
3278 :	efrank	1.1
3279 :	parrello	1.287	=back
3280 :	efrank	1.1
3281 :			=cut
3282 :
3283 :	olson	1.111	sub genus_species :scalar {
3284 :	efrank	1.1	my ($self,$genome) = @_;
3285 :	overbeek	1.13	my $ans;
3286 :	efrank	1.1
3287 :			my $genus_species = $self->cached('_genus_species');
3288 :	parrello	1.287	if (! ($ans = $genus_species->{$genome})) {
3289 :			my $rdbH = $self->db_handle;
3290 :			my $relational_db_response = $rdbH->SQL("SELECT genome,gname FROM genome");
3291 :			my $pair;
3292 :			foreach $pair (@$relational_db_response) {
3293 :			$genus_species->{$pair->[0]} = $pair->[1];
3294 :			}
3295 :			$ans = $genus_species->{$genome};
3296 :	efrank	1.1	}
3297 :			return $ans;
3298 :			}
3299 :
3300 :	parrello	1.287	=head3 org_of
3301 :
3302 :			C<< my $org = $fig->org_of($prot_id); >>
3303 :
3304 :			Return the genus/species name of the organism containing a protein. Note that in this context
3305 :			I<protein> is not a certain string of amino acids but a protein encoding region on a specific
3306 :			contig.
3307 :
3308 :			For a FIG protein ID (e.g. C<fig\|134537.1.peg.123>), the organism and strain
3309 :			information is always available. In the case of external proteins, we can usually
3310 :			determine an organism, but not anything more precise than genus/species (and
3311 :			often not that). When the organism name is not present, a null string is returned.
3312 :
3313 :			=over 4
3314 :
3315 :			=item prot_id
3316 :	efrank	1.1
3317 :	parrello	1.287	Protein or feature ID.
3318 :	efrank	1.1
3319 :	parrello	1.287	=item RETURN
3320 :
3321 :			Returns the displayable scientific name (genus, species, and strain) of the organism containing
3322 :			the identified PEG. If the name is not available, returns a null string. If the PEG is not found,
3323 :			returns C<undef>.
3324 :	efrank	1.1
3325 :	parrello	1.287	=back
3326 :	efrank	1.1
3327 :			=cut
3328 :
3329 :			sub org_of {
3330 :			my($self,$prot_id) = @_;
3331 :			my $relational_db_response;
3332 :			my $rdbH = $self->db_handle;
3333 :
3334 :	parrello	1.287	if ($prot_id =~ /^fig\\|/) {
3335 :			return $self->is_deleted_fid( $prot_id) ? undef
3336 :			: $self->genus_species( $self->genome_of( $prot_id ) ) \|\| "";
3337 :	efrank	1.1	}
3338 :
3339 :	parrello	1.287	if (($relational_db_response =
3340 :			$rdbH->SQL("SELECT org FROM external_orgs WHERE ( prot = \'$prot_id\' )")) &&
3341 :			(@$relational_db_response >= 1)) {
3342 :			$relational_db_response->[0]->[0] =~ s/^\d+://;
3343 :			return $relational_db_response->[0]->[0];
3344 :	efrank	1.1	}
3345 :			return "";
3346 :			}
3347 :
3348 :	parrello	1.287	=head3 genus_species_domain
3349 :
3350 :			C<< my ($gs, $domain) = $fig->genus_species_domain($genome_id); >>
3351 :
3352 :			Returns a genome's genus and species (and strain if that has been properly
3353 :			recorded) in a printable form, along with its domain. This method is similar
3354 :			to L</genus_species>, except it also returns the domain name (archaea,
3355 :			bacteria, etc.).
3356 :
3357 :			=over 4
3358 :
3359 :			=item genome_id
3360 :
3361 :			ID of the genome whose species and domain information is desired.
3362 :	golsen	1.130
3363 :	parrello	1.287	=item RETURN
3364 :	golsen	1.130
3365 :	parrello	1.287	Returns a two-element list. The first element is the species name and the
3366 :			second is the domain name.
3367 :	golsen	1.130
3368 :	parrello	1.287	=back
3369 :	golsen	1.130
3370 :			=cut
3371 :
3372 :			sub genus_species_domain {
3373 :			my ($self, $genome) = @_;
3374 :
3375 :			my $genus_species_domain = $self->cached('_genus_species_domain');
3376 :	parrello	1.287	if ( ! $genus_species_domain->{ $genome } ) {
3377 :			my $rdbH = $self->db_handle;
3378 :			my $relational_db_response = $rdbH->SQL("SELECT genome,gname,maindomain FROM genome");
3379 :			my $triple;
3380 :			foreach $triple ( @$relational_db_response ) {
3381 :			$genus_species_domain->{ $triple->[0] } = [ $triple->[1], $triple->[2] ];
3382 :			}
3383 :	golsen	1.130	}
3384 :			my $gsdref = $genus_species_domain->{ $genome };
3385 :			return $gsdref ? @$gsdref : ( "", "" );
3386 :			}
3387 :
3388 :	parrello	1.287	=head3 domain_color
3389 :
3390 :			C<< my $web_color = FIG::domain_color($domain); >>
3391 :
3392 :			Return the web color string associated with a specified domain. The colors are
3393 :			extremely subtle (86% luminance), so they absolutely require a black background.
3394 :			Archaea are slightly cyan, bacteria are slightly magenta, eukaryota are slightly
3395 :			yellow, viruses are slightly silver, environmental samples are slightly gray,
3396 :			and unknown or invalid domains are pure white.
3397 :
3398 :			=over 4
3399 :
3400 :			=item domain
3401 :
3402 :			Name of the domain whose color is desired.
3403 :
3404 :			=item RETURN
3405 :
3406 :			Returns a web color string for the specified domain (e.g. C<#FFDDFF> for
3407 :			bacteria).
