Annotation of /FigKernelPackages/FIG.pm

Revision 1.323 - (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	1.322	use FullLocation;
15 :	overbeek	1.36	use tree_utilities;
16 :	olson	1.93	use Subsystem;
17 :	olson	1.162	use SeedDas;
18 :	olson	1.183	use Construct;
19 :	parrello	1.200	use FIGRules;
20 :	parrello	1.210	use Tracer;
21 :	olson	1.297	use GenomeIDMap;
22 :	olson	1.260
23 :	olson	1.245	eval { require FigGFF; };
24 :	parrello	1.287	if ($@ and $ENV{USER} eq "olson") {
25 :	olson	1.260	warn $@;
26 :			}
27 :	olson	1.79
28 :			#
29 :			# Conditionally evaluate this in case its prerequisites are not available.
30 :			#
31 :
32 :			our $ClearinghouseOK = eval {
33 :			require Clearinghouse;
34 :			};
35 :	efrank	1.1
36 :	olson	1.10	use IO::Socket;
37 :
38 :	efrank	1.1	use FileHandle;
39 :
40 :			use Carp;
41 :			use Data::Dumper;
42 :	overbeek	1.25	use Time::Local;
43 :	olson	1.93	use File::Spec;
44 :	olson	1.123	use File::Copy;
45 :	olson	1.112	#
46 :			# Try to load the RPC stuff; it might fail on older versions of the software.
47 :			#
48 :			eval {
49 :			require FIGrpc;
50 :			};
51 :
52 :			my $xmlrpc_available = 1;
53 :	parrello	1.287	if ($@ ne "") {
54 :	olson	1.112	$xmlrpc_available = 0;
55 :			}
56 :
57 :	efrank	1.1
58 :	olson	1.111	use FIGAttributes;
59 :			use base 'FIGAttributes';
60 :
61 :			use vars qw(%_FunctionAttributes);
62 :
63 :			use Data::Dumper;
64 :
65 :	olson	1.124	#
66 :			# Force all new files to be all-writable.
67 :			#
68 :
69 :			umask 0;
70 :
71 :	parrello	1.210	=head1 FIG Genome Annotation System
72 :
73 :			=head2 Introduction
74 :
75 :			This is the main object for access to the SEED data store. The data store
76 :			itself is a combination of flat files and a database. The flat files can
77 :			be moved easily between systems and the database rebuilt as needed.
78 :
79 :			A reduced set of this object's functions are available via the B<SFXlate>
80 :			object. The SFXlate object uses a single database to represent all its
81 :			genomic information. It provides a much smaller capability for updating
82 :			the data, and eliminates all similarities except for bidirectional best
83 :			hits.
84 :
85 :			The key to making the FIG system work is proper configuration of the
86 :			C<FIG_Config.pm> file. This file contains names and URLs for the key
87 :			directories as well as the type and login information for the database.
88 :
89 :	parrello	1.287	FIG was designed to operate as a series of peer instances. Each instance is
90 :			updated independently by its owner, and the instances can be synchronized
91 :			using a process called a I<peer-to-peer update>. The terms
92 :			I<SEED instance> and I<peer> are used more-or-less interchangeably.
93 :
94 :			The POD documentation for this module is still in progress, and is provided
95 :			on an AS IS basis without warranty. If you have a correction and you're
96 :			not a developer, EMAIL the details to B<bruce@gigabarb.com> and I'll fold
97 :			it in.
98 :
99 :			B<NOTE>: The usage example for each method specifies whether it is static
100 :
101 :			FIG::something
102 :
103 :			or dynamic
104 :
105 :			$fig->something
106 :
107 :			If the method is static and has no parameters (C<FIG::something()>) it can
108 :	parrello	1.298	also be invoked dynamically. This is a general artifact of the
109 :	parrello	1.287	way PERL implements object-oriented programming.
110 :
111 :			=head2 Hiding/Caching in a FIG object
112 :
113 :			We save the DB handle, cache taxonomies, and put a few other odds and ends in the
114 :			FIG object. We expect users to invoke these services using the object $fig constructed
115 :			using:
116 :
117 :			use FIG;
118 :			my $fig = new FIG;
119 :
120 :			$fig is then used as the basic mechanism for accessing FIG services. It is, of course,
121 :			just a hash that is used to retain/cache data. The most commonly accessed item is the
122 :			DB filehandle, which is accessed via $self->db_handle.
123 :
124 :			We cache genus/species expansions, taxonomies, distances (very crudely estimated) estimated
125 :			between genomes, and a variety of other things.
126 :
127 :	parrello	1.210	=cut
128 :
129 :	parrello	1.287
130 :	parrello	1.210	#: Constructor FIG->new();
131 :
132 :			=head2 Public Methods
133 :
134 :			=head3 new
135 :
136 :			C<< my $fig = FIG->new(); >>
137 :
138 :	parrello	1.298	This is the constructor for a FIG object. It uses no parameters. If tracing
139 :			has not yet been turned on, it will be turned on here. The tracing type and
140 :			level are specified by the configuration variables C<$FIG_Config::trace_levels>
141 :	parrello	1.301	and C<$FIG_Config::trace_type>. These defaults can be overridden using the
142 :			environment variables C<Trace> and C<TraceType>, respectively.
143 :	parrello	1.210
144 :			=cut
145 :
146 :	efrank	1.1	sub new {
147 :			my($class) = @_;
148 :
149 :	olson	1.102	#
150 :			# Check to see if we have a FIG_URL environment variable set.
151 :			# If we do, don't actually create a FIG object, but rather
152 :			# create a FIGrpc and return that as the return from this constructor.
153 :			#
154 :
155 :	parrello	1.210	if ($ENV{FIG_URL} ne "" && $xmlrpc_available) {
156 :			Trace("Creating figrpc for '$ENV{FIG_URL}'") if T(0);
157 :			my $figrpc = new FIGrpc($ENV{FIG_URL});
158 :			return $figrpc;
159 :	olson	1.102	}
160 :	parrello	1.292	# Here we have the normal case. Check for default tracing. We only do this if
161 :			# the proper parameters are present and nobody else has set up tracing yet.
162 :	parrello	1.301	if (Tracer::Setups() == 0 && (defined $FIG_Config::trace_levels \|\| exists $ENV{Trace})) {
163 :			# Tracing is not active and the user has specified tracing levels, so it's safe for
164 :			# us to set it up using our own rules. First, the trace type: the default is WARN.
165 :			my $trace_type;
166 :			if (exists($ENV{TraceType})) {
167 :			$trace_type = $ENV{TraceType};
168 :			} elsif (defined($FIG_Config::trace_type)) {
169 :			$trace_type = $FIG_Config::trace_type;
170 :			} else {
171 :			$trace_type = "WARN";
172 :			}
173 :			# Now the trace levels. The environment variable wins over the FIG_Config value.
174 :			my $trace_levels = (exists($ENV{Trace}) ? $ENV{Trace} : $FIG_Config::trace_levels);
175 :			TSetup($trace_levels, $trace_type);
176 :	parrello	1.287	}
177 :			# Connect to the database, then return ourselves.
178 :	efrank	1.1	my $rdbH = new DBrtns;
179 :			bless {
180 :	parrello	1.210	_dbf => $rdbH,
181 :			}, $class;
182 :	efrank	1.1	}
183 :
184 :	parrello	1.287	=head3 db_handle
185 :
186 :			C<< my $dbh = $fig->db_handle; >>
187 :
188 :			Return the handle to the internal B<DBrtns> object. This allows direct access to
189 :			the database methods.
190 :
191 :			=cut
192 :
193 :			sub db_handle {
194 :			my($self) = @_;
195 :			return $self->{_dbf};
196 :			}
197 :
198 :	overbeek	1.293	sub table_exists {
199 :			my($self,$table) = @_;
200 :
201 :			my $rdbH = $self->db_handle;
202 :			return $rdbH->table_exists($table);
203 :			}
204 :	parrello	1.292
205 :	parrello	1.287	=head3 cached
206 :
207 :			C<< my $x = $fig->cached($name); >>
208 :
209 :			Return a reference to a hash containing transient data. If no hash exists with the
210 :			specified name, create an empty one under that name and return it.
211 :
212 :			The idea behind this method is to allow clients to cache data in the FIG object for
213 :			later use. (For example, a method might cache feature data so that it can be
214 :			retrieved later without using the database.) This facility should be used sparingly,
215 :			since different clients may destroy each other's data if they use the same name.
216 :
217 :			=over 4
218 :
219 :			=item name
220 :
221 :			Name assigned to the cached data.
222 :
223 :			=item RETURN
224 :
225 :			Returns a reference to a hash that is permanently associated with the specified name.
226 :			If no such hash exists, an empty one will be created for the purpose.
227 :
228 :			=back
229 :
230 :			=cut
231 :
232 :			sub cached {
233 :			my($self,$what) = @_;
234 :
235 :			my $x = $self->{$what};
236 :			if (! $x) {
237 :			$x = $self->{$what} = {};
238 :			}
239 :			return $x;
240 :			}
241 :	parrello	1.210
242 :			=head3 get_system_name
243 :
244 :			C<< my $name = $fig->get_system_name; >>
245 :
246 :			Returns C<seed>, indicating that this is object is using the SEED
247 :			database. The same method on an SFXlate object will return C<sprout>.
248 :
249 :			=cut
250 :			#: Return Type $;
251 :			sub get_system_name {
252 :	olson	1.207	return "seed";
253 :	olson	1.205	}
254 :	parrello	1.210
255 :	parrello	1.287	=head3 DESTROY
256 :
257 :			The destructor releases the database handle.
258 :
259 :			=cut
260 :	olson	1.205
261 :	parrello	1.287	sub DESTROY {
262 :	efrank	1.1	my($self) = @_;
263 :			my($rdbH);
264 :
265 :	parrello	1.210	if ($rdbH = $self->db_handle) {
266 :			$rdbH->DESTROY;
267 :	efrank	1.1	}
268 :			}
269 :
270 :	parrello	1.210	=head3 delete_genomes
271 :
272 :			C<< $fig->delete_genomes(\@genomes); >>
273 :
274 :			Delete the specified genomes from the data store. This requires making
275 :			system calls to move and delete files.
276 :
277 :			=cut
278 :			#: Return Type ;
279 :	overbeek	1.7	sub delete_genomes {
280 :			my($self,$genomes) = @_;
281 :			my $tmpD = "$FIG_Config::temp/tmp.deleted.$$";
282 :			my $tmp_Data = "$FIG_Config::temp/Data.$$";
283 :
284 :			my %to_del = map { $_ => 1 } @$genomes;
285 :			open(TMP,">$tmpD") \|\| die "could not open $tmpD";
286 :
287 :			my $genome;
288 :	parrello	1.287	foreach $genome ($self->genomes) {
289 :			if (! $to_del{$genome}) {
290 :			print TMP "$genome\n";
291 :			}
292 :	overbeek	1.7	}
293 :			close(TMP);
294 :
295 :			&run("extract_genomes $tmpD $FIG_Config::data $tmp_Data");
296 :	parrello	1.200
297 :	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");
298 :	parrello	1.200
299 :			&run("mv $FIG_Config::data $FIG_Config::data.deleted");
300 :	overbeek	1.47	&run("mv $tmp_Data $FIG_Config::data");
301 :			&run("fig load_all");
302 :			&run("rm -rf $FIG_Config::data.deleted");
303 :	overbeek	1.7	}
304 :	parrello	1.200
305 :	parrello	1.210	=head3 add_genome
306 :
307 :			C<< my $ok = $fig->add_genome($genomeF); >>
308 :
309 :			Add a new genome to the data store. A genome's data is kept in a directory
310 :	parrello	1.287	by itself, underneath the main organism directory. This method essentially
311 :			moves genome data from an external directory to the main directory and
312 :			performs some indexing tasks to integrate it.
313 :	parrello	1.210
314 :			=over 4
315 :
316 :			=item genomeF
317 :
318 :	parrello	1.287	Name of the directory containing the genome files. This should be a
319 :			fully-qualified directory name. The last segment of the directory
320 :			name should be the genome ID.
321 :	parrello	1.210
322 :			=item RETURN
323 :
324 :			Returns TRUE if successful, else FALSE.
325 :
326 :			=back
327 :
328 :			=cut
329 :			#: Return Type $;
330 :	efrank	1.1	sub add_genome {
331 :			my($self,$genomeF) = @_;
332 :
333 :			my $rc = 0;
334 :	olson	1.93
335 :			my(undef, $path, $genome) = File::Spec->splitpath($genomeF);
336 :
337 :	parrello	1.287	if ($genome !~ /^\d+\.\d+$/) {
338 :			warn "Invalid genome filename $genomeF\n";
339 :			return $rc;
340 :	olson	1.93	}
341 :
342 :	parrello	1.287	if (-d $FIG_Config::organisms/$genome) {
343 :			warn "Organism already exists for $genome\n";
344 :			return $rc;
345 :	olson	1.93	}
346 :	parrello	1.200
347 :	olson	1.93
348 :			#
349 :			# We're okay, it doesn't exist.
350 :			#
351 :
352 :			my @errors = `$FIG_Config::bin/verify_genome_directory $genomeF`;
353 :
354 :	parrello	1.287	if (@errors) {
355 :			warn "Errors found while verifying genome directory $genomeF:\n";
356 :			print join("", @errors);
357 :			return $rc;
358 :	olson	1.93	}
359 :	parrello	1.200
360 :	olson	1.93	&run("cp -r $genomeF $FIG_Config::organisms");
361 :			&run("chmod -R 777 $FIG_Config::organisms/$genome");
362 :
363 :			&run("index_contigs $genome");
364 :			&run("compute_genome_counts $genome");
365 :			&run("load_features $genome");
366 :
367 :			$rc = 1;
368 :	parrello	1.287	if (-s "$FIG_Config::organisms/$genome/Features/peg/fasta") {
369 :			&run("index_translations $genome");
370 :			my @tmp = `cut -f1 $FIG_Config::organisms/$genome/Features/peg/tbl`;
371 :			chomp @tmp;
372 :			&run("cat $FIG_Config::organisms/$genome/Features/peg/fasta >> $FIG_Config::data/Global/nr");
373 :			&enqueue_similarities(\@tmp);
374 :	olson	1.93	}
375 :			if ((-s "$FIG_Config::organisms/$genome/assigned_functions") \|\|
376 :	parrello	1.287	(-d "$FIG_Config::organisms/$genome/UserModels")) {
377 :			&run("add_assertions_of_function $genome");
378 :	efrank	1.1	}
379 :	parrello	1.200
380 :	efrank	1.1	return $rc;
381 :			}
382 :
383 :	parrello	1.287	=head3 parse_genome_args
384 :
385 :			C<< my ($mode, @genomes) = FIG::parse_genome_args(@args); >>
386 :
387 :			Extract a list of genome IDs from an argument list. If the argument list is empty,
388 :			return all the genomes in the data store.
389 :
390 :			This is a function that is performed by many of the FIG command-line utilities. The
391 :			user has the option of specifying a list of specific genome IDs or specifying none
392 :			in order to get all of them. If your command requires additional arguments in the
393 :			command line, you can still use this method if you shift them out of the argument list
394 :			before calling. The $mode return value will be C<all> if the user asked for all of
395 :			the genomes or C<some> if he specified a list of IDs. This is useful to know if,
396 :			for example, we are loading a table. If we're loading everything, we can delete the
397 :			entire table; if we're only loading some genomes, we must delete them individually.
398 :
399 :			This method uses the genome directory rather than the database because it may be used
400 :			before the database is ready.
401 :
402 :			=over 4
403 :
404 :			=item args1, args2, ... argsN
405 :
406 :			List of genome IDs. If all genome IDs are to be processed, then this list should be
407 :			empty.
408 :
409 :			=item RETURN
410 :
411 :			Returns a list. The first element of the list is C<all> if the user is asking for all
412 :			the genome IDs and C<some> otherwise. The remaining elements of the list are the
413 :			desired genome IDs.
414 :
415 :			=back
416 :
417 :			=cut
418 :
419 :			sub parse_genome_args {
420 :			# Get the parameters.
421 :			my @args = @_;
422 :			# Check the mode.
423 :			my $mode = (@args > 0 ? 'some' : 'all');
424 :			# Build the return list.
425 :			my @retVal = ($mode);
426 :			# Process according to the mode.
427 :			if ($mode eq 'all') {
428 :			# We want all the genomes, so we get them from the organism directory.
429 :			my $orgdir = "$FIG_Config::organisms";
430 :			opendir( GENOMES, $orgdir ) \|\| Confess("Could not open directory $orgdir");
431 :			push @retVal, grep { $_ =~ /^\d/ } readdir( GENOMES );
432 :			closedir( GENOMES );
433 :			} else {
434 :			# We want only the genomes specified by the user.
435 :			push @retVal, @args;
436 :			}
437 :			# Return the result.
438 :			return @retVal;
439 :			}
440 :
441 :			=head3 reload_table
442 :
443 :			C<< $fig->reload_table($mode, $table, $flds, $xflds, $fileName, $keyList, $keyName); >>
444 :
445 :			Reload a database table from a sequential file. If I<$mode> is C<all>, the table
446 :			will be dropped and re-created. If I<$mode> is C<some>, the data for the individual
447 :			items in I<$keyList> will be deleted before the table is loaded. Thus, the load
448 :			process is optimized for the type of reload.
449 :
450 :			=over 4
451 :
452 :			=item mode
453 :
454 :			C<all> if we are reloading the entire table, C<some> if we are only reloading
455 :			specific entries.
456 :
457 :			=item table
458 :
459 :			Name of the table to reload.
460 :
461 :			=item flds
462 :
463 :			String defining the table columns, in SQL format. In general, this is a
464 :			comma-delimited set of field specifiers, each specifier consisting of the
465 :			field name followed by the field type and any optional qualifiers (such as
466 :			C<NOT NULL> or C<DEFAULT>); however, it can be anything that would appear
467 :			between the parentheses in a C<CREATE TABLE> statement. The order in which
468 :			the fields are specified is important, since it is presumed that is the
469 :			order in which they are appearing in the load file.
470 :
471 :			=item xflds
472 :
473 :			Reference to a hash that describes the indexes. The hash is keyed by index name.
474 :			The value is the index's field list. This is a comma-delimited list of field names
475 :			in order from most significant to least significant. If a field is to be indexed
476 :			in descending order, its name should be followed by the qualifier C<DESC>. For
477 :			example, the following I<$xflds> value will create two indexes, one for name followed
478 :			by creation date in reverse chronological order, and one for ID.