3408 :
3409 :			=back
3410 :
3411 :			=cut
3412 :	golsen	1.130
3413 :			my %domain_color = ( AR => "#DDFFFF", BA => "#FFDDFF", EU => "#FFFFDD",
3414 :			VI => "#DDDDDD", EN => "#BBBBBB" );
3415 :
3416 :			sub domain_color {
3417 :			my ($domain) = @_;
3418 :			defined $domain \|\| return "#FFFFFF";
3419 :			return $domain_color{ uc substr($domain, 0, 2) } \|\| "#FFFFFF";
3420 :			}
3421 :
3422 :	parrello	1.287	=head3 org_and_color_of
3423 :	golsen	1.130
3424 :	parrello	1.287	C<< my ($org, $color) = $fig->org_and_domain_of($prot_id); >>
3425 :	golsen	1.130
3426 :	parrello	1.287	Return the best guess organism and domain html color string of an organism.
3427 :			In the case of external proteins, we can usually determine an organism, but not
3428 :			anything more precise than genus/species (and often not that).
3429 :
3430 :			=over 4
3431 :
3432 :			=item prot_id
3433 :
3434 :			Relevant protein or feature ID.
3435 :
3436 :			=item RETURN
3437 :	golsen	1.130
3438 :	parrello	1.287	Returns a two-element list. The first element is the displayable organism name, and the second
3439 :			is an HTML color string based on the domain (see L</domain_color>).
3440 :	golsen	1.130
3441 :	parrello	1.287	=back
3442 :	golsen	1.130
3443 :			=cut
3444 :
3445 :			sub org_and_color_of {
3446 :			my($self,$prot_id) = @_;
3447 :			my $relational_db_response;
3448 :			my $rdbH = $self->db_handle;
3449 :
3450 :	parrello	1.287	if ($prot_id =~ /^fig\\|/) {
3451 :			my( $gs, $domain ) = $self->genus_species_domain($self->genome_of($prot_id));
3452 :			return ( $gs, domain_color( $domain ) );
3453 :	golsen	1.130	}
3454 :
3455 :	parrello	1.287	if (($relational_db_response =
3456 :			$rdbH->SQL("SELECT org FROM external_orgs WHERE ( prot = \'$prot_id\' )")) &&
3457 :			(@$relational_db_response >= 1)) {
3458 :			return ($relational_db_response->[0]->[0], "#FFFFFF");
3459 :	golsen	1.130	}
3460 :			return ("", "#FFFFFF");
3461 :			}
3462 :
3463 :	parrello	1.287	=head3 abbrev
3464 :
3465 :			C<< my $abbreviated_name = FIG::abbrev($genome_name); >>
3466 :	golsen	1.130
3467 :	parrello	1.287	or
3468 :	efrank	1.1
3469 :	parrello	1.287	C<< my $abbreviated_name = $fig->abbrev($genome_name); >>
3470 :	efrank	1.1
3471 :	parrello	1.287	Abbreviate a genome name to 10 characters or less.
3472 :	efrank	1.1
3473 :			For alignments and such, it is very useful to be able to produce an abbreviation of genus/species.
3474 :			That's what this does. Note that multiple genus/species might reduce to the same abbreviation, so
3475 :			be careful (disambiguate them, if you must).
3476 :
3477 :	parrello	1.287	The abbreviation is formed from the first three letters of the species name followed by the
3478 :			first three letters of the genus name followed by the first three letters of the species name and
3479 :			then the next four nonblank characters.
3480 :
3481 :			=over 4
3482 :
3483 :			=item genome_name
3484 :
3485 :			The name to abbreviate.
3486 :
3487 :			=item RETURN
3488 :
3489 :			An abbreviated version of the specified name.
3490 :
3491 :			=back
3492 :
3493 :	efrank	1.1	=cut
3494 :
3495 :	olson	1.111	sub abbrev :scalar {
3496 :			shift if UNIVERSAL::isa($_[0],__PACKAGE__);
3497 :	efrank	1.1	my($genome_name) = @_;
3498 :
3499 :			$genome_name =~ s/^(\S{3})\S+/$1./;
3500 :	overbeek	1.198	$genome_name =~ s/^(\S+)\s+(\S{3})\S+/$1$2./;
3501 :	overbeek	1.257	$genome_name =~ s/ //g;
3502 :	parrello	1.287	if (length($genome_name) > 10) {
3503 :			$genome_name = substr($genome_name,0,10);
3504 :	efrank	1.1	}
3505 :			return $genome_name;
3506 :			}
3507 :
3508 :			################ Routines to process Features and Feature IDs ##########################
3509 :
3510 :	parrello	1.287	=head3 ftype
3511 :
3512 :			C<< my $type = FIG::ftype($fid); >>
3513 :	efrank	1.1
3514 :	parrello	1.287	or
3515 :	efrank	1.1
3516 :	parrello	1.287	C<< my $type = $fig->ftype($fid); >>
3517 :	efrank	1.1
3518 :			Returns the type of a feature, given the feature ID. This just amounts
3519 :	parrello	1.287	to lifting it out of the feature ID, since features have IDs of the form
3520 :	efrank	1.1
3521 :	parrello	1.287	fig\|x.y.f.n
3522 :	efrank	1.1
3523 :			where
3524 :			x.y is the genome ID
3525 :	parrello	1.287	f is the type of feature
3526 :	efrank	1.1	n is an integer that is unique within the genome/type
3527 :
3528 :	parrello	1.287	=over 4
3529 :
3530 :			=item fid
3531 :
3532 :			FIG ID of the feature whose type is desired.
3533 :
3534 :			=item RETURN
3535 :
3536 :			Returns the feature type (e.g. C<peg>, C<rna>, C<pi>, or C<pp>), or C<undef> if the
3537 :			feature ID is not a FIG ID.