479 :
480 :			{ name_index => "name, createDate DESC", id_index => "id" }
481 :
482 :			=item fileName
483 :
484 :			Fully-qualified name of the file containing the data to load. Each line of the
485 :			file must correspond to a record, and the fields must be arranged in order and
486 :	parrello	1.298	tab-delimited. If the file name is omitted, the table is dropped and re-created
487 :			but not loaded.
488 :	parrello	1.287
489 :			=item keyList
490 :
491 :			Reference to a list of the IDs for the objects being reloaded. This parameter is
492 :			only used if I<$mode> is C<some>.
493 :
494 :			=item keyName (optional)
495 :
496 :			Name of the key field containing the IDs in the keylist. If omitted, C<genome> is
497 :			assumed.
498 :
499 :			=back
500 :
501 :			=cut
502 :
503 :			sub reload_table {
504 :	parrello	1.298	# Get the parameters.
505 :			my ($self, $mode, $table, $flds, $xflds, $fileName, $keyList, $keyName) = @_;
506 :	parrello	1.287	if (!defined $keyName) {
507 :			$keyName = 'genome';
508 :			}
509 :			# Get the database handler.
510 :			my $dbf = $self->{_dbf};
511 :	parrello	1.298	# Call the DBKernel method.
512 :			$dbf->reload_table($mode, $table, $flds, $xflds, $fileName, $keyList, $keyName);
513 :	parrello	1.287	}
514 :
515 :	parrello	1.210	=head3 enqueue_similarities
516 :	olson	1.93
517 :	parrello	1.287	C<< FIG::enqueue_similarities(\@fids); >>
518 :
519 :			Queue the passed Feature IDs for similarity computation. The actual
520 :			computation is performed by L</create_sim_askfor_pool>. The queue is a
521 :			persistent text file in the global data directory, and this method
522 :			essentially writes new IDs on the end of it.
523 :
524 :			=over 4
525 :
526 :			=item fids
527 :
528 :			Reference to a list of feature IDs.
529 :	olson	1.93
530 :	parrello	1.287	=back
531 :	olson	1.93
532 :			=cut
533 :	parrello	1.210	#: Return Type ;
534 :	olson	1.93	sub enqueue_similarities {
535 :	efrank	1.1	my($fids) = @_;
536 :			my $fid;
537 :
538 :	olson	1.93	my $sim_q = "$FIG_Config::global/queued_similarities";
539 :
540 :			open(TMP,">>$sim_q")
541 :	parrello	1.287	\|\| die "could not open $sim_q";
542 :	olson	1.93
543 :			#
544 :			# We need to lock here so that if a computation is creating a snapshot of the
545 :			# queue, we block until it's done.
546 :			#
547 :
548 :			flock(TMP, LOCK_EX) or die "Cannot lock $sim_q\n";
549 :
550 :	parrello	1.287	foreach $fid (@$fids) {
551 :			print TMP "$fid\n";
552 :	efrank	1.1	}
553 :			close(TMP);
554 :	olson	1.10	}
555 :
556 :	olson	1.281	=head3 export_similarity_request
557 :
558 :			Creates a similarity computation request from the queued similarities and
559 :	parrello	1.287	the current NR.
560 :	olson	1.281
561 :			We keep track of the exported requests in case one gets lost.
562 :
563 :			=cut
564 :
565 :	parrello	1.287	sub export_similarity_request {
566 :	olson	1.281	my($self, $nr_file, $fasta_file) = @_;
567 :
568 :			my $req_dir = "$FIG_Config::fig/var/sim_requests";
569 :			&verify_dir("$FIG_Config::fig/var");
570 :			&verify_dir($req_dir);
571 :
572 :			$req_dir = "$req_dir/" . time;
573 :			&verify_dir($req_dir);
574 :
575 :			#
576 :			# Open all of our output files before zeroing out the sim queue, in case
577 :			# there is a problem.
578 :			#
579 :
580 :			open(my $user_fasta_fh, ">$fasta_file") or confess "Cannot open $fasta_file for writing: $!";
581 :			open(my $fasta_fh, ">$req_dir/fasta.in");
582 :
583 :			open(my $user_nr_fh, ">$nr_file") or confess "Cannot open $nr_file for writing: $!";
584 :			open(my $nr_fh, ">$req_dir/nr") or confess "Cannot open $req_dir/nr for writing: $!";
585 :
586 :			open(my $nr_read_fh, "<$FIG_Config::data/Global/nr") or die "Cannot open $FIG_Config::data/Global/nr for reading: $!";
587 :	parrello	1.287
588 :	olson	1.281	my $sim_q = "$FIG_Config::global/queued_similarities";
589 :
590 :			#
591 :			# We need to lock here so that if a computation is creating a snapshot of the
592 :			# queue, we block until it's done.
593 :			#
594 :
595 :			open(my $sim_q_lock, ">>$sim_q") or confess "could not open $sim_q";
596 :			flock($sim_q_lock, LOCK_EX) or confess "Cannot lock $sim_q\n";
597 :
598 :			#
599 :			# Everything open & locked, start copying.
600 :			#
601 :	parrello	1.287
602 :	olson	1.281	copy("$sim_q", "$req_dir/q") or confess "Copy $sim_q $req_dir/q failed: $!";
603 :	parrello	1.287
604 :	olson	1.281	my($buf);
605 :	parrello	1.287	while (1) {
606 :			my $n = read($nr_read_fh, $buf, 4096);
607 :			defined($n) or confess "Error reading nr: $!";
608 :			last unless $n;
609 :			syswrite($user_nr_fh, $buf) or confess "Error writing $nr_file: $!";
610 :			syswrite($nr_fh, $buf) or confess "Error writing $req_dir/nr: $!";
611 :	olson	1.281	}
612 :
613 :			close($nr_read_fh);
614 :			close($nr_fh);
615 :			close($user_nr_fh);
616 :
617 :			#
618 :			# We can zero out the queue and unlock now.
619 :			#
620 :
621 :			open(F, ">$sim_q") or die "Cannot open $sim_q to truncate it: $!\n";
622 :			close(F);
623 :	parrello	1.287
624 :	olson	1.281	close($sim_q_lock);
625 :
626 :			#
627 :			# Generate the fasta input from the queued ids.
628 :			#
629 :
630 :			open(my $q_fh, "<$req_dir/q");
631 :	parrello	1.287	while (my $id = <$q_fh>) {
632 :			chomp $id;
633 :	olson	1.281
634 :	parrello	1.287	my $seq = $self->get_translation($id);
635 :	olson	1.281
636 :	parrello	1.287	display_id_and_seq($id, \$seq, $user_fasta_fh);
637 :			display_id_and_seq($id, \$seq, $fasta_fh);
638 :	olson	1.281	}
639 :			close($q_fh);
640 :
641 :			close($user_fasta_fh);
642 :			close($fasta_fh);
643 :			}
644 :
645 :	parrello	1.210	=head3 create_sim_askfor_pool
646 :	olson	1.93
647 :	parrello	1.287	C<< $fig->create_sim_askfor_pool($chunk_size); >>
648 :	olson	1.93
649 :	parrello	1.287	Creates an askfor pool, which a snapshot of the current NR and similarity
650 :			queue. This process clears the old queue.
651 :	olson	1.123
652 :			The askfor pool needs to keep track of which sequences need to be
653 :			calculated, which have been handed out, etc. To simplify this task we
654 :	olson	1.279	chunk the sequences into fairly small numbers (20k characters) and
655 :	olson	1.123	allocate work on a per-chunk basis. We make use of the relational
656 :			database to keep track of chunk status as well as the seek locations
657 :			into the file of sequence data. The initial creation of the pool
658 :			involves indexing the sequence data with seek offsets and lengths and
659 :			populating the sim_askfor_index table with this information and with
660 :			initial status information.
661 :	olson	1.93
662 :	parrello	1.287	=over 4
663 :
664 :			=item chunk_size
665 :
666 :			Number of features to put into a processing chunk. The default is 15.
667 :
668 :			=back
669 :
670 :	parrello	1.200	=cut
671 :	parrello	1.210	#: Return Type $;
672 :	parrello	1.287	sub create_sim_askfor_pool {
673 :	olson	1.123	my($self, $chunk_size) = @_;
674 :
675 :	olson	1.279	$chunk_size = 20000 unless $chunk_size =~ /^\d+$/;
676 :	olson	1.93
677 :	olson	1.279	my $pool_dir = "$FIG_Config::fig/var/sim_pools";
678 :	olson	1.93	&verify_dir($pool_dir);
679 :
680 :			#
681 :			# Lock the pool directory.
682 :			#
683 :			open(my $lock, ">$pool_dir/lockfile");
684 :
685 :			flock($lock, LOCK_EX);
686 :
687 :			my $num = 0;
688 :	parrello	1.287	if (open(my $toc, "<$pool_dir/TOC")) {
689 :			while (<$toc>) {
690 :			chomp;
691 :			# print STDERR "Have toc entry $_\n";
692 :			my ($idx, $time, $str) = split(/\s+/, $_, 3);
693 :	olson	1.93
694 :	parrello	1.287	$num = max($num, $idx);
695 :			}
696 :			close($toc);
697 :	olson	1.93	}
698 :			$num++;
699 :			open(my $toc, ">>$pool_dir/TOC") or die "Cannot write $pool_dir/TOC: $!\n";
700 :
701 :			print $toc "$num ", time(), " New toc entry\n";
702 :			close($toc);
703 :
704 :	olson	1.123	my $cpool_id = sprintf "%04d", $num;
705 :			my $cpool_dir = "$pool_dir/$cpool_id";
706 :	olson	1.93
707 :			#
708 :			# All set, create the directory for this pool.
709 :			#
710 :
711 :			&verify_dir($cpool_dir);
712 :
713 :			#
714 :			# Now we can copy the nr and sim queue here.
715 :			# Do this stuff inside an eval so we can clean up
716 :			# the lockfile.
717 :			#
718 :
719 :			eval {
720 :	parrello	1.287	my $sim_q = "$FIG_Config::global/queued_similarities";
721 :	olson	1.93
722 :	parrello	1.287	copy("$sim_q", "$cpool_dir/q");
723 :			copy("$FIG_Config::data/Global/nr", "$cpool_dir/nr");
724 :	olson	1.93
725 :	parrello	1.287	open(F, ">$sim_q") or die "Cannot open $sim_q to truncate it: $!\n";
726 :			close(F);
727 :	olson	1.93	};
728 :	parrello	1.200
729 :	olson	1.93	unlink("$pool_dir/lockfile");
730 :			close($lock);
731 :	olson	1.123
732 :			#
733 :			# We've created our pool; we can now run the formatdb and
734 :			# extract the sequences for the blast run.
735 :			#
736 :	parrello	1.287	my $child_pid = $self->run_in_background(
737 :			sub {
738 :			#
739 :			# Need to close db or there's all sorts of trouble.
740 :			#
741 :
742 :			my $cmd = "$FIG_Config::ext_bin/formatdb -i $cpool_dir/nr -p T -l $cpool_dir/formatdb.log";
743 :			print "Will run '$cmd'\n";
744 :			&run($cmd);
745 :			print "finished. Logfile:\n";
746 :			print &FIG::file_read("$cpool_dir/formatdb.log");
747 :			unlink("$cpool_dir/formatdb.pid");
748 :			});
749 :	olson	1.279	warn "Running formatdb in background job $child_pid\n";
750 :	olson	1.123	open(FPID, ">$cpool_dir/formatdb.pid");
751 :			print FPID "$child_pid\n";
752 :			close(FPID);
753 :
754 :			my $db = $self->db_handle();
755 :	parrello	1.287	if (!$db->table_exists("sim_queue")) {
756 :			$db->create_table(tbl => "sim_queue",
757 :			flds => "qid varchar(32), chunk_id INTEGER, seek INTEGER, len INTEGER, " .
758 :			"assigned BOOL, finished BOOL, output_file varchar(255), " .
759 :			"assignment_expires INTEGER, worker_info varchar(255)"
760 :			);
761 :	olson	1.123	}
762 :
763 :			#
764 :			# Write the fasta input file. Keep track of how many have been written,
765 :			# and write seek info into the database as appropriate.
766 :			#
767 :
768 :			open(my $seq_fh, ">$cpool_dir/fasta.in");
769 :
770 :			my($chunk_idx, $chunk_begin, $seq_idx);
771 :
772 :	olson	1.279	my $cur_size = 0;
773 :
774 :	olson	1.123	$chunk_idx = 0;
775 :			$chunk_begin = 0;
776 :			$seq_idx = 0;
777 :
778 :			my(@seeks);
779 :
780 :	olson	1.279	my $tmpfile = "$FIG_Config::temp/simseek.$$";
781 :			open(my $tmpfh, ">$tmpfile") or confess "Cannot open tmpfile $tmpfile: $!";
782 :
783 :	olson	1.123	open(my $q_fh, "<$cpool_dir/q");
784 :	parrello	1.287	while (my $id = <$q_fh>) {
785 :			chomp $id;
786 :	olson	1.123
787 :	parrello	1.287	my $seq = $self->get_translation($id);
788 :	olson	1.123
789 :	parrello	1.287	#
790 :			# check if we're at the beginning of a chunk
791 :			#
792 :
793 :			print $seq_fh ">$id\n$seq\n";
794 :
795 :			#
796 :			# Check if we're at the end of a chunk
797 :			#
798 :
799 :			$cur_size += length($seq);
800 :			if ($cur_size >= $chunk_size) {
801 :			my $chunk_end = tell($seq_fh);
802 :			my $chunk_len = $chunk_end - $chunk_begin;
803 :
804 :			push(@seeks, [$cpool_id, $chunk_idx, $chunk_begin, $chunk_len]);
805 :			print $tmpfh join("\t", $cpool_id, $chunk_idx, $chunk_begin, $chunk_len, 'FALSE', 'FALSE'), "\n";
806 :			$chunk_idx++;
807 :			$chunk_begin = $chunk_end;
808 :			$cur_size = 0;
809 :			}
810 :			$seq_idx++;
811 :	olson	1.123	}
812 :
813 :	parrello	1.287	if ($cur_size > 0) {
814 :			my $chunk_end = tell($seq_fh);
815 :			my $chunk_len = $chunk_end - $chunk_begin;
816 :	olson	1.123
817 :	parrello	1.287	print $tmpfh join("\t", $cpool_id, $chunk_idx, $chunk_begin, $chunk_len, 'FALSE', 'FALSE'), "\n";
818 :			push(@seeks, [$cpool_id, $chunk_idx, $chunk_begin, $chunk_len]);
819 :	olson	1.123	}
820 :
821 :			close($q_fh);
822 :			close($seq_fh);
823 :	olson	1.279	close($tmpfh);
824 :	olson	1.123
825 :	olson	1.279	warn "Write seqs from $tmpfile\n";
826 :	olson	1.123
827 :	olson	1.279	$self->db_handle->load_table(tbl => 'sim_queue',
828 :	parrello	1.298	file => $tmpfile);
829 :	parrello	1.200
830 :	olson	1.279	unlink($tmpfile);
831 :	parrello	1.287
832 :	olson	1.279	# for my $seek (@seeks)
833 :			# {
834 :	parrello	1.298	# my($cpool_id, $chunk_idx, $chunk_begin, $chunk_len) = @$seek;
835 :	olson	1.279
836 :	parrello	1.298	# $db->SQL("insert into sim_queue (qid, chunk_id, seek, len, assigned, finished) " .
837 :			# "values('$cpool_id', $chunk_idx, $chunk_begin, $chunk_len, FALSE, FALSE)");
838 :	olson	1.279	# }
839 :	parrello	1.200
840 :	olson	1.123	return $cpool_id;
841 :			}
842 :
843 :	parrello	1.210	#=head3 get_sim_queue
844 :			#
845 :			#usage: get_sim_queue($pool_id, $all_sims)
846 :			#
847 :			#Returns the sims in the given pool. If $all_sims is true, return the entire queue. Otherwise,
848 :			#just return the sims awaiting processing.
849 :			#
850 :			#=cut
851 :	olson	1.123
852 :	parrello	1.287	sub get_sim_queue {
853 :	olson	1.123	my($self, $pool_id, $all_sims) = @_;
854 :	olson	1.279	}
855 :
856 :	parrello	1.287	=head3 get_sim_work
857 :	olson	1.279
858 :	parrello	1.287	C<< my ($nrPath, $fasta) = $fig->get_sim_work(); >>
859 :	olson	1.279
860 :			Get the next piece of sim computation work to be performed. Returned are
861 :			the path to the NR and a string containing the fasta data.
862 :
863 :			=cut
864 :
865 :	parrello	1.287	sub get_sim_work {
866 :
867 :			my ($self) = @_;
868 :	olson	1.279
869 :			#
870 :			# For now, just don't care about order of data that we get back.
871 :			#
872 :
873 :			my $db = $self->db_handle();
874 :			my $lock = FIG::SimLock->new;
875 :
876 :			my $work = $db->SQL(qq(SELECT qid, chunk_id, seek, len
877 :	parrello	1.298	FROM sim_queue
878 :			WHERE not finished
879 :			LIMIT 1));
880 :	olson	1.279	print "Got work ", Dumper($work), "\n";
881 :
882 :	parrello	1.287	if (not $work or @$work == 0) {
883 :			return undef;
884 :	olson	1.279	}
885 :
886 :			my($cpool_id, $chunk_id, $seek, $len) = @{$work->[0]};
887 :	parrello	1.287
888 :	olson	1.279	my $pool_dir = "$FIG_Config::fig/var/sim_pools";
889 :			my $cpool_dir = "$pool_dir/$cpool_id";
890 :
891 :			my $nr = "$cpool_dir/nr";
892 :			open(my $fh, "<$cpool_dir/fasta.in");
893 :			seek($fh, $seek, 0);
894 :			my $fasta;
895 :			read($fh, $fasta, $len);
896 :
897 :			return($cpool_id, $chunk_id, $nr, $fasta, "$cpool_dir/out.$chunk_id");
898 :			}
899 :
900 :			=head3 sim_work_done
901 :
902 :	parrello	1.287	C<< $fig->sim_work_done($pool_id, $chunk_id, $out_file); >>
903 :
904 :	olson	1.279	Declare that the work in pool_id/chunk_id has been completed, and output written
905 :			to the pool directory (get_sim_work gave it the path).
906 :
907 :	parrello	1.287	=over 4
908 :
909 :			=item pool_id
910 :
911 :			The ID number of the pool containing the work that just completed.
912 :
913 :			=item chunk_id
914 :
915 :			The ID number of the chunk completed.
916 :
917 :			=item out_file
918 :
919 :			The file into which the work was placed.
920 :
921 :			=back
922 :
923 :	olson	1.279	=cut
924 :
925 :	parrello	1.287	sub sim_work_done {
926 :			my ($self, $pool_id, $chunk_id, $out_file) = @_;
927 :	olson	1.279
928 :	parrello	1.287	if (! -f $out_file) {
929 :			Confess("sim_work_done: output file $out_file does not exist");
930 :	olson	1.279	}
931 :
932 :			my $db = $self->db_handle();
933 :			my $lock = FIG::SimLock->new;
934 :
935 :			my $dbh = $db->{_dbh};
936 :
937 :			my $rows = $dbh->do(qq(UPDATE sim_queue
938 :	parrello	1.298	SET finished = TRUE, output_file = ?
939 :			WHERE qid = ? and chunk_id = ?), undef, $out_file, $pool_id, $chunk_id);
940 :	parrello	1.287	if ($rows != 1) {
941 :			if ($dbh->errstr) {
942 :			Confess("Update not able to set finished=TRUE: ", $dbh->errstr);
943 :			} else {
944 :			Confess("Update not able to set finished=TRUE");
945 :			}
946 :	olson	1.279	}
947 :			#
948 :			# Determine if this was the last piece of work for this pool. If so, we can
949 :	parrello	1.287	# schedule the postprocessing work.
950 :	olson	1.279	#
951 :			# Note we're still holding the lock.
952 :			#
953 :
954 :			my $out = $db->SQL(qq(SELECT chunk_id
955 :	parrello	1.298	FROM sim_queue
956 :			WHERE qid = ? AND not finished), undef, $pool_id);
957 :	parrello	1.287	if (@$out == 0) {
958 :			#
959 :			# Pool is done.
960 :			#
961 :			$self->schedule_sim_pool_postprocessing($pool_id);
962 :	olson	1.279	}
963 :	olson	1.123	}
964 :
965 :	olson	1.279	=head3 schedule_sim_pool_postprocessing
966 :
967 :	parrello	1.287	C<< $fig->schedule_sim_pool_postprocessing($pool_id); >>
968 :
969 :			Schedule a job to do the similarity postprocessing for the specified pool.
970 :
971 :			=over 4
972 :
973 :			=item pool_id
974 :
975 :			ID of the pool whose similarity postprocessing needs to be scheduled.
976 :	olson	1.279
977 :	parrello	1.287	=back
978 :	olson	1.279
979 :			=cut
980 :
981 :	parrello	1.287	sub schedule_sim_pool_postprocessing {
982 :
983 :	olson	1.279	my($self, $pool_id) = @_;
984 :
985 :			my $pool_dir = "$FIG_Config::fig/var/sim_pools";
986 :			my $cpool_dir = "$pool_dir/$pool_id";
987 :
988 :			my $js = JobScheduler->new();
989 :			my $job = $js->job_create();
990 :
991 :			my $spath = $job->get_script_path();
992 :			open(my $sfh, ">$spath");
993 :			print $sfh <<END;
994 :			#!/bin/sh
995 :			. $FIG_Config::fig_disk/config/fig-user-env.sh
996 :			$FIG_Config::bin/postprocess_computed_sims $pool_id
997 :			END
998 :
999 :			close($sfh);
1000 :			chmod(0775, $spath);
1001 :
1002 :			#
1003 :			# Write the job ID to the subsystem queue dir.
1004 :			#
1005 :
1006 :			open(J, ">$cpool_dir/postprocess_jobid");
1007 :			print J $job->get_id(), "\n";
1008 :			close(J);
1009 :
1010 :			$job->enqueue();
1011 :			}
1012 :
1013 :			=head3 postprocess_computed_sims
1014 :
1015 :	parrello	1.287	C<< $fig->postprocess_computed_sims($pool_id); >>
1016 :
1017 :			Set up to reduce, reformat, and split the similarities in a given pool. We build
1018 :			a pipe to this pipeline:
1019 :	olson	1.279
1020 :			reduce_sims peg.synonyms 300 \| reformat_sims nr \| split_sims dest prefix
1021 :
1022 :	parrello	1.287	Then we put the new sims in the pool directory, and then copy to NewSims.
1023 :
1024 :			=over 4
1025 :
1026 :			=item pool_id
1027 :
1028 :			ID of the pool whose similarities are to be post-processed.
1029 :
1030 :			=back
1031 :	olson	1.279
1032 :			=cut
1033 :
1034 :	parrello	1.287	sub postprocess_computed_sims {
1035 :	olson	1.279	my($self, $pool_id) = @_;
1036 :
1037 :			#
1038 :			# We don't lock here because the job is already done, and we
1039 :			# shouldn't (ha, ha) ever postprocess twice.
1040 :			#
1041 :
1042 :			my $pool_dir = "$FIG_Config::fig/var/sim_pools";
1043 :			my $cpool_dir = "$pool_dir/$pool_id";
1044 :
1045 :			my $sim_dir = "$cpool_dir/NewSims";
1046 :			&verify_dir($sim_dir);
1047 :
1048 :			#
1049 :			# Open the processing pipeline.
1050 :			#
1051 :
1052 :			my $reduce = "$FIG_Config::bin/reduce_sims $FIG_Config::global/peg.synonyms 300";
1053 :			my $reformat = "$FIG_Config::bin/reformat_sims $cpool_dir/nr";
1054 :			my $split = "$FIG_Config::bin/split_sims $sim_dir sims.$pool_id";
1055 :			open(my $process, "\| $reduce \| $reformat \| $split");
1056 :
1057 :			#
1058 :			# Iterate over all the sims files, taken from the database.
1059 :			#
1060 :
1061 :			my $dbh = $self->db_handle()->{_dbh};
1062 :			my $files = $dbh->selectcol_arrayref(qq(SELECT output_file
1063 :	parrello	1.298	FROM sim_queue
1064 :			WHERE qid = ? and output_file IS NOT NULL
1065 :			ORDER BY chunk_id), undef, $pool_id);
1066 :	parrello	1.287	for my $file (@$files) {
1067 :			my $buf;
1068 :			open(my $fh, "<$file") or confess "Cannot sim input file $file: $!";
1069 :			while (read($fh, $buf, 4096)) {
1070 :			print $process $buf;
1071 :			}
1072 :			close($fh);
1073 :	olson	1.279	}
1074 :			my $res = close($process);
1075 :	parrello	1.287	if (!$res) {
1076 :			if ($!) {
1077 :			confess "Error closing process pipeline: $!";
1078 :			} else {
1079 :			confess "Process pipeline exited with status $?";
1080 :			}
1081 :	olson	1.279	}
1082 :
1083 :			#
1084 :			# If we got here, it worked. Copy the new sims files over to NewSims.
1085 :			#
1086 :
1087 :			opendir(my $simdh, $sim_dir) or confess "Cannot open $sim_dir: $!";
1088 :			my @new_sims = grep { $_ !~ /^\./ } readdir($simdh);
1089 :			closedir($simdh);
1090 :
1091 :			&verify_dir("$FIG_Config::data/NewSims");
1092 :
1093 :	parrello	1.287	for my $sim_file (@new_sims) {
1094 :			my $target = "$FIG_Config::data/NewSims/$sim_file";
1095 :			if (-s $target) {
1096 :			Confess("$target already exists");
1097 :			}
1098 :			print "copying sim file $sim_file\n";
1099 :			&FIG::run("cp $sim_dir/$sim_file $target");
1100 :			&FIG::run("$FIG_Config::bin/index_sims $target");
1101 :	olson	1.279	}
1102 :			}
1103 :
1104 :	parrello	1.210	=head3 get_active_sim_pools
1105 :	olson	1.123
1106 :	parrello	1.287	C<< @pools = $fig->get_active_sim_pools(); >>
1107 :	olson	1.123
1108 :	parrello	1.287	Return a list of the pool IDs for the sim processing queues that have
1109 :			entries awaiting computation.
1110 :	olson	1.123
1111 :			=cut
1112 :	parrello	1.210	#: Return Type @;
1113 :	parrello	1.287	sub get_active_sim_pools {
1114 :	olson	1.123	my($self) = @_;
1115 :
1116 :			my $dbh = $self->db_handle();
1117 :
1118 :			my $res = $dbh->SQL("select distinct qid from sim_queue where not finished");
1119 :			return undef unless $res;
1120 :
1121 :			return map { $_->[0] } @$res;
1122 :			}
1123 :
1124 :	parrello	1.210	=head3 get_sim_pool_info
1125 :	olson	1.123
1126 :	parrello	1.287	C<< my ($total_entries, $n_finished, $n_assigned, $n_unassigned) = $fig->get_sim_pool_info($pool_id); >>
1127 :
1128 :			Return information about the given sim pool.
1129 :
1130 :			=over 4
1131 :
1132 :			=item pool_id
1133 :
1134 :			Pool ID of the similarity processing queue whose information is desired.
1135 :
1136 :			=item RETURN
1137 :
1138 :			Returns a four-element list. The first is the number of features in the
1139 :			queue; the second is the number of features that have been processed; the
1140 :			third is the number of features that have been assigned to a
1141 :			processor, and the fourth is the number of features left over.
1142 :	olson	1.123
1143 :	parrello	1.287	=back
1144 :	olson	1.123
1145 :			=cut
1146 :	parrello	1.210	#: Return Type @;
1147 :	parrello	1.287	sub get_sim_pool_info {
1148 :
1149 :	olson	1.123	my($self, $pool_id) = @_;
1150 :			my($dbh, $res, $total_entries, $n_finished, $n_assigned, $n_unassigned);
1151 :
1152 :			$dbh = $self->db_handle();
1153 :
1154 :			$res = $dbh->SQL("select count(chunk_id) from sim_queue where qid = '$pool_id'");
1155 :	parrello	1.200	$total_entries = $res->[0]->[0];
1156 :	olson	1.123
1157 :			$res = $dbh->SQL("select count(chunk_id) from sim_queue where qid = '$pool_id' and finished");
1158 :			$n_finished = $res->[0]->[0];
1159 :
1160 :			$res = $dbh->SQL("select count(chunk_id) from sim_queue where qid = '$pool_id' and assigned and not finished");
1161 :			$n_assigned = $res->[0]->[0];
1162 :
1163 :			$res = $dbh->SQL("select count(chunk_id) from sim_queue where qid = '$pool_id' and not finished and not assigned");
1164 :			$n_unassigned = $res->[0]->[0];
1165 :
1166 :			return ($total_entries, $n_finished, $n_assigned, $n_unassigned);
1167 :	olson	1.93	}
1168 :
1169 :	parrello	1.210	#=head3 get_sim_chunk
1170 :			#
1171 :			#usage: get_sim_chunk($n_seqs, $worker_id)
1172 :			#
1173 :			#Returns a chunk of $n_seqs of work.
1174 :			#
1175 :			#From Ross, about how sims are processed:
1176 :			#
1177 :			#Here is how I process them:
1178 :			#
1179 :			#
1180 :			# bash$ cd /Volumes/seed/olson/Sims/June22.out
1181 :			# bash$ for i in really*
1182 :			# > do
1183 :			# > cat < $i >> /Volumes/laptop/new.sims
1184 :			# > done
1185 :			#
1186 :			#
1187 :			#Then, I need to "reformat" them by adding to columns to each one
1188 :			# and split the result into files of about 3M each This I do using
1189 :			#
1190 :			#reduce_sims /Volumes/laptop/NR/NewNR/peg.synonyms.june21 300 < /Volumes/laptop/new.sims \|
1191 :			# reformat_sims /Volumes/laptop/NR/NewNR/checked.nr.june21 > /Volumes/laptop/reformated.sims
1192 :			#rm /Volumes/laptop/new.sims
1193 :			#split_sims /Volumes/laptop/NewSims sims.june24 reformated.sims
1194 :			#rm reformatted.sims
1195 :			#
1196 :			#=cut
1197 :	olson	1.93
1198 :	parrello	1.287	sub get_sim_chunk {
1199 :	parrello	1.210	my($self, $n_seqs, $worker_id) = @_;
1200 :			}
1201 :	olson	1.123
1202 :	parrello	1.210	=head3 get_local_hostname
1203 :	parrello	1.200
1204 :	parrello	1.287	C<< my $result = FIG::get_local_hostname(); >>
1205 :
1206 :			Return the local host name for the current processor. The name may be
1207 :			stored in a configuration file, or we may have to get it from the
1208 :			operating system.
1209 :	olson	1.123
1210 :	olson	1.93	=cut
1211 :	parrello	1.213	#: Return Type $;
1212 :	olson	1.10	sub get_local_hostname {
1213 :	olson	1.52
1214 :			#
1215 :			# See if there is a FIGdisk/config/hostname file. If there
1216 :			# is, force the hostname to be that.
1217 :			#
1218 :
1219 :			my $hostfile = "$FIG_Config::fig_disk/config/hostname";
1220 :	parrello	1.287	if (-f $hostfile) {
1221 :			my $fh;
1222 :			if (open($fh, $hostfile)) {
1223 :			my $hostname = <$fh>;
1224 :			chomp($hostname);
1225 :			return $hostname;
1226 :			}
1227 :	olson	1.52	}
1228 :	parrello	1.200
1229 :	olson	1.10	#
1230 :			# First check to see if we our hostname is correct.
1231 :			#
1232 :			# Map it to an IP address, and try to bind to that ip.
1233 :			#
1234 :
1235 :			my $tcp = getprotobyname('tcp');
1236 :	parrello	1.200
1237 :	olson	1.10	my $hostname = `hostname`;
1238 :	golsen	1.44	chomp($hostname);
1239 :	olson	1.10
1240 :			my @hostent = gethostbyname($hostname);
1241 :
1242 :	parrello	1.287	if (@hostent > 0) {
1243 :			my $sock;
1244 :			my $ip = $hostent[4];
1245 :
1246 :			socket($sock, PF_INET, SOCK_STREAM, $tcp);
1247 :			if (bind($sock, sockaddr_in(0, $ip))) {
1248 :			#
1249 :			# It worked. Reverse-map back to a hopefully fqdn.
1250 :			#
1251 :
1252 :			my @rev = gethostbyaddr($ip, AF_INET);
1253 :			if (@rev > 0) {
1254 :			my $host = $rev[0];
1255 :			#
1256 :			# Check to see if we have a FQDN.
1257 :			#
1258 :
1259 :			if ($host =~ /\./) {
1260 :			#
1261 :			# Good.
1262 :			#
1263 :			return $host;
1264 :			} else {
1265 :			#
1266 :			# We didn't get a fqdn; bail and return the IP address.
1267 :			#
1268 :			return get_hostname_by_adapter()
1269 :			}
1270 :			} else {
1271 :			return inet_ntoa($ip);
1272 :			}
1273 :			} else {
1274 :			#
1275 :			# Our hostname must be wrong; we can't bind to the IP
1276 :			# address it maps to.
1277 :			# Return the name associated with the adapter.
1278 :			#
1279 :			return get_hostname_by_adapter()
1280 :			}
1281 :			} else {
1282 :			#
1283 :			# Our hostname isn't known to DNS. This isn't good.
1284 :			# Return the name associated with the adapter.
1285 :			#
1286 :			return get_hostname_by_adapter()
1287 :			}
1288 :			}
1289 :
1290 :			=head3 get_hostname_by_adapter
1291 :	parrello	1.200
1292 :	parrello	1.287	C<< my $name = FIG::get_hostname_by_adapter(); >>
1293 :	olson	1.10
1294 :	parrello	1.287	Return the local host name for the current network environment.
1295 :	parrello	1.213
1296 :			=cut
1297 :			#: Return Type $;
1298 :	olson	1.10	sub get_hostname_by_adapter {
1299 :			#
1300 :			# Attempt to determine our local hostname based on the
1301 :			# network environment.
1302 :			#
1303 :			# This implementation reads the routing table for the default route.
1304 :			# We then look at the interface config for the interface that holds the default.
1305 :			#
1306 :			#
1307 :			# Linux routing table:
1308 :			# [olson@yips 0.0.0]$ netstat -rn
1309 :			# Kernel IP routing table
1310 :			# Destination Gateway Genmask Flags MSS Window irtt Iface
1311 :			# 140.221.34.32 0.0.0.0 255.255.255.224 U 0 0 0 eth0
1312 :			# 169.254.0.0 0.0.0.0 255.255.0.0 U 0 0 0 eth0
1313 :			# 127.0.0.0 0.0.0.0 255.0.0.0 U 0 0 0 lo
1314 :			# 0.0.0.0 140.221.34.61 0.0.0.0 UG 0 0 0 eth0
1315 :	parrello	1.200	#
1316 :	olson	1.10	# Mac routing table:
1317 :	parrello	1.200	#
1318 :	olson	1.10	# bash-2.05a$ netstat -rn
1319 :			# Routing tables
1320 :	parrello	1.200	#
1321 :	olson	1.10	# Internet:
1322 :			# Destination Gateway Flags Refs Use Netif Expire
1323 :			# default 140.221.11.253 UGSc 12 120 en0
1324 :			# 127.0.0.1 127.0.0.1 UH 16 8415486 lo0
1325 :			# 140.221.8/22 link#4 UCS 12 0 en0
1326 :			# 140.221.8.78 0:6:5b:f:51:c4 UHLW 0 183 en0 408
1327 :			# 140.221.8.191 0:3:93:84:ab:e8 UHLW 0 92 en0 622
1328 :			# 140.221.8.198 0:e0:98:8e:36:e2 UHLW 0 5 en0 691
1329 :			# 140.221.9.6 0:6:5b:f:51:d6 UHLW 1 63 en0 1197
1330 :			# 140.221.10.135 0:d0:59:34:26:34 UHLW 2 2134 en0 1199
1331 :			# 140.221.10.152 0:30:1b:b0:ec:dd UHLW 1 137 en0 1122
1332 :			# 140.221.10.153 127.0.0.1 UHS 0 0 lo0
1333 :			# 140.221.11.37 0:9:6b:53:4e:4b UHLW 1 624 en0 1136
1334 :			# 140.221.11.103 0:30:48:22:59:e6 UHLW 3 973 en0 1016
1335 :			# 140.221.11.224 0:a:95:6f:7:10 UHLW 1 1 en0 605
1336 :			# 140.221.11.237 0:1:30:b8:80:c0 UHLW 0 0 en0 1158
1337 :			# 140.221.11.250 0:1:30:3:1:0 UHLW 0 0 en0 1141
1338 :			# 140.221.11.253 0:d0:3:e:70:a UHLW 13 0 en0 1199
1339 :			# 169.254 link#4 UCS 0 0 en0
1340 :	parrello	1.200	#
1341 :	olson	1.10	# Internet6:
1342 :			# Destination Gateway Flags Netif Expire
1343 :			# UH lo0
1344 :			# fe80::%lo0/64 Uc lo0
1345 :			# link#1 UHL lo0
1346 :			# fe80::%en0/64 link#4 UC en0
1347 :			# 0:a:95:a8:26:68 UHL lo0
1348 :			# ff01::/32 U lo0
1349 :			# ff02::%lo0/32 UC lo0
1350 :			# ff02::%en0/32 link#4 UC en0
1351 :
1352 :			my($fh);
1353 :
1354 :	parrello	1.287	if (!open($fh, "netstat -rn \|")) {
1355 :			warn "Cannot run netstat to determine local IP address\n";
1356 :			return "localhost";
1357 :	olson	1.10	}
1358 :
1359 :			my $interface_name;
1360 :	parrello	1.200
1361 :	parrello	1.287	while (<$fh>) {
1362 :			my @cols = split();
1363 :	olson	1.10
1364 :	parrello	1.287	if ($cols[0] eq "default" \|\| $cols[0] eq "0.0.0.0") {
1365 :			$interface_name = $cols[$#cols];
1366 :			}
1367 :	olson	1.10	}
1368 :			close($fh);
1369 :	parrello	1.200
1370 :	olson	1.11	# print "Default route on $interface_name\n";
1371 :	olson	1.10
1372 :			#
1373 :			# Find ifconfig.