3538 :
3539 :			=back
3540 :
3541 :	efrank	1.1	=cut
3542 :
3543 :			sub ftype {
3544 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
3545 :	efrank	1.1	my($feature_id) = @_;
3546 :
3547 :	parrello	1.287	if ($feature_id =~ /^fig\\|\d+\.\d+\.([^\.]+)/) {
3548 :			return $1;
3549 :	efrank	1.1	}
3550 :			return undef;
3551 :			}
3552 :
3553 :	parrello	1.287	=head3 genome_of
3554 :
3555 :			C<< my $genome_id = $fig->genome_of($fid); >>
3556 :
3557 :			or
3558 :
3559 :			C<< my $genome_id = FIG::genome_of($fid); >>
3560 :
3561 :			Return the genome ID from a feature ID.
3562 :	efrank	1.1
3563 :	parrello	1.287	=over 4
3564 :
3565 :			=item fid
3566 :
3567 :			ID of the feature whose genome ID is desired.
3568 :
3569 :			=item RETURN
3570 :	efrank	1.1
3571 :	parrello	1.287	If the feature ID is a FIG ID, returns the genome ID embedded inside it; otherwise, it
3572 :			returns C<undef>.
3573 :	efrank	1.1
3574 :	parrello	1.287	=back
3575 :	efrank	1.1
3576 :			=cut
3577 :
3578 :
3579 :	olson	1.113	sub genome_of :scalar {
3580 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
3581 :	parrello	1.200	my $prot_id = (@_ == 1) ? $_[0] : $_[1];
3582 :	efrank	1.1
3583 :			if ($prot_id =~ /^fig\\|(\d+\.\d+)/) { return $1; }
3584 :			return undef;
3585 :			}
3586 :
3587 :	parrello	1.287	=head3 genome_and_peg_of
3588 :
3589 :			C<< my ($genome_id, $peg_number = FIG::genome_and_peg_of($fid); >>
3590 :
3591 :			C<< my ($genome_id, $peg_number = $fig->genome_and_peg_of($fid); >>
3592 :	olson	1.96
3593 :	parrello	1.287	Return the genome ID and peg number from a feature ID.
3594 :	olson	1.96
3595 :	parrello	1.287	=over 4
3596 :
3597 :			=item prot_id
3598 :
3599 :			ID of the feature whose genome and PEG number as desired.
3600 :
3601 :			=item RETURN
3602 :
3603 :			Returns the genome ID and peg number associated with a feature if the feature
3604 :			is represented by a FIG ID, else C<undef>.
3605 :
3606 :			=back
3607 :	olson	1.96
3608 :			=cut
3609 :
3610 :			sub genome_and_peg_of {
3611 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
3612 :	parrello	1.200	my $prot_id = (@_ == 1) ? $_[0] : $_[1];
3613 :	olson	1.96
3614 :	parrello	1.287	if ($prot_id =~ /^fig\\|(\d+\.\d+)\.peg\.(\d+)/) {
3615 :			return ($1, $2);
3616 :	olson	1.96	}
3617 :			return undef;
3618 :			}
3619 :
3620 :	parrello	1.287	=head3 by_fig_id
3621 :
3622 :			C<< my @sorted_by_fig_id = sort { FIG::by_fig_id($a,$b) } @fig_ids; >>
3623 :
3624 :			Compare two feature IDs.
3625 :
3626 :			This function is designed to assist in sorting features by ID. The sort is by
3627 :			genome ID followed by feature type and then feature number.
3628 :
3629 :			=over 4
3630 :
3631 :			=item a
3632 :	efrank	1.1
3633 :	parrello	1.287	First feature ID.
3634 :	efrank	1.1
3635 :	parrello	1.287	=item b
3636 :	efrank	1.1
3637 :	parrello	1.287	Second feature ID.
3638 :
3639 :			=item RETURN
3640 :
3641 :			Returns a negative number if the first parameter is smaller, zero if both parameters
3642 :			are equal, and a positive number if the first parameter is greater.
3643 :
3644 :			=back
3645 :	efrank	1.1
3646 :			=cut
3647 :
3648 :			sub by_fig_id {
3649 :			my($a,$b) = @_;
3650 :			my($g1,$g2,$t1,$t2,$n1,$n2);
3651 :			if (($a =~ /^fig\\|(\d+\.\d+).([^\.]+)\.(\d+)$/) && (($g1,$t1,$n1) = ($1,$2,$3)) &&
3652 :	parrello	1.287	($b =~ /^fig\\|(\d+\.\d+).([^\.]+)\.(\d+)$/) && (($g2,$t2,$n2) = ($1,$2,$3))) {
3653 :			($g1 <=> $g2) or ($t1 cmp $t2) or ($n1 <=> $n2);
3654 :			} else {
3655 :			$a cmp $b;
3656 :	efrank	1.1	}
3657 :			}
3658 :
3659 :	parrello	1.287	=head3 genes_in_region
3660 :	efrank	1.1
3661 :	parrello	1.287	C<< my ($features_in_region, $beg1, $end1) = $fig->genes_in_region($genome, $contig, $beg, $end, size_limit); >>
3662 :	efrank	1.1
3663 :	parrello	1.287	Locate features that overlap a specified region of a contig. This includes features that begin or end
3664 :			outside that region, just so long as some part of the feature can be found in the region of interest.
3665 :	efrank	1.1
3666 :			It is often important to be able to find the genes that occur in a specific region on
3667 :			a chromosome. This routine is designed to provide this information. It returns all genes
3668 :	parrello	1.287	that overlap positions from I<$beg> through I<$end> in the specified contig.
3669 :
3670 :			The I<$size_limit> parameter limits the search process. It is presumed that no features are longer than the
3671 :			specified size limit. A shorter size limit means you'll miss some features; a longer size limit significantly
3672 :			slows the search process. For prokaryotes, a value of C<10000> (the default) seems to work best.
3673 :
3674 :			=over 4
3675 :
3676 :			=item genome
3677 :
3678 :			ID of the genome containing the relevant contig.