1374 :			#
1375 :
1376 :			my $ifconfig;
1377 :
1378 :	parrello	1.287	for my $dir ((split(":", $ENV{PATH}), "/sbin", "/usr/sbin")) {
1379 :			if (-x "$dir/ifconfig") {
1380 :			$ifconfig = "$dir/ifconfig";
1381 :			last;
1382 :			}
1383 :	olson	1.10	}
1384 :
1385 :	parrello	1.287	if ($ifconfig eq "") {
1386 :			warn "Ifconfig not found\n";
1387 :			return "localhost";
1388 :	olson	1.10	}
1389 :	olson	1.11	# print "Foudn $ifconfig\n";
1390 :	olson	1.10
1391 :	parrello	1.287	if (!open($fh, "$ifconfig $interface_name \|")) {
1392 :			warn "Could not run $ifconfig: $!\n";
1393 :			return "localhost";
1394 :	olson	1.10	}
1395 :
1396 :			my $ip;
1397 :	parrello	1.287	while (<$fh>) {
1398 :			#
1399 :			# Mac:
1400 :			# inet 140.221.10.153 netmask 0xfffffc00 broadcast 140.221.11.255
1401 :			# Linux:
1402 :			# inet addr:140.221.34.37 Bcast:140.221.34.63 Mask:255.255.255.224
1403 :			#
1404 :
1405 :			chomp;
1406 :			s/^\s*//;
1407 :
1408 :			# print "Have '$_'\n";
1409 :			if (/inet\s+addr:(\d+\.\d+\.\d+\.\d+)\s+/) {
1410 :			#
1411 :			# Linux hit.
1412 :			#
1413 :			$ip = $1;
1414 :			# print "Got linux $ip\n";
1415 :			last;
1416 :			} elsif (/inet\s+(\d+\.\d+\.\d+\.\d+)\s+/) {
1417 :			#
1418 :			# Mac hit.
1419 :			#
1420 :			$ip = $1;
1421 :			# print "Got mac $ip\n";
1422 :			last;
1423 :			}
1424 :	olson	1.10	}
1425 :			close($fh);
1426 :
1427 :	parrello	1.287	if ($ip eq "") {
1428 :			warn "Didn't find an IP\n";
1429 :			return "localhost";
1430 :	olson	1.10	}
1431 :
1432 :			return $ip;
1433 :	efrank	1.1	}
1434 :
1435 :	parrello	1.213	=head3 get_seed_id
1436 :
1437 :	parrello	1.287	C<< my $id = FIG::get_seed_id(); >>
1438 :
1439 :			Return the Universally Unique ID for this SEED instance. If one
1440 :			does not exist, it will be created.
1441 :	parrello	1.213
1442 :			=cut
1443 :			#: Return type $;
1444 :	olson	1.38	sub get_seed_id {
1445 :			#
1446 :			# Retrieve the seed identifer from FIGdisk/config/seed_id.
1447 :			#
1448 :			# If it's not there, create one, and make it readonly.
1449 :			#
1450 :			my $id;
1451 :			my $id_file = "$FIG_Config::fig_disk/config/seed_id";
1452 :	parrello	1.287	if (! -f $id_file) {
1453 :			my $newid = `uuidgen`;
1454 :			if (!$newid) {
1455 :			die "Cannot run uuidgen: $!";
1456 :			}
1457 :	olson	1.38
1458 :	parrello	1.287	chomp($newid);
1459 :			my $fh = new FileHandle(">$id_file");
1460 :			if (!$fh) {
1461 :			die "error creating $id_file: $!";
1462 :			}
1463 :			print $fh "$newid\n";
1464 :			$fh->close();
1465 :			chmod(0444, $id_file);
1466 :	olson	1.38	}
1467 :			my $fh = new FileHandle("<$id_file");
1468 :			$id = <$fh>;
1469 :			chomp($id);
1470 :			return $id;
1471 :			}
1472 :
1473 :	parrello	1.287	=head3 get_release_info
1474 :	olson	1.155
1475 :	parrello	1.287	C<< my ($name, $id, $inst, $email, $parent_id, $description) = FIG::get_release_info(); >>
1476 :	olson	1.155
1477 :	parrello	1.287	Return the current data release information..
1478 :	olson	1.195
1479 :			The release info comes from the file FIG/Data/RELEASE. It is formatted as:
1480 :
1481 :	parrello	1.287	<release-name>
1482 :			<unique id>
1483 :			<institution>
1484 :			<contact email>
1485 :			<unique id of data release this release derived from>
1486 :			<description>
1487 :	olson	1.195
1488 :			For instance:
1489 :
1490 :	parrello	1.287	-----
1491 :			SEED Data Release, 09/15/2004.
1492 :			4148208C-1DF2-11D9-8417-000A95D52EF6
1493 :			ANL/FIG
1494 :			olson@mcs.anl.gov
1495 :
1496 :			Test release.
1497 :			-----
1498 :	olson	1.195
1499 :			If no RELEASE file exists, this routine will create one with a new unique ID. This
1500 :			lets a peer optimize the data transfer by being able to cache ID translations
1501 :			from this instance.
1502 :	olson	1.155
1503 :			=cut
1504 :	parrello	1.213	#: Return Type @;
1505 :	parrello	1.287	sub get_release_info {
1506 :	olson	1.196	my($fig, $no_create) = @_;
1507 :	olson	1.195
1508 :			my $rel_file = "$FIG_Config::data/RELEASE";
1509 :
1510 :	parrello	1.287	if (! -f $rel_file and !$no_create) {
1511 :	parrello	1.298	#
1512 :			# Create a new one.
1513 :			#
1514 :	olson	1.195
1515 :	parrello	1.287	my $newid = `uuidgen`;
1516 :			if (!$newid) {
1517 :			die "Cannot run uuidgen: $!";
1518 :			}
1519 :	olson	1.195
1520 :	parrello	1.287	chomp($newid);
1521 :	olson	1.195
1522 :	parrello	1.287	my $relinfo = "Automatically generated release info " . localtime();
1523 :			my $inst = "Unknown";
1524 :			my $contact = "Unknown";
1525 :			my $parent = "";
1526 :			my( $a, $b, $e, $v, $env ) = $fig->genome_counts;
1527 :			my $description = "Automatically generated release info\n";
1528 :			$description .= "Contains $a archaeal, $b bacterial, $e eukaryal, $v viral and $env environmental genomes.\n";
1529 :
1530 :			my $fh = new FileHandle(">$rel_file");
1531 :			if (!$fh) {
1532 :			warn "error creating $rel_file: $!";
1533 :			return undef;
1534 :			}
1535 :			print $fh "$relinfo\n";
1536 :			print $fh "$newid\n";
1537 :			print $fh "$inst\n";
1538 :			print $fh "$contact\n";
1539 :			print $fh "$parent\n";
1540 :			print $fh $description;
1541 :			$fh->close();
1542 :			chmod(0444, $rel_file);
1543 :	olson	1.195	}
1544 :
1545 :	parrello	1.287	if (open(my $fh, $rel_file)) {
1546 :			my(@lines) = <$fh>;
1547 :			close($fh);
1548 :	parrello	1.200
1549 :	parrello	1.287	chomp(@lines);
1550 :	parrello	1.200
1551 :	parrello	1.287	my($info, $id, $inst, $contact, $parent, @desc) = @lines;
1552 :	olson	1.195
1553 :	parrello	1.287	return ($info, $id, $inst, $contact, $parent, join("\n", @desc));
1554 :	olson	1.195	}
1555 :	olson	1.155
1556 :			return undef;
1557 :			}
1558 :
1559 :	parrello	1.287	=head3 get_peer_last_update
1560 :	olson	1.155
1561 :	parrello	1.287	C<< my $date = $fig->get_peer_last_update($peer_id); >>
1562 :	parrello	1.213
1563 :	olson	1.155	Return the timestamp from the last successful peer-to-peer update with
1564 :	parrello	1.287	the given peer. If the specified peer has made updates, comparing this
1565 :			timestamp to the timestamp of the updates can tell you whether or not
1566 :			the updates have been integrated into your SEED data store.
1567 :	olson	1.155
1568 :			We store this information in FIG/Data/Global/Peers/<peer-id>.
1569 :
1570 :	parrello	1.287	=over 4
1571 :
1572 :			=item peer_id
1573 :
1574 :			Universally Unique ID for the desired peer.
1575 :
1576 :			=item RETURN
1577 :
1578 :			Returns the date/time stamp for the last peer-to-peer updated performed
1579 :			with the identified SEED instance.
1580 :
1581 :			=back
1582 :
1583 :	olson	1.155	=cut
1584 :	parrello	1.213	#: Return Type $;
1585 :	parrello	1.287	sub get_peer_last_update {
1586 :	olson	1.155	my($self, $peer_id) = @_;
1587 :
1588 :			my $dir = "$FIG_Config::data/Global/Peers";
1589 :			&verify_dir($dir);
1590 :			$dir .= "/$peer_id";
1591 :			&verify_dir($dir);
1592 :
1593 :			my $update_file = "$dir/last_update";
1594 :	parrello	1.287	if (-f $update_file) {
1595 :			my $time = file_head($update_file, 1);
1596 :			chomp $time;
1597 :			return $time;
1598 :			} else {
1599 :			return undef;
1600 :	olson	1.155	}
1601 :			}
1602 :
1603 :	parrello	1.287	=head3 set_peer_last_update
1604 :	parrello	1.213
1605 :	parrello	1.287	C<< $fig->set_peer_last_update($peer_id, $time); >>
1606 :	parrello	1.213
1607 :	parrello	1.287	Manually set the update timestamp for a specified peer. This informs
1608 :			the SEED that you have all of the assignments and updates from a
1609 :			particular SEED instance as of a certain date.
1610 :	parrello	1.213
1611 :			=cut
1612 :			#: Return Type ;
1613 :
1614 :	parrello	1.287	sub set_peer_last_update {
1615 :	olson	1.155	my($self, $peer_id, $time) = @_;
1616 :
1617 :			my $dir = "$FIG_Config::data/Global/Peers";
1618 :			&verify_dir($dir);
1619 :			$dir .= "/$peer_id";
1620 :			&verify_dir($dir);
1621 :
1622 :			my $update_file = "$dir/last_update";
1623 :			open(F, ">$update_file");
1624 :			print F "$time\n";
1625 :			close(F);
1626 :			}
1627 :
1628 :	redwards	1.302	=head3 clean_spaces
1629 :
1630 :	parrello	1.320	Remove any extra spaces from input fields. This will (currently) remove ^\s, \s$, and concatenate multiple spaces into one.
1631 :	redwards	1.302
1632 :			my $input=$fig->clean_spaces($cgi->param('input'));
1633 :
1634 :			=cut
1635 :
1636 :			sub clean_spaces
1637 :			{
1638 :			my ($self, $s)=@_;
1639 :			# note at the moment I do not use \s because that recognizes \t and \n too. This should only remove multiple spaces.
1640 :	parrello	1.320	$s =~ s/^ +//;
1641 :	redwards	1.302	$s =~ s/ +$//;
1642 :			$s =~ s/ +/ /g;
1643 :			return $s;
1644 :			}
1645 :
1646 :
1647 :
1648 :	parrello	1.213	=head3 cgi_url
1649 :
1650 :	parrello	1.287	C<< my $url = FIG::$fig->cgi_url(); >>
1651 :
1652 :			Return the URL for the CGI script directory.
1653 :	parrello	1.213
1654 :			=cut
1655 :			#: Return Type $;
1656 :	efrank	1.1	sub cgi_url {
1657 :			return &plug_url($FIG_Config::cgi_url);
1658 :			}
1659 :	parrello	1.200
1660 :	parrello	1.213	=head3 temp_url
1661 :
1662 :	parrello	1.287	C<< my $url = FIG::temp_url(); >>
1663 :
1664 :			Return the URL of the temporary file directory.
1665 :	parrello	1.213
1666 :			=cut
1667 :			#: Return Type $;
1668 :	efrank	1.1	sub temp_url {
1669 :			return &plug_url($FIG_Config::temp_url);
1670 :			}
1671 :	parrello	1.200
1672 :	parrello	1.213	=head3 plug_url
1673 :
1674 :	parrello	1.287	C<< my $url2 = $fig->plug_url($url); >>
1675 :
1676 :			or
1677 :
1678 :			C<< my $url2 = $fig->plug_url($url); >>
1679 :
1680 :			Change the domain portion of a URL to point to the current domain. This essentially
1681 :			relocates URLs into the current environment.
1682 :
1683 :			=over 4
1684 :
1685 :			=item url
1686 :
1687 :			URL to relocate.
1688 :
1689 :			=item RETURN
1690 :
1691 :			Returns a new URL with the base portion converted to the current operating host.
1692 :			If the URL does not begin with C<http://>, the URL will be returned unmodified.
1693 :
1694 :			=back
1695 :	parrello	1.213
1696 :			=cut
1697 :			#: Return Type $;
1698 :	efrank	1.1	sub plug_url {
1699 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1700 :	efrank	1.1	my($url) = @_;
1701 :
1702 :	golsen	1.44	my $name;
1703 :
1704 :			# Revised by GJO
1705 :			# First try to get url from the current http request
1706 :
1707 :			if ( defined( $ENV{ 'HTTP_HOST' } ) # This is where $cgi->url gets its value
1708 :			&& ( $name = $ENV{ 'HTTP_HOST' } )
1709 :			&& ( $url =~ s~^http://[^/]*~http://$name~ ) # ~ is delimiter
1710 :			) {}
1711 :
1712 :			# Otherwise resort to alternative sources
1713 :
1714 :			elsif ( ( $name = &get_local_hostname )
1715 :			&& ( $url =~ s~^http://[^/]*~http://$name~ ) # ~ is delimiter
1716 :			) {}
1717 :
1718 :	efrank	1.1	return $url;
1719 :			}
1720 :
1721 :	parrello	1.213	=head3 file_read
1722 :
1723 :	parrello	1.287	C<< my $text = $fig->file_read($fileName); >>
1724 :
1725 :			or
1726 :
1727 :			C<< my @lines = $fig->file_read($fileName); >>
1728 :
1729 :			or
1730 :
1731 :			C<< my $text = FIG::file_read($fileName); >>
1732 :
1733 :			or
1734 :
1735 :			C<< my @lines = FIG::file_read($fileName); >>
1736 :
1737 :			Read an entire file into memory. In a scalar context, the file is returned
1738 :			as a single text string with line delimiters included. In a list context, the
1739 :			file is returned as a list of lines, each line terminated by a line
1740 :			delimiter. (For a method that automatically strips the line delimiters,
1741 :			use C<Tracer::GetFile>.)
1742 :
1743 :			=over 4
1744 :
1745 :			=item fileName
1746 :
1747 :			Fully-qualified name of the file to read.
1748 :
1749 :			=item RETURN
1750 :
1751 :			In a list context, returns a list of the file lines. In a scalar context, returns
1752 :			a string containing all the lines of the file with delimiters included.
1753 :	parrello	1.213
1754 :	parrello	1.287	=back
1755 :	parrello	1.213
1756 :			=cut
1757 :			#: Return Type $;
1758 :			#: Return Type @;
1759 :	parrello	1.287	sub file_read {
1760 :
1761 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1762 :	parrello	1.287	my($fileName) = @_;
1763 :			return file_head($fileName, '*');
1764 :	olson	1.90
1765 :			}
1766 :
1767 :
1768 :	parrello	1.213	=head3 file_head
1769 :
1770 :	parrello	1.287	C<< my $text = $fig->file_head($fileName, $count); >>
1771 :
1772 :			or
1773 :
1774 :			C<< my @lines = $fig->file_head($fileName, $count); >>
1775 :	parrello	1.213
1776 :	parrello	1.287	or
1777 :	parrello	1.213
1778 :	parrello	1.287	C<< my $text = FIG::file_head($fileName, $count); >>
1779 :	olson	1.90
1780 :	parrello	1.287	or
1781 :	olson	1.90
1782 :	parrello	1.287	C<< my @lines = FIG::file_head($fileName, $count); >>
1783 :	olson	1.90
1784 :	parrello	1.287	Read a portion of a file into memory. In a scalar context, the file portion is
1785 :			returned as a single text string with line delimiters included. In a list
1786 :			context, the file portion is returned as a list of lines, each line terminated
1787 :			by a line delimiter.
1788 :	olson	1.155
1789 :	parrello	1.287	=over 4
1790 :	olson	1.90
1791 :	parrello	1.287	=item fileName
1792 :	olson	1.90
1793 :	parrello	1.287	Fully-qualified name of the file to read.
1794 :	efrank	1.1
1795 :	parrello	1.287	=item count (optional)
1796 :	efrank	1.1
1797 :	parrello	1.287	Number of lines to read from the file. If omitted, C<1> is assumed. If the
1798 :			non-numeric string C<*> is specified, the entire file will be read.
1799 :	efrank	1.1
1800 :	parrello	1.287	=item RETURN
1801 :	efrank	1.1
1802 :	parrello	1.287	In a list context, returns a list of the desired file lines. In a scalar context, returns
1803 :			a string containing the desired lines of the file with delimiters included.
1804 :	efrank	1.1
1805 :	parrello	1.287	=back
1806 :	efrank	1.1
1807 :			=cut
1808 :	parrello	1.287	#: Return Type $;
1809 :			#: Return Type @;
1810 :			sub file_head {
1811 :	efrank	1.1
1812 :	parrello	1.287	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1813 :			my($file, $count) = @_;
1814 :	efrank	1.1
1815 :	parrello	1.287	my ($n, $allFlag);
1816 :			if ($count eq '*') {
1817 :	olson	1.304	Trace("Full file read for \"$file\".") if T(3);
1818 :	parrello	1.287	$allFlag = 1;
1819 :			$n = 0;
1820 :			} else {
1821 :			$allFlag = 0;
1822 :			$n = (!$count ? 1 : $count);
1823 :	olson	1.304	Trace("Reading $n record(s) from \"$file\".") if T(3);
1824 :	parrello	1.287	}
1825 :	efrank	1.1
1826 :	parrello	1.287	if (open(my $fh, "<$file")) {
1827 :	parrello	1.298	my(@ret, $i);
1828 :	parrello	1.287	$i = 0;
1829 :			while (<$fh>) {
1830 :			push(@ret, $_);
1831 :			$i++;
1832 :			last if !$allFlag && $i >= $n;
1833 :			}
1834 :			close($fh);
1835 :			if (wantarray) {
1836 :			return @ret;
1837 :			} else {
1838 :			return join("", @ret);
1839 :			}
1840 :	efrank	1.1	}
1841 :			}
1842 :
1843 :			################ Basic Routines [ existed since WIT ] ##########################
1844 :
1845 :	parrello	1.287	=head3 min
1846 :
1847 :			C<< my $min = FIG::min(@x); >>
1848 :
1849 :			or
1850 :
1851 :			C<< my $min = $fig->min(@x); >>
1852 :
1853 :			Return the minimum numeric value from a list.
1854 :
1855 :			=over 4
1856 :
1857 :			=item x1, x2, ... xN
1858 :	efrank	1.1
1859 :	parrello	1.287	List of numbers to process.
1860 :	efrank	1.1
1861 :	parrello	1.287	=item RETURN
1862 :	efrank	1.1
1863 :	parrello	1.287	Returns the numeric value of the list entry possessing the lowest value. Returns
1864 :			C<undef> if the list is empty.
1865 :	efrank	1.1
1866 :	parrello	1.287	=back
1867 :	efrank	1.1
1868 :			=cut
1869 :	parrello	1.213	#: Return Type $;
1870 :	efrank	1.1	sub min {
1871 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1872 :	efrank	1.1	my(@x) = @_;
1873 :			my($min,$i);
1874 :
1875 :			(@x > 0) \|\| return undef;
1876 :			$min = $x[0];
1877 :	parrello	1.287	for ($i=1; ($i < @x); $i++) {
1878 :			$min = ($min > $x[$i]) ? $x[$i] : $min;
1879 :	efrank	1.1	}
1880 :			return $min;
1881 :			}
1882 :
1883 :	parrello	1.287	=head3 max
1884 :
1885 :			C<< my $max = FIG::max(@x); >>
1886 :
1887 :			or
1888 :
1889 :			C<< my $max = $fig->max(@x); >>
1890 :	efrank	1.1
1891 :	parrello	1.287	Return the maximum numeric value from a list.
1892 :	efrank	1.1
1893 :	parrello	1.287	=over 4
1894 :
1895 :			=item x1, x2, ... xN
1896 :
1897 :			List of numbers to process.
1898 :
1899 :			=item RETURN
1900 :
1901 :			Returns the numeric value of t/he list entry possessing the highest value. Returns
1902 :			C<undef> if the list is empty.
1903 :	efrank	1.1
1904 :	parrello	1.287	=back
1905 :	efrank	1.1
1906 :			=cut
1907 :	parrello	1.213	#: Return Type $;
1908 :	efrank	1.1	sub max {
1909 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1910 :	efrank	1.1	my(@x) = @_;
1911 :			my($max,$i);
1912 :
1913 :			(@x > 0) \|\| return undef;
1914 :			$max = $x[0];
1915 :	parrello	1.287	for ($i=1; ($i < @x); $i++) {
1916 :			$max = ($max < $x[$i]) ? $x[$i] : $max;
1917 :	efrank	1.1	}
1918 :			return $max;
1919 :			}
1920 :
1921 :	parrello	1.287	=head3 between
1922 :	efrank	1.1
1923 :	parrello	1.287	C<< my $flag = FIG::between($x, $y, $z); >>
1924 :	efrank	1.1
1925 :	parrello	1.287	or
1926 :
1927 :			C<< my $flag = $fig->between($x, $y, $z); >>
1928 :
1929 :			Determine whether or not $y is between $x and $z.
1930 :
1931 :			=over 4
1932 :
1933 :			=item x
1934 :
1935 :			First edge number.
1936 :
1937 :			=item y
1938 :	efrank	1.1
1939 :	parrello	1.287	Number to examine.
1940 :
1941 :			=item z
1942 :
1943 :			Second edge number.
1944 :
1945 :			=item RETURN
1946 :
1947 :			Return TRUE if the number I<$y> is between the numbers I<$x> and I<$z>. The check
1948 :			is inclusive (that is, if I<$y> is equal to I<$x> or I<$z> the function returns
1949 :			TRUE), and the order of I<$x> and I<$z> does not matter. If I<$x> is lower than
1950 :			I<$z>, then the return is TRUE if I<$x> <= I<$y> <= I<$z>. If I<$z> is lower,
1951 :			then the return is TRUE if I<$x> >= I$<$y> >= I<$z>.
1952 :
1953 :			=back
1954 :	efrank	1.1
1955 :			=cut
1956 :	parrello	1.213	#: Return Type $;
1957 :	efrank	1.1	sub between {
1958 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1959 :	efrank	1.1	my($x,$y,$z) = @_;
1960 :
1961 :	parrello	1.287	if ($x < $z) {
1962 :			return (($x <= $y) && ($y <= $z));
1963 :			} else {
1964 :			return (($x >= $y) && ($y >= $z));
1965 :	efrank	1.1	}
1966 :			}
1967 :
1968 :	parrello	1.287	=head3 standard_genetic_code
1969 :	efrank	1.1
1970 :	parrello	1.287	C<< my $code = FIG::standard_genetic_code(); >>
1971 :	efrank	1.1
1972 :	parrello	1.287	Return a hash containing the standard translation of nucleotide triples to proteins.
1973 :			Methods such as L</translate> can take a translation scheme as a parameter. This method
1974 :			returns the default translation scheme. The scheme is implemented as a reference to a
1975 :			hash that contains nucleotide triplets as keys and has protein letters as values.
1976 :	efrank	1.1
1977 :			=cut
1978 :	parrello	1.213	#: Return Type $;
1979 :	efrank	1.1	sub standard_genetic_code {
1980 :	parrello	1.200
1981 :	efrank	1.1	my $code = {};
1982 :
1983 :			$code->{"AAA"} = "K";
1984 :			$code->{"AAC"} = "N";
1985 :			$code->{"AAG"} = "K";
1986 :			$code->{"AAT"} = "N";
1987 :			$code->{"ACA"} = "T";
1988 :			$code->{"ACC"} = "T";
1989 :			$code->{"ACG"} = "T";
1990 :			$code->{"ACT"} = "T";
1991 :			$code->{"AGA"} = "R";
1992 :			$code->{"AGC"} = "S";
1993 :			$code->{"AGG"} = "R";
1994 :			$code->{"AGT"} = "S";
1995 :			$code->{"ATA"} = "I";
1996 :			$code->{"ATC"} = "I";
1997 :			$code->{"ATG"} = "M";
1998 :			$code->{"ATT"} = "I";
1999 :			$code->{"CAA"} = "Q";
2000 :			$code->{"CAC"} = "H";
2001 :			$code->{"CAG"} = "Q";
2002 :			$code->{"CAT"} = "H";
2003 :			$code->{"CCA"} = "P";
2004 :			$code->{"CCC"} = "P";
2005 :			$code->{"CCG"} = "P";
2006 :			$code->{"CCT"} = "P";
2007 :			$code->{"CGA"} = "R";
2008 :			$code->{"CGC"} = "R";
2009 :			$code->{"CGG"} = "R";
2010 :			$code->{"CGT"} = "R";
2011 :			$code->{"CTA"} = "L";
2012 :			$code->{"CTC"} = "L";
2013 :			$code->{"CTG"} = "L";
2014 :			$code->{"CTT"} = "L";
2015 :			$code->{"GAA"} = "E";
2016 :			$code->{"GAC"} = "D";
2017 :			$code->{"GAG"} = "E";
2018 :			$code->{"GAT"} = "D";
2019 :			$code->{"GCA"} = "A";
2020 :			$code->{"GCC"} = "A";
2021 :			$code->{"GCG"} = "A";
2022 :			$code->{"GCT"} = "A";
2023 :			$code->{"GGA"} = "G";
2024 :			$code->{"GGC"} = "G";
2025 :			$code->{"GGG"} = "G";
2026 :			$code->{"GGT"} = "G";
2027 :			$code->{"GTA"} = "V";
2028 :			$code->{"GTC"} = "V";
2029 :			$code->{"GTG"} = "V";
2030 :			$code->{"GTT"} = "V";
2031 :			$code->{"TAA"} = "*";
2032 :			$code->{"TAC"} = "Y";
2033 :			$code->{"TAG"} = "*";
2034 :			$code->{"TAT"} = "Y";
2035 :			$code->{"TCA"} = "S";
2036 :			$code->{"TCC"} = "S";
2037 :			$code->{"TCG"} = "S";
2038 :			$code->{"TCT"} = "S";
2039 :			$code->{"TGA"} = "*";
2040 :			$code->{"TGC"} = "C";
2041 :			$code->{"TGG"} = "W";
2042 :			$code->{"TGT"} = "C";
2043 :			$code->{"TTA"} = "L";
2044 :			$code->{"TTC"} = "F";
2045 :			$code->{"TTG"} = "L";
2046 :			$code->{"TTT"} = "F";
2047 :	parrello	1.200
2048 :	efrank	1.1	return $code;
2049 :			}
2050 :
2051 :	parrello	1.287	=head3 translate
2052 :
2053 :			C<< my $aa_seq = &FIG::translate($dna_seq, $code, $fix_start); >>
2054 :
2055 :			Translate a DNA sequence to a protein sequence using the specified genetic code.
2056 :			If I<$fix_start> is TRUE, will translate an initial C<TTG> or C<GTG> code to
2057 :			C<M>. (In the standard genetic code, these two combinations normally translate
2058 :			to C<V> and C<L>, respectively.)
2059 :
2060 :			=over 4
2061 :	efrank	1.1
2062 :	parrello	1.287	=item dna_seq
2063 :	efrank	1.1
2064 :	parrello	1.287	DNA sequence to translate. Note that the DNA sequence can only contain
2065 :			known nucleotides.
2066 :	efrank	1.1
2067 :	parrello	1.287	=item code
2068 :	efrank	1.1
2069 :	parrello	1.287	Reference to a hash specifying the translation code. The hash is keyed by
2070 :			nucleotide triples, and the value for each key is the corresponding protein
2071 :			letter. If this parameter is omitted, the L</standard_genetic_code> will be
2072 :			used.
2073 :	efrank	1.1
2074 :	parrello	1.287	=item fix_start
2075 :
2076 :			TRUE if the first triple is to get special treatment, else FALSE. If TRUE,
2077 :			then a value of C<TTG> or C<GTG> in the first position will be translated to
2078 :			C<M> instead of the value specified in the translation code.
2079 :
2080 :			=item RETURN
2081 :
2082 :			Returns a string resulting from translating each nucleotide triple into a
2083 :			protein letter.
2084 :
2085 :			=back
2086 :
2087 :			=cut
2088 :			#: Return Type $;
2089 :			sub translate {
2090 :			shift if UNIVERSAL::isa($_[0],__PACKAGE__);
2091 :
2092 :			my( $dna,$code,$start ) = @_;
2093 :			my( $i,$j,$ln );
2094 :			my( $x,$y );
2095 :			my( $prot );
2096 :
2097 :			if (! defined($code)) {
2098 :			$code = &FIG::standard_genetic_code;
2099 :	efrank	1.1	}
2100 :			$ln = length($dna);
2101 :			$prot = "X" x ($ln/3);
2102 :			$dna =~ tr/a-z/A-Z/;
2103 :
2104 :	parrello	1.287	for ($i=0,$j=0; ($i < ($ln-2)); $i += 3,$j++) {
2105 :			$x = substr($dna,$i,3);
2106 :			if ($y = $code->{$x}) {
2107 :			substr($prot,$j,1) = $y;
2108 :	efrank	1.1	}
2109 :			}
2110 :	parrello	1.200
2111 :	parrello	1.287	if (($start) && ($ln >= 3) && (substr($dna,0,3) =~ /^[GT]TG$/)) {
2112 :			substr($prot,0,1) = 'M';
2113 :	efrank	1.1	}
2114 :			return $prot;
2115 :			}
2116 :
2117 :	parrello	1.287	=head3 reverse_comp
2118 :
2119 :			C<< my $dnaR = FIG::reverse_comp($dna); >>
2120 :
2121 :			or
2122 :
2123 :			C<< my $dnaR = $fig->reverse_comp($dna); >>
2124 :
2125 :			Return the reverse complement os the specified DNA sequence.
2126 :	efrank	1.1
2127 :	parrello	1.287	NOTE: for extremely long DNA strings, use L</rev_comp>, which allows you to
2128 :			pass the strings around in the form of pointers.
2129 :	efrank	1.1
2130 :	parrello	1.287	=over 4
2131 :
2132 :			=item dna
2133 :	efrank	1.1
2134 :	parrello	1.287	DNA sequence whose reverse complement is desired.
2135 :
2136 :			=item RETURN
2137 :
2138 :			Returns the reverse complement of the incoming DNA sequence.
2139 :
2140 :			=back
2141 :	efrank	1.1
2142 :			=cut
2143 :	parrello	1.213	#: Return Type $;
2144 :	efrank	1.1	sub reverse_comp {
2145 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
2146 :	efrank	1.1	my($seq) = @_;
2147 :
2148 :			return ${&rev_comp(\$seq)};
2149 :			}
2150 :
2151 :	parrello	1.287	=head3 rev_comp
2152 :
2153 :			C<< my $dnaRP = FIG::rev_comp(\$dna); >>
2154 :
2155 :			or
2156 :
2157 :			C<< my $dnaRP = $fig->rev_comp(\$dna); >>
2158 :
2159 :			Return the reverse complement of the specified DNA sequence. The DNA sequence
2160 :			is passed in as a string reference rather than a raw string for performance
2161 :			reasons. If this is unnecessary, use L</reverse_comp>, which processes strings
2162 :			instead of references to strings.
2163 :
2164 :			=over 4
2165 :
2166 :			=item dna
2167 :
2168 :			Reference to the DNA sequence whose reverse complement is desired.
2169 :
2170 :			=item RETURN
2171 :
2172 :			Returns a reference to the reverse complement of the incoming DNA sequence.
2173 :
2174 :			=back
2175 :	parrello	1.213
2176 :			=cut
2177 :			#: Return Type $;
2178 :	efrank	1.1	sub rev_comp {
2179 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
2180 :	efrank	1.1	my( $seqP ) = @_;
2181 :			my( $rev );
2182 :
2183 :			$rev = reverse( $$seqP );
2184 :	overbeek	1.317	$rev =~ tr/A-Z/a-z/;
2185 :			$rev =~ tr/acgtumrwsykbdhv/tgcaakywsrmvhdb/;
2186 :	efrank	1.1	return \$rev;
2187 :			}
2188 :
2189 :	parrello	1.287	=head3 verify_dir
2190 :
2191 :			C<< FIG::verify_dir($dir); >>
2192 :	efrank	1.1
2193 :	parrello	1.287	or
2194 :	efrank	1.1
2195 :	parrello	1.287	C<< $fig->verify_dir($dir); >>
2196 :	efrank	1.1
2197 :	parrello	1.287	Insure that the specified directory exists. If it must be created, the permissions will
2198 :			be set to C<0777>.
2199 :	efrank	1.1
2200 :			=cut
2201 :
2202 :			sub verify_dir {
2203 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
2204 :	efrank	1.1	my($dir) = @_;
2205 :
2206 :	parrello	1.287	if (-d $dir) {
2207 :			return
2208 :			}
2209 :			if ($dir =~ /^(.*)\/[^\/]+$/) {
2210 :			&verify_dir($1);
2211 :	efrank	1.1	}
2212 :	parrello	1.287	mkdir($dir,0777) \|\| Confess("Could not make directory $dir: $!");
2213 :	efrank	1.1	}
2214 :
2215 :	parrello	1.287	=head3 run
2216 :	efrank	1.1
2217 :	parrello	1.287	C<< FIG::run($cmd); >>
2218 :	overbeek	1.283
2219 :	parrello	1.287	or
2220 :
2221 :			C<< $fig->run($cmd); >>
2222 :	overbeek	1.283
2223 :	parrello	1.287	Run a command. If the command fails, the error will be traced.
2224 :	overbeek	1.283
2225 :			=cut
2226 :
2227 :	parrello	1.287	sub run {
2228 :			shift if UNIVERSAL::isa($_[0],__PACKAGE__);
2229 :			my($cmd) = @_;
2230 :
2231 :			if ($ENV{VERBOSE}) {
2232 :			my @tmp = `date`;
2233 :			chomp @tmp;
2234 :			print STDERR "$tmp[0]: running $cmd\n";
2235 :			}
2236 :			Trace("Running command: $cmd") if T(3);
2237 :			(system($cmd) == 0) \|\| Confess("FAILED: $cmd");
2238 :			}
2239 :
2240 :			=head3 augment_path
2241 :
2242 :			C<< FIG::augment_path($dirName); >>
2243 :	overbeek	1.283
2244 :	parrello	1.287	Add a directory to the system path.
2245 :	overbeek	1.283
2246 :	parrello	1.287	This method adds a new directory to the front of the system path. It looks in the
2247 :			configuration file to determine whether this is Windows or Unix, and uses the
2248 :			appropriate separator.
2249 :	efrank	1.1
2250 :	parrello	1.287	=over 4
2251 :	efrank	1.1
2252 :	parrello	1.287	=item dirName
2253 :
2254 :			Name of the directory to add to the path.
2255 :
2256 :			=back
2257 :	efrank	1.1
2258 :			=cut
2259 :
2260 :	parrello	1.287	sub augment_path {
2261 :			my ($dirName) = @_;
2262 :			if ($FIG_Config::win_mode) {
2263 :			$ENV{PATH} = "$dirName;$ENV{PATH}";
2264 :			} else {
2265 :			$ENV{PATH} = "$dirName:$ENV{PATH}";
2266 :	overbeek	1.278	}
2267 :	efrank	1.1	}
2268 :
2269 :	parrello	1.287	=head3 read_fasta_record
2270 :	gdpusch	1.45
2271 :	parrello	1.287	C<< my ($seq_id, $seq_pointer, $comment) = FIG::read_fasta_record(\*FILEHANDLE); >>
2272 :	gdpusch	1.45
2273 :	parrello	1.287	or
2274 :	gdpusch	1.45
2275 :	parrello	1.287	C<< my ($seq_id, $seq_pointer, $comment) = $fig->read_fasta_record(\*FILEHANDLE); >>
2276 :	gdpusch	1.45
2277 :	parrello	1.287	Read and parse the next logical record of a FASTA file. A FASTA logical record
2278 :			consists of multiple lines of text. The first line begins with a C<< > >> symbol
2279 :			and contains the sequence ID followed by an optional comment. (NOTE: comments
2280 :			are currently deprecated, because not all tools handle them properly.) The
2281 :			remaining lines contain the sequence data.