3679 :
3680 :			=item contig
3681 :
3682 :			ID of the relevant contig.
3683 :
3684 :			=item beg
3685 :
3686 :			Position of the first base pair in the region of interest.
3687 :
3688 :			=item end
3689 :
3690 :			Position of the last base pair in the region of interest.
3691 :
3692 :			=item size_limit
3693 :
3694 :			Maximum allowable size for a feature. If omitted, C<10000> is assumed.
3695 :
3696 :			=item RETURN
3697 :	efrank	1.1
3698 :	parrello	1.287	Returns a three-element list. The first element is a reference to a list of the feature IDs found. The second
3699 :			element is the position of the leftmost base pair in any feature found. This may be well before the region of
3700 :			interest begins or it could be somewhere inside. The third element is the position of the rightmost base pair
3701 :			in any feature found. Again, this can be somewhere inside the region or it could be well to the right of it.
3702 :
3703 :			=back
3704 :	efrank	1.1
3705 :			=cut
3706 :	parrello	1.213	#: Return Type @;
3707 :	efrank	1.1	sub genes_in_region {
3708 :	parrello	1.287	my($self, $genome, $contig, $beg, $end, $pad) = @_;
3709 :			if (!defined $pad) { $pad = 10000; }
3710 :	efrank	1.1	my($x,$relational_db_response,$feature_id,$b1,$e1,@feat,@tmp,$l,$u);
3711 :
3712 :			my $rdbH = $self->db_handle;
3713 :
3714 :	parrello	1.200	my $minV = $beg - $pad;
3715 :	efrank	1.1	my $maxV = $end + $pad;
3716 :	parrello	1.287	if (($relational_db_response = $rdbH->SQL("SELECT id FROM features "
3717 :			. " WHERE ( minloc > $minV ) AND ( minloc < $maxV ) AND ( maxloc < $maxV) AND "
3718 :			. " ( genome = \'$genome\' ) AND ( contig = \'$contig\' );")) &&
3719 :			(@$relational_db_response >= 1)) {
3720 :			@tmp = sort { ($a->[1] cmp $b->[1]) or (($a->[2]+$a->[3]) <=> ($b->[2]+$b->[3])) }
3721 :			map { $feature_id = $_->[0]; $x = $self->feature_location($feature_id); $x ? [$feature_id,&boundaries_of($x)] : ()
3722 :			} @$relational_db_response;
3723 :	efrank	1.1
3724 :
3725 :	parrello	1.287	($l,$u) = (10000000000,0);
3726 :			foreach $x (@tmp)
3727 :			{
3728 :			($feature_id,undef,$b1,$e1) = @$x;
3729 :			if (&between($beg,&min($b1,$e1),$end) \|\| &between(&min($b1,$e1),$beg,&max($b1,$e1)))
3730 :			{
3731 :			if (! $self->is_deleted_fid($feature_id))
3732 :			{
3733 :			push(@feat,$feature_id);
3734 :			$l = &min($l,&min($b1,$e1));
3735 :			$u = &max($u,&max($b1,$e1));
3736 :			}
3737 :			}
3738 :			}
3739 :			(@feat <= 0) \|\| return ([@feat],$l,$u);
3740 :	efrank	1.1	}
3741 :			return ([],$l,$u);
3742 :			}
3743 :
3744 :	golsen	1.141
3745 :			#=============================================================================
3746 :			# Using the following version is better, but it brings out a very annoying
3747 :			# issue with some genomes. It already exists in the current code (above)
3748 :			# for some genes in some genomes. For example, visit fig\|70601.1.peg.1.
3749 :			# This is true for any genome that has a feature that crosses the origin.
3750 :			# The root of the problem lies in boundaries_of. I am working on a fix that
3751 :			# replaces boundaries_of with a more sophisticated function. When it is
3752 :			# all done, genes_in_retion should behave as desired. -- GJO, Aug. 22, 2004
3753 :			#=============================================================================
3754 :	parrello	1.200	#
3755 :	golsen	1.141	# =pod
3756 :	parrello	1.200	#
3757 :	parrello	1.287	# =head3 genes_in_region
3758 :	parrello	1.200	#
3759 :	golsen	1.141	# usage: ( $features_in_region, $min_coord, $max_coord )
3760 :			# = $fig->genes_in_region( $genome, $contig, $beg, $end )
3761 :	parrello	1.200	#
3762 :	golsen	1.141	# It is often important to be able to find the genes that occur in a specific
3763 :			# region on a chromosome. This routine is designed to provide this information.
3764 :			# It returns all genes that overlap the region ( $genome, $contig, $beg, $end ).
3765 :			# $min_coord is set to the minimum coordinate of the returned genes (which may
3766 :			# preceed the given region), and $max_coord the maximum coordinate. Because
3767 :			# the database is indexed by the leftmost and rightmost coordinates of each
3768 :			# feature, the function makes no assumption about the length of the feature, but
3769 :			# it can (and probably will) miss features spanning multiple contigs.