2282 :
2283 :			This method uses a trick to smooth its operation: the line terminator character
2284 :			is temporarily changed to C<< \n> >> so that a single read operation brings in
2285 :			the entire logical record.
2286 :	gdpusch	1.45
2287 :	parrello	1.287	=over 4
2288 :	gdpusch	1.45
2289 :	parrello	1.287	=item FILEHANDLE
2290 :	gdpusch	1.45
2291 :	parrello	1.287	Open handle of the FASTA file. If not specified, C<STDIN> is assumed.
2292 :
2293 :			=item RETURN
2294 :
2295 :			If we are at the end of the file, returns C<undef>. Otherwise, returns a
2296 :			three-element list. The first element is the sequence ID, the second is
2297 :			a pointer to the sequence data (that is, a string reference as opposed to
2298 :			as string), and the third is the comment.
2299 :
2300 :			=back
2301 :	gdpusch	1.45
2302 :			=cut
2303 :	parrello	1.213	#: Return Type @;
2304 :	parrello	1.287	sub read_fasta_record {
2305 :
2306 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
2307 :	gdpusch	1.45	my ($file_handle) = @_;
2308 :	parrello	1.287	my ($old_end_of_record, $fasta_record, @lines, $head, $sequence, $seq_id, $comment, @parsed_fasta_record);
2309 :	parrello	1.200
2310 :	gdpusch	1.45	if (not defined($file_handle)) { $file_handle = \*STDIN; }
2311 :	parrello	1.200
2312 :	gdpusch	1.45	$old_end_of_record = $/;
2313 :			$/ = "\n>";
2314 :	parrello	1.200
2315 :	parrello	1.287	if (defined($fasta_record = <$file_handle>)) {
2316 :			chomp $fasta_record;
2317 :			@lines = split( /\n/, $fasta_record );
2318 :			$head = shift @lines;
2319 :			$head =~ s/^>?//;
2320 :			$head =~ m/^(\S+)/;
2321 :			$seq_id = $1;
2322 :			if ($head =~ m/^\S+\s+(.*)$/) { $comment = $1; } else { $comment = ""; }
2323 :			$sequence = join( "", @lines );
2324 :			@parsed_fasta_record = ( $seq_id, \$sequence, $comment );
2325 :			} else {
2326 :			@parsed_fasta_record = ();
2327 :	gdpusch	1.45	}
2328 :	parrello	1.200
2329 :	gdpusch	1.45	$/ = $old_end_of_record;
2330 :	parrello	1.200
2331 :	gdpusch	1.45	return @parsed_fasta_record;
2332 :			}
2333 :
2334 :	parrello	1.287	=head3 display_id_and_seq
2335 :
2336 :			C<< FIG::display_id_and_seq($id_and_comment, $seqP, $fh); >>
2337 :
2338 :			or
2339 :
2340 :			C<< $fig->display_id_and_seq($id_and_comment, $seqP, $fh); >>
2341 :
2342 :			Display a fasta ID and sequence to the specified open file. This method is designed
2343 :			to work well with L</read_fasta_sequence> and L</rev_comp>, because it takes as
2344 :			input a string pointer rather than a string. If the file handle is omitted it
2345 :			defaults to STDOUT.
2346 :
2347 :			The output is formatted into a FASTA record. The first line of the output is
2348 :			preceded by a C<< > >> symbol, and the sequence is split into 60-character
2349 :			chunks displayed one per line. Thus, this method can be used to produce
2350 :			FASTA files from data gathered by the rest of the system.
2351 :
2352 :			=over 4
2353 :
2354 :			=item id_and_comment
2355 :
2356 :			The sequence ID and (optionally) the comment from the sequence's FASTA record.
2357 :			The ID
2358 :	gdpusch	1.45
2359 :	parrello	1.287	=item seqP
2360 :	efrank	1.1
2361 :	parrello	1.287	Reference to a string containing the sequence. The sequence is automatically
2362 :			formatted into 60-character chunks displayed one per line.
2363 :	efrank	1.1
2364 :	parrello	1.287	=item fh
2365 :	efrank	1.1
2366 :	parrello	1.287	Open file handle to which the ID and sequence should be output. If omitted,
2367 :			C<STDOUT> is assumed.
2368 :
2369 :			=back
2370 :	efrank	1.1
2371 :			=cut
2372 :
2373 :	parrello	1.287	sub display_id_and_seq {
2374 :	mkubal	1.53
2375 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
2376 :	parrello	1.287
2377 :	efrank	1.1	my( $id, $seq, $fh ) = @_;
2378 :	parrello	1.200
2379 :	efrank	1.1	if (! defined($fh) ) { $fh = \*STDOUT; }
2380 :	parrello	1.200
2381 :	efrank	1.1	print $fh ">$id\n";
2382 :			&display_seq($seq, $fh);
2383 :			}
2384 :
2385 :	parrello	1.287	=head3 display_id_and_seq
2386 :
2387 :			C<< FIG::display_seq($seqP, $fh); >>
2388 :
2389 :			or
2390 :
2391 :			C<< $fig->display_seq($seqP, $fh); >>
2392 :
2393 :			Display a fasta sequence to the specified open file. This method is designed
2394 :			to work well with L</read_fasta_sequence> and L</rev_comp>, because it takes as
2395 :			input a string pointer rather than a string. If the file handle is omitted it
2396 :			defaults to STDOUT.
2397 :
2398 :			The sequence is split into 60-character chunks displayed one per line for
2399 :			readability.
2400 :
2401 :			=over 4
2402 :
2403 :			=item seqP
2404 :
2405 :			Reference to a string containing the sequence.
2406 :
2407 :			=item fh
2408 :
2409 :			Open file handle to which the sequence should be output. If omitted,
2410 :			C<STDOUT> is assumed.
2411 :
2412 :			=back
2413 :
2414 :			=cut
2415 :
2416 :	efrank	1.1	sub display_seq {
2417 :	parrello	1.287
2418 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
2419 :	parrello	1.287
2420 :	efrank	1.1	my ( $seq, $fh ) = @_;
2421 :			my ( $i, $n, $ln );
2422 :	parrello	1.200
2423 :	efrank	1.1	if (! defined($fh) ) { $fh = \*STDOUT; }
2424 :
2425 :			$n = length($$seq);
2426 :			# confess "zero-length sequence ???" if ( (! defined($n)) \|\| ($n == 0) );
2427 :	parrello	1.287	for ($i=0; ($i < $n); $i += 60) {
2428 :			if (($i + 60) <= $n) {
2429 :			$ln = substr($$seq,$i,60);
2430 :			} else {
2431 :			$ln = substr($$seq,$i,($n-$i));
2432 :			}
2433 :			print $fh "$ln\n";
2434 :	efrank	1.1	}
2435 :			}
2436 :
2437 :			########## I commented the pods on the following routines out, since they should not
2438 :			########## be part of the SOAP/WSTL interface
2439 :			#=pod
2440 :			#
2441 :	parrello	1.287	#=head3 file2N
2442 :	efrank	1.1	#
2443 :			#usage: $n = $fig->file2N($file)
2444 :			#
2445 :			#In some of the databases I need to store filenames, which can waste a lot of
2446 :			#space. Hence, I maintain a database for converting filenames to/from integers.
2447 :			#
2448 :			#=cut
2449 :			#
2450 :	olson	1.111	sub file2N :scalar {
2451 :	efrank	1.1	my($self,$file) = @_;
2452 :			my($relational_db_response);
2453 :
2454 :			my $rdbH = $self->db_handle;
2455 :
2456 :			if (($relational_db_response = $rdbH->SQL("SELECT fileno FROM file_table WHERE ( file = \'$file\')")) &&
2457 :	parrello	1.298	(@$relational_db_response == 1)) {
2458 :	parrello	1.287	return $relational_db_response->[0]->[0];
2459 :			} elsif (($relational_db_response = $rdbH->SQL("SELECT MAX(fileno) FROM file_table ")) && (@$relational_db_response == 1) && ($relational_db_response->[0]->[0])) {
2460 :			my $fileno = $relational_db_response->[0]->[0] + 1;
2461 :			if ($rdbH->SQL("INSERT INTO file_table ( file, fileno ) VALUES ( \'$file\', $fileno )")) {
2462 :			return $fileno;
2463 :			}
2464 :			} elsif ($rdbH->SQL("INSERT INTO file_table ( file, fileno ) VALUES ( \'$file\', 1 )")) {
2465 :			return 1;
2466 :	efrank	1.1	}
2467 :			return undef;
2468 :			}
2469 :
2470 :			#=pod
2471 :			#
2472 :	parrello	1.287	#=head3 N2file
2473 :	efrank	1.1	#
2474 :			#usage: $filename = $fig->N2file($n)
2475 :			#
2476 :			#In some of the databases I need to store filenames, which can waste a lot of
2477 :			#space. Hence, I maintain a database for converting filenames to/from integers.
2478 :			#
2479 :			#=cut
2480 :			#
2481 :	olson	1.111	sub N2file :scalar {
2482 :	efrank	1.1	my($self,$fileno) = @_;
2483 :			my($relational_db_response);
2484 :
2485 :			my $rdbH = $self->db_handle;
2486 :
2487 :			if (($relational_db_response = $rdbH->SQL("SELECT file FROM file_table WHERE ( fileno = $fileno )")) &&
2488 :	parrello	1.298	(@$relational_db_response == 1)) {
2489 :	parrello	1.287	return $relational_db_response->[0]->[0];
2490 :	efrank	1.1	}
2491 :			return undef;
2492 :			}
2493 :
2494 :
2495 :			#=pod
2496 :			#
2497 :	parrello	1.287	#=head3 openF
2498 :	efrank	1.1	#
2499 :			#usage: $fig->openF($filename)
2500 :			#
2501 :			#Parts of the system rely on accessing numerous different files. The most obvious case is
2502 :			#the situation with similarities. It is important that the system be able to run in cases in
2503 :			#which an arbitrary number of files cannot be open simultaneously. This routine (with closeF) is
2504 :			#a hack to handle this. I should probably just pitch them and insist that the OS handle several
2505 :			#hundred open filehandles.
2506 :			#
2507 :			#=cut
2508 :			#
2509 :			sub openF {
2510 :			my($self,$file) = @_;
2511 :			my($fxs,$x,@fxs,$fh);
2512 :
2513 :			$fxs = $self->cached('_openF');
2514 :	parrello	1.287	if ($x = $fxs->{$file}) {
2515 :			$x->[1] = time();
2516 :			return $x->[0];
2517 :	efrank	1.1	}
2518 :	parrello	1.200
2519 :	efrank	1.1	@fxs = keys(%$fxs);
2520 :	parrello	1.287	if (defined($fh = new FileHandle "<$file")) {
2521 :			if (@fxs >= 50) {
2522 :			@fxs = sort { $fxs->{$a}->[1] <=> $fxs->{$b}->[1] } @fxs;
2523 :			$x = $fxs->{$fxs[0]};
2524 :			undef $x->[0];
2525 :			delete $fxs->{$fxs[0]};
2526 :			}
2527 :			$fxs->{$file} = [$fh,time()];
2528 :			return $fh;
2529 :	efrank	1.1	}
2530 :			return undef;
2531 :			}
2532 :
2533 :			#=pod
2534 :			#
2535 :	parrello	1.287	#=head3 closeF
2536 :	efrank	1.1	#
2537 :			#usage: $fig->closeF($filename)
2538 :			#
2539 :			#Parts of the system rely on accessing numerous different files. The most obvious case is
2540 :			#the situation with similarities. It is important that the system be able to run in cases in
2541 :			#which an arbitrary number of files cannot be open simultaneously. This routine (with openF) is
2542 :			#a hack to handle this. I should probably just pitch them and insist that the OS handle several
2543 :			#hundred open filehandles.
2544 :			#
2545 :			#=cut
2546 :			#
2547 :			sub closeF {
2548 :			my($self,$file) = @_;
2549 :			my($fxs,$x);
2550 :
2551 :	parrello	1.287	if (($fxs = $self->{_openF}) && ($x = $fxs->{$file})) {
2552 :			undef $x->[0];
2553 :			delete $fxs->{$file};
2554 :	efrank	1.1	}
2555 :			}
2556 :
2557 :	parrello	1.287	=head3 ec_name
2558 :
2559 :			C<< my $enzymatic_function = $fig->ec_name($ec); >>
2560 :	efrank	1.1
2561 :	parrello	1.287	Returns the enzymatic name corresponding to the specified enzyme code.
2562 :	efrank	1.1
2563 :	parrello	1.287	=over 4
2564 :
2565 :			=item ec
2566 :	efrank	1.1
2567 :	parrello	1.287	Code number for the enzyme whose name is desired. The code number is actually
2568 :			a string of digits and periods (e.g. C<1.2.50.6>).
2569 :
2570 :			=item RETURN
2571 :
2572 :			Returns the name of the enzyme specified by the indicated code, or a null string
2573 :			if the code is not found in the database.
2574 :
2575 :			=back
2576 :	efrank	1.1
2577 :			=cut
2578 :
2579 :			sub ec_name {
2580 :			my($self,$ec) = @_;
2581 :
2582 :			($ec =~ /^\d+\.\d+\.\d+\.\d+$/) \|\| return "";
2583 :			my $rdbH = $self->db_handle;
2584 :			my $relational_db_response = $rdbH->SQL("SELECT name FROM ec_names WHERE ( ec = \'$ec\' )");
2585 :
2586 :			return (@$relational_db_response == 1) ? $relational_db_response->[0]->[0] : "";
2587 :			return "";
2588 :			}
2589 :
2590 :	parrello	1.287	=head3 all_roles
2591 :	efrank	1.1
2592 :	parrello	1.287	C<< my @roles = $fig->all_roles; >>
2593 :	efrank	1.1
2594 :	parrello	1.287	Return a list of the known roles. Currently, this is a list of the enzyme codes and names.
2595 :	efrank	1.1
2596 :	parrello	1.287	The return value is a list of list references. Each element of the big list contains an
2597 :			enzyme code (EC) followed by the enzymatic name.
2598 :	efrank	1.1
2599 :			=cut
2600 :
2601 :			sub all_roles {
2602 :			my($self) = @_;
2603 :
2604 :			my $rdbH = $self->db_handle;
2605 :			my $relational_db_response = $rdbH->SQL("SELECT ec,name FROM ec_names");
2606 :
2607 :			return @$relational_db_response;
2608 :			}
2609 :
2610 :	parrello	1.287	=head3 expand_ec
2611 :	efrank	1.1
2612 :	parrello	1.287	C<< my $expanded_ec = $fig->expand_ec($ec); >>
2613 :	efrank	1.1
2614 :			Expands "1.1.1.1" to "1.1.1.1 - alcohol dehydrogenase" or something like that.
2615 :
2616 :			=cut
2617 :
2618 :			sub expand_ec {
2619 :			my($self,$ec) = @_;
2620 :			my($name);
2621 :
2622 :			return ($name = $self->ec_name($ec)) ? "$ec - $name" : $ec;
2623 :			}
2624 :
2625 :	parrello	1.287	=head3 clean_tmp
2626 :	efrank	1.1
2627 :	parrello	1.287	C<< FIG::clean_tmp(); >>
2628 :	efrank	1.1
2629 :	parrello	1.287	Delete temporary files more than two days old.
2630 :	efrank	1.1
2631 :			We store temporary files in $FIG_Config::temp. There are specific classes of files
2632 :			that are created and should be saved for at least a few days. This routine can be
2633 :			invoked to clean out those that are over two days old.
2634 :
2635 :			=cut
2636 :
2637 :			sub clean_tmp {
2638 :
2639 :			my($file);
2640 :	parrello	1.287	if (opendir(TMP,"$FIG_Config::temp")) {
2641 :			# change the pattern to pick up other files that need to be cleaned up
2642 :			my @temp = grep { $_ =~ /^(Geno\|tmp)/ } readdir(TMP);
2643 :			foreach $file (@temp) {
2644 :			if (-M "$FIG_Config::temp/$file" > 2) {
2645 :			unlink("$FIG_Config::temp/$file");
2646 :			}
2647 :			}
2648 :	efrank	1.1	}
2649 :			}
2650 :
2651 :			################ Routines to process genomes and genome IDs ##########################
2652 :
2653 :
2654 :	parrello	1.287	=head3 genomes
2655 :	efrank	1.1
2656 :	parrello	1.287	C<< my @genome_ids = $fig->genomes($complete, $restrictions, $domain); >>
2657 :	efrank	1.1
2658 :	parrello	1.287	Return a list of genome IDs. If called with no parameters, all genome IDs
2659 :			in the database will be returned.
2660 :	efrank	1.1
2661 :			Genomes are assigned ids of the form X.Y where X is the taxonomic id maintained by
2662 :			NCBI for the species (not the specific strain), and Y is a sequence digit assigned to
2663 :			this particular genome (as one of a set with the same genus/species). Genomes also
2664 :			have versions, but that is a separate issue.
2665 :
2666 :	parrello	1.287	=over 4
2667 :
2668 :			=item complete
2669 :
2670 :			TRUE if only complete genomes should be returned, else FALSE.
2671 :
2672 :			=item restrictions
2673 :
2674 :			TRUE if only restriction genomes should be returned, else FALSE.
2675 :
2676 :			=item domain
2677 :
2678 :			Name of the domain from which the genomes should be returned. Possible values are
2679 :			C<Bacteria>, C<Virus>, C<Eukaryota>, C<unknown>, C<Archaea>, and
2680 :			C<Environmental Sample>. If no domain is specified, all domains will be
2681 :			eligible.
2682 :
2683 :			=item RETURN
2684 :
2685 :			Returns a list of all the genome IDs with the specified characteristics.
2686 :
2687 :			=back
2688 :
2689 :	efrank	1.1	=cut
2690 :	parrello	1.320	#: Return Type @;
2691 :	olson	1.111	sub genomes :remote :list {
2692 :	golsen	1.150	my( $self, $complete, $restrictions, $domain ) = @_;
2693 :	overbeek	1.13
2694 :			my $rdbH = $self->db_handle;
2695 :
2696 :			my @where = ();
2697 :	parrello	1.287	if ($complete) {
2698 :			push(@where, "( complete = \'1\' )")
2699 :	overbeek	1.13	}
2700 :
2701 :	parrello	1.287	if ($restrictions) {
2702 :			push(@where, "( restrictions = \'1\' )")
2703 :	overbeek	1.13	}
2704 :	golsen	1.150
2705 :	parrello	1.287	if ($domain) {
2706 :			push( @where, "( maindomain = '$domain' )" )
2707 :	golsen	1.150	}
2708 :
2709 :	overbeek	1.13	my $relational_db_response;
2710 :	parrello	1.287	if (@where > 0) {
2711 :			my $where = join(" AND ",@where);
2712 :			$relational_db_response = $rdbH->SQL("SELECT genome FROM genome where $where");
2713 :			} else {
2714 :			$relational_db_response = $rdbH->SQL("SELECT genome FROM genome");
2715 :	overbeek	1.13	}
2716 :			my @genomes = sort { $a <=> $b } map { $_->[0] } @$relational_db_response;
2717 :	efrank	1.1	return @genomes;
2718 :			}
2719 :
2720 :	parrello	1.287	=head3 is_complete
2721 :
2722 :			C<< my $flag = $fig->is_complete($genome); >>
2723 :
2724 :			Return TRUE if the genome with the specified ID is complete, else FALSE.
2725 :
2726 :			=over 4
2727 :
2728 :			=item genome
2729 :
2730 :			ID of the relevant genome.
2731 :
2732 :			=item RETURN
2733 :
2734 :			Returns TRUE if there is a complete genome in the database with the specified ID,
2735 :			else FALSE.
2736 :
2737 :			=back
2738 :
2739 :			=cut
2740 :
2741 :	overbeek	1.180	sub is_complete {
2742 :			my($self,$genome) = @_;
2743 :
2744 :			my $rdbH = $self->db_handle;
2745 :			my $relational_db_response = $rdbH->SQL("SELECT genome FROM genome where (genome = '$genome') AND (complete = '1')");
2746 :			return (@$relational_db_response == 1)
2747 :	parrello	1.287	}
2748 :
2749 :			=head3 genome_counts
2750 :
2751 :			C<< my ($arch, $bact, $euk, $vir, $env, $unk) = $fig->genome_counts($complete); >>
2752 :
2753 :			Count the number of genomes in each domain. If I<$complete> is TRUE, only complete
2754 :			genomes will be included in the counts.
2755 :
2756 :			=over 4
2757 :
2758 :			=item complete
2759 :
2760 :			TRUE if only complete genomes are to be counted, FALSE if all genomes are to be
2761 :			counted
2762 :
2763 :			=item RETURN
2764 :
2765 :			A six-element list containing the number of genomes in each of six categories--
2766 :			Archaea, Bacteria, Eukaryota, Viral, Environmental, and Unknown, respectively.
2767 :
2768 :			=back
2769 :
2770 :			=cut
2771 :	golsen	1.150
2772 :	efrank	1.2	sub genome_counts {
2773 :	overbeek	1.13	my($self,$complete) = @_;
2774 :			my($x,$relational_db_response);
2775 :	efrank	1.2
2776 :	overbeek	1.13	my $rdbH = $self->db_handle;
2777 :
2778 :	parrello	1.287	if ($complete) {
2779 :			$relational_db_response = $rdbH->SQL("SELECT genome, maindomain FROM genome where complete = '1'");
2780 :			} else {
2781 :			$relational_db_response = $rdbH->SQL("SELECT genome,maindomain FROM genome");
2782 :	overbeek	1.13	}
2783 :
2784 :	gdpusch	1.107	my ($arch, $bact, $euk, $vir, $env, $unk) = (0, 0, 0, 0, 0, 0);
2785 :	parrello	1.287	if (@$relational_db_response > 0) {
2786 :			foreach $x (@$relational_db_response) {
2787 :			if ($x->[1] =~ /^archaea/i) { ++$arch }
2788 :			elsif ($x->[1] =~ /^bacter/i) { ++$bact }
2789 :			elsif ($x->[1] =~ /^eukar/i) { ++$euk }
2790 :			elsif ($x->[1] =~ /^vir/i) { ++$vir }
2791 :			elsif ($x->[1] =~ /^env/i) { ++$env }
2792 :			else { ++$unk }
2793 :	parrello	1.298	}
2794 :	efrank	1.2	}
2795 :	parrello	1.200
2796 :	gdpusch	1.107	return ($arch, $bact, $euk, $vir, $env, $unk);
2797 :			}
2798 :
2799 :
2800 :	parrello	1.287	=head3 genome_domain
2801 :
2802 :			C<< my $domain = $fig->genome_domain($genome_id); >>
2803 :
2804 :			Find the domain of a genome.
2805 :	gdpusch	1.107
2806 :	parrello	1.287	=over 4
2807 :
2808 :			=item genome_id
2809 :	gdpusch	1.107
2810 :	parrello	1.287	ID of the genome whose domain is desired.
2811 :	gdpusch	1.107
2812 :	parrello	1.287	=item RETURN
2813 :
2814 :			Returns the name of the genome's domain (archaea, bacteria, etc.), or C<undef> if
2815 :			the genome is not in the database.
2816 :	gdpusch	1.107
2817 :	parrello	1.292	=back
2818 :
2819 :	gdpusch	1.107	=cut
2820 :
2821 :			sub genome_domain {
2822 :			my($self,$genome) = @_;
2823 :			my $relational_db_response;
2824 :			my $rdbH = $self->db_handle;
2825 :	parrello	1.200
2826 :	parrello	1.287	if ($genome) {
2827 :			if (($relational_db_response = $rdbH->SQL("SELECT genome,maindomain FROM genome WHERE ( genome = \'$genome\' )"))
2828 :			&& (@$relational_db_response == 1)) {
2829 :			# die Dumper($relational_db_response);
2830 :			return $relational_db_response->[0]->[1];
2831 :			}
2832 :	gdpusch	1.107	}
2833 :			return undef;
2834 :	efrank	1.2	}
2835 :
2836 :	gdpusch	1.92
2837 :	parrello	1.287	=head3 genome_pegs
2838 :	gdpusch	1.92
2839 :	parrello	1.287	C<< my $num_pegs = $fig->genome_pegs($genome_id); >>
2840 :	gdpusch	1.92
2841 :	parrello	1.287	Return the number of protein-encoding genes (PEGs) for a specified
2842 :			genome.
2843 :	gdpusch	1.92
2844 :	parrello	1.287	=over 4
2845 :
2846 :			=item genome_id
2847 :
2848 :			ID of the genome whose PEG count is desired.
2849 :
2850 :			=item RETURN
2851 :
2852 :			Returns the number of PEGs for the specified genome, or C<undef> if the genome
2853 :			is not indexed in the database.
2854 :
2855 :			=back
2856 :	gdpusch	1.92
2857 :			=cut
2858 :
2859 :			sub genome_pegs {
2860 :			my($self,$genome) = @_;
2861 :			my $relational_db_response;
2862 :			my $rdbH = $self->db_handle;
2863 :	parrello	1.200
2864 :	parrello	1.287	if ($genome) {
2865 :			if (($relational_db_response = $rdbH->SQL("SELECT pegs FROM genome WHERE ( genome = \'$genome\' )"))
2866 :			&& (@$relational_db_response == 1)) {
2867 :			return $relational_db_response->[0]->[0];
2868 :			}
2869 :	gdpusch	1.92	}
2870 :			return undef;
2871 :			}
2872 :
2873 :
2874 :	parrello	1.287	=head3 genome_rnas
2875 :
2876 :			C<< my $num_rnas = $fig->genome_rnas($genome_id); >>
2877 :
2878 :			Return the number of RNA-encoding genes for a genome.
2879 :			"$genome_id" is indexed in the "genome" database, and 'undef' otherwise.
2880 :	efrank	1.1
2881 :	parrello	1.287	=over 4
2882 :
2883 :			=item genome_id
2884 :
2885 :			ID of the genome whose RNA count is desired.
2886 :
2887 :			=item RETURN
2888 :	gdpusch	1.92
2889 :	parrello	1.287	Returns the number of RNAs for the specified genome, or C<undef> if the genome
2890 :			is not indexed in the database.
2891 :	gdpusch	1.92
2892 :	parrello	1.287	=back
2893 :	gdpusch	1.92
2894 :			=cut
2895 :
2896 :			sub genome_rnas {
2897 :			my($self,$genome) = @_;
2898 :			my $relational_db_response;
2899 :			my $rdbH = $self->db_handle;
2900 :	parrello	1.200
2901 :	parrello	1.287	if ($genome) {
2902 :			if (($relational_db_response = $rdbH->SQL("SELECT rnas FROM genome WHERE ( genome = \'$genome\' )"))
2903 :			&& (@$relational_db_response == 1)) {
2904 :			return $relational_db_response->[0]->[0];
2905 :			}
2906 :	gdpusch	1.92	}
2907 :			return undef;
2908 :			}
2909 :
2910 :
2911 :	parrello	1.287	=head3 genome_szdna
2912 :
2913 :			usage: $szdna = $fig->genome_szdna($genome_id);
2914 :
2915 :			Return the number of DNA base-pairs in a genome's contigs.
2916 :
2917 :			=over 4
2918 :
2919 :			=item genome_id
2920 :
2921 :			ID of the genome whose base-pair count is desired.
2922 :	gdpusch	1.92
2923 :	parrello	1.287	=item RETURN
2924 :	efrank	1.1
2925 :	parrello	1.287	Returns the number of base pairs in the specified genome's contigs, or C<undef>
2926 :			if the genome is not indexed in the database.
2927 :	gdpusch	1.91
2928 :	parrello	1.287	=back
2929 :	gdpusch	1.91
2930 :			=cut
2931 :
2932 :	gdpusch	1.92	sub genome_szdna {
2933 :	gdpusch	1.91	my($self,$genome) = @_;
2934 :			my $relational_db_response;
2935 :			my $rdbH = $self->db_handle;
2936 :	parrello	1.200
2937 :	parrello	1.287	if ($genome) {
2938 :			if (($relational_db_response =
2939 :			$rdbH->SQL("SELECT szdna FROM genome WHERE ( genome = \'$genome\' )"))
2940 :			&& (@$relational_db_response == 1)) {
2941 :
2942 :			return $relational_db_response->[0]->[0];
2943 :
2944 :			}
2945 :	gdpusch	1.91	}
2946 :			return undef;
2947 :			}
2948 :
2949 :	parrello	1.287	=head3 genome_version
2950 :	gdpusch	1.91
2951 :	parrello	1.287	C<< my $version = $fig->genome_version($genome_id); >>
2952 :	gdpusch	1.91
2953 :	parrello	1.287	Return the version number of the specified genome.
2954 :	efrank	1.1
2955 :			Versions are incremented for major updates. They are put in as major
2956 :			updates of the form 1.0, 2.0, ...
2957 :
2958 :			Users may do local "editing" of the DNA for a genome, but when they do,
2959 :			they increment the digits to the right of the decimal. Two genomes remain
2960 :	parrello	1.200	comparable only if the versions match identically. Hence, minor updating should be
2961 :	efrank	1.1	committed only by the person/group responsible for updating that genome.
2962 :
2963 :			We can, of course, identify which genes are identical between any two genomes (by matching
2964 :			the DNA or amino acid sequences). However, the basic intent of the system is to
2965 :			support editing by the main group issuing periodic major updates.
2966 :
2967 :	parrello	1.287	=over 4
2968 :
2969 :			=item genome_id
2970 :
2971 :			ID of the genome whose version is desired.
2972 :
2973 :			=item RETURN
2974 :
2975 :			Returns the version number of the specified genome, or C<undef> if the genome is not in
2976 :			the data store or no version number has been assigned.
2977 :
2978 :			=back
2979 :
2980 :	efrank	1.1	=cut
2981 :
2982 :	olson	1.113	sub genome_version :scalar {
2983 :	efrank	1.1	my($self,$genome) = @_;
2984 :
2985 :			my(@tmp);
2986 :			if ((-s "$FIG_Config::organisms/$genome/VERSION") &&
2987 :	parrello	1.298	(@tmp = `cat $FIG_Config::organisms/$genome/VERSION`) &&
2988 :			($tmp[0] =~ /^(\S+)$/)) {
2989 :			return $1;
2990 :	efrank	1.1	}
2991 :			return undef;
2992 :			}
2993 :
2994 :	parrello	1.287	=head3 genome_md5sum
2995 :	olson	1.236
2996 :	parrello	1.287	C<< my $md5sum = $fig->genome_md5sum($genome_id); >>
2997 :	olson	1.236
2998 :	parrello	1.287	Returns the MD5 checksum of the specified genome.
2999 :	olson	1.236
3000 :			The checksum of a genome is defined as the checksum of its signature file. The signature
3001 :			file consists of tab-separated lines, one for each contig, ordered by the contig id.
3002 :	parrello	1.287	Each line contains the contig ID, the length of the contig in nucleotides, and the
3003 :	olson	1.236	MD5 checksum of the nucleotide data, with uppercase letters forced to lower case.
3004 :
3005 :	parrello	1.287	The checksum is indexed in the database. If you know a genome's checksum, you can use
3006 :			the L</genome_with_md5sum> method to find its ID in the database.
3007 :
3008 :			=over 4
3009 :
3010 :			=item genome
3011 :
3012 :			ID of the genome whose checksum is desired.
3013 :
3014 :			=item RETURN
3015 :
3016 :			Returns the specified genome's checksum, or C<undef> if the genome is not in the
3017 :			database.
3018 :
3019 :			=back
3020 :	olson	1.236
3021 :			=cut
3022 :
3023 :	olson	1.237	sub genome_md5sum :scalar {
3024 :	olson	1.236	my($self,$genome) = @_;
3025 :			my $relational_db_response;
3026 :			my $rdbH = $self->db_handle;
3027 :
3028 :	parrello	1.287	if ($genome) {
3029 :			if (($relational_db_response =
3030 :			$rdbH->SQL("SELECT md5sum FROM genome_md5sum WHERE ( genome = \'$genome\' )"))
3031 :			&& (@$relational_db_response == 1)) {
3032 :			return $relational_db_response->[0]->[0];
3033 :			}
3034 :	olson	1.236	}
3035 :			return undef;
3036 :			}
3037 :
3038 :	parrello	1.287	=head3 genome_with_md5sum
3039 :
3040 :			C<< my $genome = $fig->genome_with_md5sum($cksum); >>
3041 :
3042 :			Find a genome with the specified checksum.
3043 :
3044 :			The MD5 checksum is computed from the content of the genome (see L</genome_md5sum>). This method
3045 :			can be used to determine if a genome already exists for a specified content.
3046 :
3047 :			=over 4
3048 :
3049 :			=item cksum
3050 :
3051 :			Checksum to use for searching the genome table.
3052 :	olson	1.260
3053 :	parrello	1.287	=item RETURN
3054 :
3055 :			The ID of a genome with the specified checksum, or C<undef> if no such genome exists.
3056 :	olson	1.260
3057 :	parrello	1.287	=back
3058 :	olson	1.260
3059 :			=cut
3060 :
3061 :			sub genome_with_md5sum :scalar {
3062 :			my($self,$cksum) = @_;
3063 :			my $relational_db_response;
3064 :			my $rdbH = $self->db_handle;
3065 :
3066 :	parrello	1.287	if (($relational_db_response =
3067 :			$rdbH->SQL("SELECT genome FROM genome_md5sum WHERE ( md5sum = \'$cksum\' )"))
3068 :	parrello	1.298	&& (@$relational_db_response == 1)) {
3069 :			return $relational_db_response->[0]->[0];
3070 :	olson	1.260	}
3071 :
3072 :			return undef;
3073 :			}
3074 :
3075 :	parrello	1.287	=head3 contig_md5sum
3076 :
3077 :			C<< my $cksum = $fig->contig_md5sum($genome, $contig); >>
3078 :
3079 :			Return the MD5 checksum for a contig. The MD5 checksum is computed from the content
3080 :			of the contig. This method retrieves the checksum stored in the database. The checksum
3081 :			can be compared to the checksum of an external contig as a cheap way of seeing if they
3082 :			match.
3083 :
3084 :			=over 4
3085 :
3086 :			=item genome
3087 :
3088 :			ID of the genome containing the contig.
3089 :
3090 :			=item contig
3091 :
3092 :			ID of the relevant contig.
3093 :
3094 :			=item RETURN
3095 :
3096 :			Returns the checksum of the specified contig, or C<undef> if the contig is not in the
3097 :			database.
3098 :
3099 :			=back
3100 :
3101 :			=cut
3102 :
3103 :	olson	1.237	sub contig_md5sum :scalar {
3104 :			my($self, $genome, $contig) = @_;
3105 :			my $relational_db_response;
3106 :			my $rdbH = $self->db_handle;
3107 :
3108 :	parrello	1.287	if ($genome) {
3109 :			if (($relational_db_response =
3110 :			$rdbH->SQL(qq(SELECT md5 FROM contig_md5sums WHERE (genome = ? AND contig = ?)), undef, $genome, $contig))
3111 :			&& (@$relational_db_response == 1)) {
3112 :			return $relational_db_response->[0]->[0];
3113 :			}
3114 :	olson	1.237	}
3115 :			return undef;
3116 :			}
3117 :
3118 :	parrello	1.287	=head3 genus_species
3119 :
3120 :			C<< my $gs = $fig->genus_species($genome_id); >>
3121 :
3122 :			Return the genus, species, and possibly also the strain of a specified genome.
3123 :
3124 :			This method converts a genome ID into a more recognizble species name. The species name
3125 :			is stored directly in the genome table of the database. Essentially, if the strain is
3126 :			present in the database, it will be returned by this method, and if it's not present,
3127 :			it won't.
3128 :	efrank	1.1
3129 :	parrello	1.287	=over 4
3130 :
3131 :			=item genome_id
3132 :
3133 :			ID of the genome whose name is desired.
3134 :	efrank	1.1
3135 :	parrello	1.287	=item RETURN
3136 :
3137 :			Returns the scientific species name associated with the specified ID, or C<undef> if the
3138 :			ID is not in the database.