3770 :	parrello	1.200	#
3771 :	golsen	1.141	# =cut
3772 :	parrello	1.200	#
3773 :			#
3774 :	golsen	1.141	# sub genes_in_region {
3775 :			# my ( $self, $genome, $contig, $beg, $end ) = @_;
3776 :			# my ( $x, $db_response, $feature_id, $b1, $e1, @tmp, @bounds );
3777 :			# my ( $min_coord, $max_coord );
3778 :	parrello	1.200	#
3779 :	golsen	1.141	# my @features = ();
3780 :			# my $rdbH = $self->db_handle;
3781 :	parrello	1.200	#
3782 :	golsen	1.141	# if ( ( $db_response = $rdbH->SQL( "SELECT id
3783 :			# FROM features
3784 :			# WHERE ( contig = '$contig' )
3785 :			# AND ( genome = '$genome' )
3786 :	parrello	1.200	# AND ( minloc <= $end )
3787 :	golsen	1.141	# AND ( maxloc >= $beg );"
3788 :			# )
3789 :			# )
3790 :			# && ( @$db_response > 0 )
3791 :			# )
3792 :			# {
3793 :			# # The sort is unnecessary, but provides a consistent ordering
3794 :	parrello	1.200	#
3795 :	golsen	1.141	# @tmp = sort { ( $a->[1] cmp $b->[1] ) # contig
3796 :			# \|\| ( ($a->[2] + $a->[3] ) <=> ( $b->[2] + $b->[3] ) ) # midpoint
3797 :			# }
3798 :			# map { $feature_id = $_->[0];
3799 :			# ( ( ! $self->is_deleted_fid( $feature_id ) ) # not deleted
3800 :			# && ( $x = $self->feature_location( $feature_id ) ) # and has location
3801 :			# && ( ( @bounds = boundaries_of( $x ) ) == 3 ) # and has bounds
3802 :	parrello	1.200	# ) ? [ $feature_id, @bounds ] : ()
3803 :	golsen	1.141	# } @$db_response;
3804 :	parrello	1.200	#
3805 :	golsen	1.141	# ( $min_coord, $max_coord ) = ( 10000000000, 0 );
3806 :	parrello	1.200	#
3807 :	golsen	1.141	# foreach $x ( @tmp )
3808 :			# {
3809 :			# ( $feature_id, undef, $b1, $e1 ) = @$x;
3810 :			# push @features, $feature_id;
3811 :			# my ( $min, $max ) = ( $b1 <= $e1 ) ? ( $b1, $e1 ) : ( $e1, $b1 );
3812 :			# ( $min_coord <= $min ) \|\| ( $min_coord = $min );
3813 :			# ( $max_coord >= $max ) \|\| ( $max_coord = $max );
3814 :			# }
3815 :			# }
3816 :	parrello	1.200	#
3817 :	golsen	1.141	# return ( @features ) ? ( [ @features ], $min_coord, $max_coord )
3818 :			# : ( [], undef, undef );
3819 :			# }
3820 :
3821 :			# These will be part of the fix to genes_in_region. -- GJO
3822 :
3823 :	parrello	1.287	=head3 regions_spanned
3824 :
3825 :			C<< my ( [ $contig, $beg, $end ], ... ) = $fig->regions_spanned( $loc ); >>
3826 :	golsen	1.141
3827 :	parrello	1.287	or
3828 :	golsen	1.141
3829 :	parrello	1.287	C<< my ( [ $contig, $beg, $end ], ... ) = FIG::regions_spanned( $loc ); >>
3830 :	golsen	1.141
3831 :			The location of a feature in a scalar context is
3832 :
3833 :	parrello	1.287	contig_b1_e1, contig_b2_e2, ... [one contig_b_e for each segment]
3834 :
3835 :			This routine takes as input a scalar location in the above form
3836 :			and reduces it to one or more regions spanned by the gene. This
3837 :			involves combining regions in the location string that are on the
3838 :			same contig and going in the same direction. Unlike L</boundaries_of>,
3839 :			which returns one region in which the entire gene can be found,
3840 :			B<regions_spanned> handles wrapping through the orgin, features
3841 :			split over contigs and exons that are not ordered nicely along
3842 :			the chromosome (ugly but true).
3843 :	golsen	1.141
3844 :	parrello	1.287	=over 4
3845 :
3846 :			=item loc
3847 :
3848 :			The location string for a feature.
3849 :
3850 :			=item RETURN
3851 :
3852 :			Returns a list of list references. Each inner list contains a contig ID, a starting
3853 :			position, and an ending position. The starting position may be numerically greater
3854 :			than the ending position (which indicates a backward-traveling gene). It is
3855 :			guaranteed that the entire feature is covered by the regions in the list.
3856 :
3857 :			=back
3858 :	golsen	1.141
3859 :			=cut
3860 :
3861 :			sub regions_spanned {
3862 :			shift if UNIVERSAL::isa( $_[0], __PACKAGE__ );
3863 :			my( $location ) = ( @_ == 1 ) ? $_[0] : $_[1];
3864 :			defined( $location ) \|\| return undef;
3865 :
3866 :			my @regions = ();
3867 :
3868 :			my ( $cur_contig, $cur_beg, $cur_end, $cur_dir );
3869 :			my ( $contig, $beg, $end, $dir );
3870 :			my @segs = split( /\s,\s/, $location ); # should not have space, but ...
3871 :			@segs \|\| return undef;
3872 :
3873 :			# Process the first segment
3874 :
3875 :			my $seg = shift @segs;
3876 :			( ( $cur_contig, $cur_beg, $cur_end ) = ( $seg =~ /^(\S+)_(\d+)_\d+$/ ) )
3877 :			\|\| return undef;
3878 :			$cur_dir = ( $cur_end >= $cur_beg ) ? 1 : -1;
3879 :
3880 :			foreach $seg ( @segs ) {
3881 :	parrello	1.287	( ( $contig, $beg, $end ) = ( $seg =~ /^(\S+)_(\d+)_\d+$/ ) ) \|\| next;
3882 :			$dir = ( $end >= $beg ) ? 1 : -1;
3883 :	golsen	1.141
3884 :	parrello	1.287	# Is this a continuation? Update end
3885 :	golsen	1.141
3886 :	parrello	1.287	if ( ( $contig eq $cur_contig )
3887 :			&& ( $dir == $cur_dir )
3888 :			&& ( ( ( $dir > 0 ) && ( $end > $cur_end ) )
3889 :			\|\| ( ( $dir < 0 ) && ( $end < $cur_end ) ) )
3890 :			)
3891 :			{
3892 :			$cur_end = $end;
3893 :			}
3894 :	golsen	1.141
3895 :	parrello	1.287	# Not a continuation. Report previous and update current.
3896 :	golsen	1.141
3897 :	parrello	1.287	else
3898 :			{
3899 :			push @regions, [ $cur_contig, $cur_beg, $cur_end ];
3900 :			( $cur_contig, $cur_beg, $cur_end, $cur_dir )
3901 :			= ( $contig, $beg, $end, $dir );
3902 :			}
3903 :	golsen	1.141	}
3904 :
3905 :			# There should alwasy be a valid, unreported region.
3906 :
3907 :			push @regions, [ $cur_contig, $cur_beg, $cur_end ];
3908 :
3909 :			return wantarray ? @regions : \@regions;
3910 :			}
3911 :
3912 :	parrello	1.287	=head3 filter_regions
3913 :
3914 :			C<< my @regions = FIG::filter_regions( $contig, $min, $max, @regions ); >>
3915 :
3916 :			or
3917 :
3918 :			C<< my \@regions = FIG::filter_regions( $contig, $min, $max, @regions ); >>
3919 :
3920 :			or
3921 :
3922 :			C<< my @regions = FIG::filter_regions( $contig, $min, $max, \@regions ); >>
3923 :
3924 :			or
3925 :
3926 :			C<< my \@regions = FIG::filter_regions( $contig, $min, $max, \@regions ); >>
3927 :
3928 :			Filter a list of regions to those that overlap a specified section of a
3929 :			particular contig. Region definitions correspond to those produced
3930 :			by L</regions_spanned>. That is, C<[>I<contig>C<,>I<beg>C<,>I<end>C<]>.
3931 :			In the function call, either I<$contig> or I<$min> and I<$max> can be
3932 :			undefined (permitting anything). So, for example,
3933 :
3934 :			my @regions = FIG::filter_regions(undef, 1, 5000, $regionList);
3935 :
3936 :			would return all regions in C<$regionList> that overlap the first
3937 :			5000 base pairs in any contig. Conversely,
3938 :
3939 :			my @regions = FIG::filter_regions('NC_003904', undef, undef, $regionList);
3940 :	golsen	1.141
3941 :	parrello	1.287	would return all regions on the contig C<NC_003904>.
3942 :	golsen	1.141
3943 :	parrello	1.287	=over 4
3944 :
3945 :			=item contig
3946 :
3947 :			ID of the contig whose regions are to be passed by the filter, or C<undef>
3948 :			if the contig doesn't matter.
3949 :
3950 :			=item min
3951 :
3952 :			Leftmost position of the region used for filtering. Only regions which contain
3953 :			at least one base pair at or beyond this position will be passed. A value
3954 :			of C<undef> is equivalent to zero.
3955 :
3956 :			=item max
3957 :
3958 :			Rightmost position of the region used for filtering. Only regions which contain
3959 :			at least one base pair on or before this position will be passed. A value
3960 :			of C<undef> is equivalent to the length of the contig.
3961 :
3962 :			=item regionList
3963 :	golsen	1.141
3964 :	parrello	1.287	A list of regions, or a reference to a list of regions. Each region is a
3965 :			reference to a three-element list, the first element of which is a contig
3966 :			ID, the second element of which is the start position, and the third
3967 :			element of which is the ending position. (The ending position can be
3968 :			before the starting position if the region is backward-traveling.)
3969 :
3970 :			=item RETURN
3971 :
3972 :			In a scalar context, returns a reference to a list of the filtered regions.
3973 :			In a list context, returns the list itself.
3974 :
3975 :			=back
3976 :	golsen	1.141
3977 :			=cut
3978 :
3979 :			sub filter_regions {
3980 :			my ( $contig, $min, $max, @regions ) = @_;
3981 :
3982 :			@regions \|\| return ();
3983 :			( ref( $regions[0] ) eq "ARRAY" ) \|\| return undef;
3984 :
3985 :			# Is it a region list, or a reference to a region list?
3986 :
3987 :			if ( ref( $regions[0]->[0] ) eq "ARRAY" ) { @regions = @{ $regions[0] } }
3988 :
3989 :			if ( ! defined( $contig ) )
3990 :			{
3991 :			( defined( $min ) && defined( $max ) ) \|\| return undef;
3992 :			}
3993 :			else # with a defined contig name, allow undefined range
3994 :			{
3995 :			defined( $min ) \|\| ( $min = 1 );
3996 :			defined( $max ) \|\| ( $max = 1000000000 );
3997 :			}
3998 :			( $min <= $max ) \|\| return ();
3999 :
4000 :			my ( $c, $b, $e );
4001 :			my @filtered = grep { ( @$_ >= 3 ) # Allow extra fields?
4002 :			&& ( ( $c, $b, $e ) = @$_ )
4003 :			&& ( ( ! defined( $contig ) ) \|\| ( $c eq $contig ) )
4004 :			&& ( ( $e >= $b ) \|\| ( ( $b, $e ) = ( $e, $b ) ) )
4005 :			&& ( ( $b <= $max ) && ( $e >= $min ) )
4006 :			} @regions;
4007 :
4008 :			return wantarray ? @filtered : \@filtered;
4009 :			}
4010 :
4011 :	parrello	1.287	=head3 close_genes
4012 :
4013 :			C<< my @features = $fig->close_genes($fid, $dist); >>
4014 :
4015 :			Return all features within a certain distance of a specified other feature.
4016 :
4017 :			This method is a quick way to get genes that are near another gene. It calls
4018 :			L</boundaries_of> to get the boundaries of the incoming gene, then passes
4019 :			the region computed to L</genes_in_region>.
4020 :
4021 :			So, for example, if the specified I<$dist> is 500, the method would select
4022 :			a region that extends 500 base pairs to either side of the boundaries for
4023 :			the gene I<$fid>, and pass it to C<genes_in_region> for analysis. The
4024 :			features returned would be those that overlap the selected region. Note
4025 :			that the flaws inherent in C<genes_in_region> are also inherent in this
4026 :			method: if a feature is more than 10000 base pairs long, it may not
4027 :			be caught even though it has an overlap in the specified region.
4028 :
4029 :			=over 4
4030 :
4031 :			=item fid
4032 :
4033 :			ID of the relevant feature.
4034 :
4035 :			=item dist
4036 :
4037 :			Desired maximum distance.
4038 :
4039 :			=item RETURN
4040 :
4041 :			Returns a list of feature IDs for genes that overlap or are close to the boundaries
4042 :			for the specified incoming feature.
4043 :
4044 :			=back
4045 :
4046 :			=cut
4047 :	golsen	1.141
4048 :	efrank	1.1	sub close_genes {
4049 :			my($self,$fid,$dist) = @_;
4050 :	parrello	1.200
4051 :	mkubal	1.147	# warn "In close_genes, self=$self, fid=$fid";
4052 :	parrello	1.200
4053 :	efrank	1.1	my $loc = $self->feature_location($fid);
4054 :			if ($loc)
4055 :			{
4056 :	parrello	1.287	my($contig,$beg,$end) = &FIG::boundaries_of($loc);
4057 :			if ($contig && $beg && $end)
4058 :			{
4059 :			my $min = &min($beg,$end) - $dist;
4060 :			my $max = &max($beg,$end) + $dist;
4061 :			my $feat;
4062 :			($feat,undef,undef) = $self->genes_in_region(&FIG::genome_of($fid),$contig,$min,$max);
4063 :			return @$feat;
4064 :			}
4065 :	efrank	1.1	}
4066 :			return ();
4067 :			}
4068 :
4069 :	parrello	1.287	=head3 adjacent_genes
4070 :
4071 :			C<< my ($left_fid, $right_fid) = $fig->adjacent_genes($fid, $dist); >>
4072 :
4073 :			Return the IDs of the genes immediately to the left and right of a specified
4074 :			feature.
4075 :
4076 :			This method gets a list of the features within the specified distance of
4077 :			the incoming feature (using L</close_genes>), and then chooses the two
4078 :			closest to the feature found. If the incoming feature is on the + strand,
4079 :			these are features to the left and the right. If the incoming feature is
4080 :			on the - strand, the features will be returned in reverse order.
4081 :
4082 :			=over 4
4083 :
4084 :			=item fid
4085 :
4086 :			ID of the feature whose neighbors are desired.
4087 :
4088 :			=item dist
4089 :
4090 :			Maximum permissible distance to the neighbors.
4091 :
4092 :			=item RETURN
4093 :
4094 :			Returns a two-element list containing the IDs of the features on either side
4095 :			of the incoming feature.
4096 :
4097 :			=back
4098 :
4099 :			=cut
4100 :
4101 :	mkubal	1.147	sub adjacent_genes
4102 :			{
4103 :			my ($self, $fid, $dist) = @_;
4104 :			my (@close, $strand, $i);
4105 :	parrello	1.200
4106 :	mkubal	1.147	# warn "In adjacent_genes, self=$self, fid=$fid";
4107 :	parrello	1.200
4108 :
4109 :	mkubal	1.147	$strand = $self->strand_of($fid);
4110 :	parrello	1.200
4111 :	mkubal	1.147	$dist = $dist \|\| 2000;
4112 :			@close = $self->close_genes($fid, $dist);
4113 :			for ($i=0; $i < @close; ++$i) { last if ($close[$i] eq $fid); }
4114 :	parrello	1.200
4115 :	redwards	1.157	# RAE note that if $self->strand_of($close[$i-1]) ne $strand then left/right neighbors
4116 :			# were never set! oops!
4117 :	parrello	1.200
4118 :	redwards	1.157	# I think the concept of Left and right is confused here. In my mind, left and right
4119 :			# are independent of strand ?? E.g. take a look at PEG fig\|196600.1.peg.1806
4120 :			# this is something like
4121 :			#
4122 :			# ---> <--1805--- --1806--> <--1807-- <----
4123 :			#
4124 :			# 1805 is always the left neighbor, no?
4125 :
4126 :			my ($left_neighbor, $right_neighbor) = ($close[$i-1], $close[$i+1]);
4127 :	parrello	1.200
4128 :	parrello	1.287	# if (0) # this was if ($i > 0) I just skip this whole section!
4129 :			# {
4130 :			# if ($self->strand_of($close[$i-1]) eq $strand) { $left_neighbor = $close[$i-1]; }
4131 :			# }
4132 :
4133 :			if ($i < $#close)
4134 :	mkubal	1.147	{
4135 :	parrello	1.287	if ($self->strand_of($close[$i+1]) eq $strand) { $right_neighbor = $close[$i+1]; }
4136 :	mkubal	1.147	}
4137 :	parrello	1.200
4138 :	parrello	1.287	# ...return genes in transcription order...
4139 :			if ($strand eq '-')
4140 :	mkubal	1.147	{
4141 :	parrello	1.287	($left_neighbor, $right_neighbor) = ($right_neighbor, $left_neighbor);
4142 :	mkubal	1.147	}
4143 :	parrello	1.200
4144 :	parrello	1.287	return ($left_neighbor, $right_neighbor) ;
4145 :			}
4146 :
4147 :			=head3 feature_location
4148 :
4149 :			C<< my $loc = $fig->feature_location($fid); >>
4150 :
4151 :			or
4152 :
4153 :			C<< my @loc = $fig->feature_location($fid);; >>
4154 :
4155 :			Return the location of a feature. The location consists
4156 :			of a list of (contigID, begin, end) triples encoded
4157 :			as strings with an underscore delimiter. So, for example,
4158 :			C<NC_002755_100_199> indicates a location starting at position
4159 :			100 and extending through 199 on the contig C<NC_002755>. If
4160 :			the location goes backward, the start location will be higher
4161 :			than the end location (e.g. C<NC_002755_199_100>).
4162 :
4163 :			In a scalar context, this method returns the locations as a
4164 :			comma-delimited string
4165 :	parrello	1.200
4166 :	parrello	1.287	NC_002755_100_199,NC_002755_210_498
4167 :	mkubal	1.147
4168 :	parrello	1.287	In a list context, the locations are returned as a list
4169 :	efrank	1.1
4170 :	parrello	1.287	(NC_002755_100_199, NC_002755_210_498)
4171 :	efrank	1.1
4172 :	parrello	1.287	=over 4
4173 :	efrank	1.1
4174 :	parrello	1.287	=item fid
4175 :	efrank	1.1
4176 :	parrello	1.287	ID of the feature whose location is desired.
4177 :	efrank	1.1
4178 :	parrello	1.287	=item RETURN
4179 :	efrank	1.1
4180 :	parrello	1.287	Returns the locations of a feature, either as a comma-delimited
4181 :			string or a list.
4182 :	efrank	1.1
4183 :	parrello	1.287	=back
4184 :	efrank	1.1
4185 :			=cut
4186 :
4187 :	olson	1.111	sub feature_location :scalar :list {
4188 :	efrank	1.1	my($self,$feature_id) = @_;
4189 :			my($relational_db_response,$locations,$location);
4190 :	parrello	1.200
4191 :	mkubal	1.147	# warn "In feature_location, self=$self, fid=$feature_id";
4192 :	parrello	1.200
4193 :	overbeek	1.136	if ($self->is_deleted_fid($feature_id)) { return undef }
4194 :
4195 :	efrank	1.1	$locations = $self->cached('_location');
4196 :	parrello	1.287	if (! ($location = $locations->{$feature_id})) {
4197 :			my $rdbH = $self->db_handle;
4198 :			if (($relational_db_response = $rdbH->SQL("SELECT location FROM features WHERE ( id = \'$feature_id\' )")) &&
4199 :			(@$relational_db_response == 1)) {
4200 :			$locations->{$feature_id} = $location = $relational_db_response->[0]->[0];
4201 :			}
4202 :	efrank	1.1	}
4203 :
4204 :	parrello	1.287	if ($location) {
4205 :			return wantarray() ? split(/,/,$location) : $location;
4206 :	efrank	1.1	}
4207 :			return undef;
4208 :			}
4209 :
4210 :	parrello	1.287	#TODO: BRUCE IS HERE
4211 :
4212 :	mkubal	1.147	sub contig_of
4213 :			{
4214 :			my ($self, $locus) = @_;
4215 :	parrello	1.200
4216 :	olson	1.159	$locus =~ m/^([^,]+)_\d+_\d+/;
4217 :	parrello	1.200
4218 :	mkubal	1.147	return $1;
4219 :			}
4220 :
4221 :			sub beg_of
4222 :			{
4223 :			my ($self, $locus) = @_;
4224 :	parrello	1.200
4225 :	olson	1.159	$locus =~ m/^[^,]+_(\d+)_\d+/;
4226 :	parrello	1.200
4227 :	mkubal	1.147	return $1;
4228 :			}
4229 :
4230 :			sub end_of
4231 :			{
4232 :			my ($self, $locus) = @_;
4233 :	parrello	1.200
4234 :	mkubal	1.147	$locus =~ m/\S+_\d+_(\d+)$/;
4235 :	parrello	1.200
4236 :	mkubal	1.147	return $1;
4237 :			}
4238 :
4239 :	parrello	1.200	sub strand_of
4240 :	mkubal	1.147	{
4241 :			my ($self, $fid) = @_;
4242 :			my ($beg, $end);
4243 :	parrello	1.200
4244 :	mkubal	1.147	# warn "In strand_of, self=$self, fid=$fid";
4245 :	parrello	1.200
4246 :	mkubal	1.147	(undef, $beg, $end) = $self->boundaries_of($self->feature_location($fid));
4247 :	parrello	1.200
4248 :	mkubal	1.147	if ($beg < $end) { return '+'; } else { return '-'; }
4249 :			}
4250 :
4251 :	parrello	1.287	=head3 find_contig_with_checksum
4252 :	olson	1.158
4253 :			Find a contig in the given genome with the given checksum.
4254 :
4255 :			=cut
4256 :
4257 :			sub find_contig_with_checksum
4258 :			{
4259 :			my($self, $genome, $checksum) = @_;
4260 :	parrello	1.200
4261 :	olson	1.158	#
4262 :			# This implementation scans all the contig files for the organism; when
4263 :			# we have contig checksums in the database this will simplify
4264 :			# significantly.
4265 :			#
4266 :			# For some efficiency, we cache the checksums we compute along the way since
4267 :			# it's probably likely we'll poke at other contigs for this organism.
4268 :			#
4269 :
4270 :			my $gdir = "$FIG_Config::organisms/$genome";
4271 :
4272 :			my $cached_cksum = $self->cached('_contig_checksum');
4273 :	parrello	1.200
4274 :	olson	1.158	if (opendir(my $dh, $gdir))
4275 :			{
4276 :			for my $file (map { "$gdir/$_" } grep { $_ =~ /^contigs\d*$/ } readdir($dh))
4277 :			{
4278 :			local $/ = "\n>";
4279 :	parrello	1.200
4280 :	olson	1.158	if (open(my $fh, "<$file"))
4281 :			{
4282 :			while (<$fh>)
4283 :			{
4284 :			chomp;
4285 :	olson	1.160
4286 :			#
4287 :			# Pull the contig identifier from the first line.
4288 :			# We need the >? to handle the first line in the file;
4289 :			# the others are removed by the chomp above because
4290 :			# $/ is set to "\n>";
4291 :			#
4292 :	parrello	1.200
4293 :	olson	1.160	if (s/^>?\s(\S+)([^\n])\n//)