3139 :	efrank	1.1
3140 :	parrello	1.287	=back
3141 :	efrank	1.1
3142 :			=cut
3143 :	parrello	1.320	#: Return Type $;
3144 :	olson	1.111	sub genus_species :scalar {
3145 :	efrank	1.1	my ($self,$genome) = @_;
3146 :	overbeek	1.13	my $ans;
3147 :	efrank	1.1
3148 :			my $genus_species = $self->cached('_genus_species');
3149 :	parrello	1.287	if (! ($ans = $genus_species->{$genome})) {
3150 :			my $rdbH = $self->db_handle;
3151 :			my $relational_db_response = $rdbH->SQL("SELECT genome,gname FROM genome");
3152 :			my $pair;
3153 :			foreach $pair (@$relational_db_response) {
3154 :			$genus_species->{$pair->[0]} = $pair->[1];
3155 :			}
3156 :			$ans = $genus_species->{$genome};
3157 :	efrank	1.1	}
3158 :			return $ans;
3159 :			}
3160 :
3161 :	parrello	1.287	=head3 org_of
3162 :
3163 :			C<< my $org = $fig->org_of($prot_id); >>
3164 :
3165 :			Return the genus/species name of the organism containing a protein. Note that in this context
3166 :			I<protein> is not a certain string of amino acids but a protein encoding region on a specific
3167 :			contig.
3168 :
3169 :			For a FIG protein ID (e.g. C<fig\|134537.1.peg.123>), the organism and strain
3170 :			information is always available. In the case of external proteins, we can usually
3171 :			determine an organism, but not anything more precise than genus/species (and
3172 :			often not that). When the organism name is not present, a null string is returned.
3173 :
3174 :			=over 4
3175 :
3176 :			=item prot_id
3177 :	efrank	1.1
3178 :	parrello	1.287	Protein or feature ID.
3179 :	efrank	1.1
3180 :	parrello	1.287	=item RETURN
3181 :
3182 :			Returns the displayable scientific name (genus, species, and strain) of the organism containing
3183 :			the identified PEG. If the name is not available, returns a null string. If the PEG is not found,
3184 :			returns C<undef>.
3185 :	efrank	1.1
3186 :	parrello	1.287	=back
3187 :	efrank	1.1
3188 :			=cut
3189 :
3190 :			sub org_of {
3191 :			my($self,$prot_id) = @_;
3192 :			my $relational_db_response;
3193 :			my $rdbH = $self->db_handle;
3194 :
3195 :	parrello	1.287	if ($prot_id =~ /^fig\\|/) {
3196 :			return $self->is_deleted_fid( $prot_id) ? undef
3197 :			: $self->genus_species( $self->genome_of( $prot_id ) ) \|\| "";
3198 :	efrank	1.1	}
3199 :
3200 :	parrello	1.287	if (($relational_db_response =
3201 :			$rdbH->SQL("SELECT org FROM external_orgs WHERE ( prot = \'$prot_id\' )")) &&
3202 :			(@$relational_db_response >= 1)) {
3203 :			$relational_db_response->[0]->[0] =~ s/^\d+://;
3204 :			return $relational_db_response->[0]->[0];
3205 :	efrank	1.1	}
3206 :			return "";
3207 :			}
3208 :
3209 :	parrello	1.287	=head3 genus_species_domain
3210 :
3211 :			C<< my ($gs, $domain) = $fig->genus_species_domain($genome_id); >>
3212 :
3213 :			Returns a genome's genus and species (and strain if that has been properly
3214 :			recorded) in a printable form, along with its domain. This method is similar
3215 :			to L</genus_species>, except it also returns the domain name (archaea,
3216 :			bacteria, etc.).
3217 :
3218 :			=over 4
3219 :
3220 :			=item genome_id
3221 :
3222 :			ID of the genome whose species and domain information is desired.
3223 :	golsen	1.130
3224 :	parrello	1.287	=item RETURN
3225 :	golsen	1.130
3226 :	parrello	1.287	Returns a two-element list. The first element is the species name and the
3227 :			second is the domain name.
3228 :	golsen	1.130
3229 :	parrello	1.287	=back
3230 :	golsen	1.130
3231 :			=cut
3232 :
3233 :			sub genus_species_domain {
3234 :			my ($self, $genome) = @_;
3235 :
3236 :			my $genus_species_domain = $self->cached('_genus_species_domain');
3237 :	parrello	1.287	if ( ! $genus_species_domain->{ $genome } ) {
3238 :			my $rdbH = $self->db_handle;
3239 :			my $relational_db_response = $rdbH->SQL("SELECT genome,gname,maindomain FROM genome");
3240 :			my $triple;
3241 :			foreach $triple ( @$relational_db_response ) {
3242 :			$genus_species_domain->{ $triple->[0] } = [ $triple->[1], $triple->[2] ];
3243 :			}
3244 :	golsen	1.130	}
3245 :			my $gsdref = $genus_species_domain->{ $genome };
3246 :			return $gsdref ? @$gsdref : ( "", "" );
3247 :			}
3248 :
3249 :	parrello	1.287	=head3 domain_color
3250 :
3251 :			C<< my $web_color = FIG::domain_color($domain); >>
3252 :
3253 :			Return the web color string associated with a specified domain. The colors are
3254 :			extremely subtle (86% luminance), so they absolutely require a black background.
3255 :			Archaea are slightly cyan, bacteria are slightly magenta, eukaryota are slightly
3256 :			yellow, viruses are slightly silver, environmental samples are slightly gray,
3257 :			and unknown or invalid domains are pure white.
3258 :
3259 :			=over 4
3260 :
3261 :			=item domain
3262 :
3263 :			Name of the domain whose color is desired.
3264 :
3265 :			=item RETURN
3266 :
3267 :			Returns a web color string for the specified domain (e.g. C<#FFDDFF> for
3268 :			bacteria).
3269 :
3270 :			=back
3271 :
3272 :			=cut
3273 :	golsen	1.130
3274 :			my %domain_color = ( AR => "#DDFFFF", BA => "#FFDDFF", EU => "#FFFFDD",
3275 :			VI => "#DDDDDD", EN => "#BBBBBB" );
3276 :
3277 :			sub domain_color {
3278 :			my ($domain) = @_;
3279 :			defined $domain \|\| return "#FFFFFF";
3280 :			return $domain_color{ uc substr($domain, 0, 2) } \|\| "#FFFFFF";
3281 :			}
3282 :
3283 :	parrello	1.287	=head3 org_and_color_of
3284 :	golsen	1.130
3285 :	parrello	1.287	C<< my ($org, $color) = $fig->org_and_domain_of($prot_id); >>
3286 :	golsen	1.130
3287 :	parrello	1.287	Return the best guess organism and domain html color string of an organism.
3288 :			In the case of external proteins, we can usually determine an organism, but not
3289 :			anything more precise than genus/species (and often not that).
3290 :
3291 :			=over 4
3292 :
3293 :			=item prot_id
3294 :
3295 :			Relevant protein or feature ID.
3296 :
3297 :			=item RETURN
3298 :	golsen	1.130
3299 :	parrello	1.287	Returns a two-element list. The first element is the displayable organism name, and the second
3300 :			is an HTML color string based on the domain (see L</domain_color>).
3301 :	golsen	1.130
3302 :	parrello	1.287	=back
3303 :	golsen	1.130
3304 :			=cut
3305 :
3306 :			sub org_and_color_of {
3307 :			my($self,$prot_id) = @_;
3308 :			my $relational_db_response;
3309 :			my $rdbH = $self->db_handle;
3310 :
3311 :	parrello	1.287	if ($prot_id =~ /^fig\\|/) {
3312 :			my( $gs, $domain ) = $self->genus_species_domain($self->genome_of($prot_id));
3313 :			return ( $gs, domain_color( $domain ) );
3314 :	golsen	1.130	}
3315 :
3316 :	parrello	1.287	if (($relational_db_response =
3317 :			$rdbH->SQL("SELECT org FROM external_orgs WHERE ( prot = \'$prot_id\' )")) &&
3318 :			(@$relational_db_response >= 1)) {
3319 :			return ($relational_db_response->[0]->[0], "#FFFFFF");
3320 :	golsen	1.130	}
3321 :			return ("", "#FFFFFF");
3322 :			}
3323 :
3324 :	redwards	1.310	=head3 partial_genus_matching
3325 :
3326 :			Return a list of genome IDs that match a partial genus.
3327 :
3328 :	redwards	1.311	For example partial_genus_matching("Listeria") will return all genome IDs that begin with Listeria, and this can also be restricted to complete genomes with another argument like this partial_genus_matching("Listeria", 1)
3329 :	redwards	1.310
3330 :			=cut
3331 :
3332 :			sub partial_genus_matching {
3333 :	redwards	1.311	my ($self, $gen, $complete)=@_;
3334 :			return grep {$self->genus_species($_) =~ /$gen/i} $self->genomes($complete);
3335 :	redwards	1.310	}
3336 :
3337 :
3338 :	parrello	1.287	=head3 abbrev
3339 :
3340 :			C<< my $abbreviated_name = FIG::abbrev($genome_name); >>
3341 :	golsen	1.130
3342 :	parrello	1.287	or
3343 :	efrank	1.1
3344 :	parrello	1.287	C<< my $abbreviated_name = $fig->abbrev($genome_name); >>
3345 :	efrank	1.1
3346 :	parrello	1.287	Abbreviate a genome name to 10 characters or less.
3347 :	efrank	1.1
3348 :			For alignments and such, it is very useful to be able to produce an abbreviation of genus/species.
3349 :			That's what this does. Note that multiple genus/species might reduce to the same abbreviation, so
3350 :			be careful (disambiguate them, if you must).
3351 :
3352 :	parrello	1.287	The abbreviation is formed from the first three letters of the species name followed by the
3353 :			first three letters of the genus name followed by the first three letters of the species name and
3354 :			then the next four nonblank characters.
3355 :
3356 :			=over 4
3357 :
3358 :			=item genome_name
3359 :
3360 :			The name to abbreviate.
3361 :
3362 :			=item RETURN
3363 :
3364 :			An abbreviated version of the specified name.
3365 :
3366 :			=back
3367 :
3368 :	efrank	1.1	=cut
3369 :
3370 :	olson	1.111	sub abbrev :scalar {
3371 :			shift if UNIVERSAL::isa($_[0],__PACKAGE__);
3372 :	efrank	1.1	my($genome_name) = @_;
3373 :
3374 :			$genome_name =~ s/^(\S{3})\S+/$1./;
3375 :	overbeek	1.198	$genome_name =~ s/^(\S+)\s+(\S{3})\S+/$1$2./;
3376 :	overbeek	1.257	$genome_name =~ s/ //g;
3377 :	parrello	1.287	if (length($genome_name) > 10) {
3378 :	parrello	1.298	$genome_name = substr($genome_name,0,10);
3379 :	efrank	1.1	}
3380 :			return $genome_name;
3381 :			}
3382 :
3383 :			################ Routines to process Features and Feature IDs ##########################
3384 :
3385 :	parrello	1.287	=head3 ftype
3386 :
3387 :			C<< my $type = FIG::ftype($fid); >>
3388 :	efrank	1.1
3389 :	parrello	1.287	or
3390 :	efrank	1.1
3391 :	parrello	1.287	C<< my $type = $fig->ftype($fid); >>
3392 :	efrank	1.1
3393 :			Returns the type of a feature, given the feature ID. This just amounts
3394 :	parrello	1.287	to lifting it out of the feature ID, since features have IDs of the form
3395 :	efrank	1.1
3396 :	parrello	1.287	fig\|x.y.f.n
3397 :	efrank	1.1
3398 :			where
3399 :			x.y is the genome ID
3400 :	parrello	1.287	f is the type of feature
3401 :	efrank	1.1	n is an integer that is unique within the genome/type
3402 :
3403 :	parrello	1.287	=over 4
3404 :
3405 :			=item fid
3406 :
3407 :			FIG ID of the feature whose type is desired.
3408 :
3409 :			=item RETURN
3410 :
3411 :			Returns the feature type (e.g. C<peg>, C<rna>, C<pi>, or C<pp>), or C<undef> if the
3412 :			feature ID is not a FIG ID.
3413 :
3414 :			=back
3415 :
3416 :	efrank	1.1	=cut
3417 :
3418 :			sub ftype {
3419 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
3420 :	efrank	1.1	my($feature_id) = @_;
3421 :
3422 :	parrello	1.287	if ($feature_id =~ /^fig\\|\d+\.\d+\.([^\.]+)/) {
3423 :			return $1;
3424 :	efrank	1.1	}
3425 :			return undef;
3426 :			}
3427 :
3428 :	parrello	1.287	=head3 genome_of
3429 :
3430 :			C<< my $genome_id = $fig->genome_of($fid); >>
3431 :
3432 :			or
3433 :
3434 :			C<< my $genome_id = FIG::genome_of($fid); >>
3435 :
3436 :			Return the genome ID from a feature ID.
3437 :	efrank	1.1
3438 :	parrello	1.287	=over 4
3439 :
3440 :			=item fid
3441 :
3442 :			ID of the feature whose genome ID is desired.
3443 :
3444 :			=item RETURN
3445 :	efrank	1.1
3446 :	parrello	1.287	If the feature ID is a FIG ID, returns the genome ID embedded inside it; otherwise, it
3447 :			returns C<undef>.
3448 :	efrank	1.1
3449 :	parrello	1.287	=back
3450 :	efrank	1.1
3451 :			=cut
3452 :
3453 :
3454 :	olson	1.113	sub genome_of :scalar {
3455 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
3456 :	parrello	1.200	my $prot_id = (@_ == 1) ? $_[0] : $_[1];
3457 :	efrank	1.1
3458 :			if ($prot_id =~ /^fig\\|(\d+\.\d+)/) { return $1; }
3459 :			return undef;
3460 :			}
3461 :
3462 :	parrello	1.287	=head3 genome_and_peg_of
3463 :
3464 :			C<< my ($genome_id, $peg_number = FIG::genome_and_peg_of($fid); >>
3465 :
3466 :			C<< my ($genome_id, $peg_number = $fig->genome_and_peg_of($fid); >>
3467 :	olson	1.96
3468 :	parrello	1.287	Return the genome ID and peg number from a feature ID.
3469 :	olson	1.96
3470 :	parrello	1.287	=over 4
3471 :
3472 :			=item prot_id
3473 :
3474 :			ID of the feature whose genome and PEG number as desired.
3475 :
3476 :			=item RETURN
3477 :
3478 :			Returns the genome ID and peg number associated with a feature if the feature
3479 :			is represented by a FIG ID, else C<undef>.
3480 :
3481 :			=back
3482 :	olson	1.96
3483 :			=cut
3484 :
3485 :			sub genome_and_peg_of {
3486 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
3487 :	parrello	1.200	my $prot_id = (@_ == 1) ? $_[0] : $_[1];
3488 :	olson	1.96
3489 :	parrello	1.287	if ($prot_id =~ /^fig\\|(\d+\.\d+)\.peg\.(\d+)/) {
3490 :	parrello	1.298	return ($1, $2);
3491 :	olson	1.96	}
3492 :			return undef;
3493 :			}
3494 :
3495 :	parrello	1.287	=head3 by_fig_id
3496 :
3497 :			C<< my @sorted_by_fig_id = sort { FIG::by_fig_id($a,$b) } @fig_ids; >>
3498 :
3499 :			Compare two feature IDs.
3500 :
3501 :			This function is designed to assist in sorting features by ID. The sort is by
3502 :			genome ID followed by feature type and then feature number.
3503 :
3504 :			=over 4
3505 :
3506 :			=item a
3507 :	efrank	1.1
3508 :	parrello	1.287	First feature ID.
3509 :	efrank	1.1
3510 :	parrello	1.287	=item b
3511 :	efrank	1.1
3512 :	parrello	1.287	Second feature ID.
3513 :
3514 :			=item RETURN
3515 :
3516 :			Returns a negative number if the first parameter is smaller, zero if both parameters
3517 :			are equal, and a positive number if the first parameter is greater.
3518 :
3519 :			=back
3520 :	efrank	1.1
3521 :			=cut
3522 :
3523 :			sub by_fig_id {
3524 :			my($a,$b) = @_;
3525 :			my($g1,$g2,$t1,$t2,$n1,$n2);
3526 :			if (($a =~ /^fig\\|(\d+\.\d+).([^\.]+)\.(\d+)$/) && (($g1,$t1,$n1) = ($1,$2,$3)) &&
3527 :	parrello	1.298	($b =~ /^fig\\|(\d+\.\d+).([^\.]+)\.(\d+)$/) && (($g2,$t2,$n2) = ($1,$2,$3))) {
3528 :			($g1 <=> $g2) or ($t1 cmp $t2) or ($n1 <=> $n2);
3529 :	parrello	1.287	} else {
3530 :	parrello	1.298	$a cmp $b;
3531 :	efrank	1.1	}
3532 :			}
3533 :
3534 :	parrello	1.287	=head3 genes_in_region
3535 :	efrank	1.1
3536 :	parrello	1.287	C<< my ($features_in_region, $beg1, $end1) = $fig->genes_in_region($genome, $contig, $beg, $end, size_limit); >>
3537 :	efrank	1.1
3538 :	parrello	1.287	Locate features that overlap a specified region of a contig. This includes features that begin or end
3539 :			outside that region, just so long as some part of the feature can be found in the region of interest.
3540 :	efrank	1.1
3541 :			It is often important to be able to find the genes that occur in a specific region on
3542 :			a chromosome. This routine is designed to provide this information. It returns all genes
3543 :	parrello	1.287	that overlap positions from I<$beg> through I<$end> in the specified contig.
3544 :
3545 :			The I<$size_limit> parameter limits the search process. It is presumed that no features are longer than the
3546 :			specified size limit. A shorter size limit means you'll miss some features; a longer size limit significantly
3547 :			slows the search process. For prokaryotes, a value of C<10000> (the default) seems to work best.
3548 :
3549 :			=over 4
3550 :
3551 :			=item genome
3552 :
3553 :			ID of the genome containing the relevant contig.
3554 :
3555 :			=item contig
3556 :
3557 :			ID of the relevant contig.
3558 :
3559 :			=item beg
3560 :
3561 :			Position of the first base pair in the region of interest.
3562 :
3563 :			=item end
3564 :
3565 :			Position of the last base pair in the region of interest.
3566 :
3567 :			=item size_limit
3568 :
3569 :			Maximum allowable size for a feature. If omitted, C<10000> is assumed.
3570 :
3571 :			=item RETURN
3572 :	efrank	1.1
3573 :	parrello	1.287	Returns a three-element list. The first element is a reference to a list of the feature IDs found. The second
3574 :			element is the position of the leftmost base pair in any feature found. This may be well before the region of
3575 :			interest begins or it could be somewhere inside. The third element is the position of the rightmost base pair
3576 :			in any feature found. Again, this can be somewhere inside the region or it could be well to the right of it.
3577 :
3578 :			=back
3579 :	efrank	1.1
3580 :			=cut
3581 :	parrello	1.213	#: Return Type @;
3582 :	efrank	1.1	sub genes_in_region {
3583 :	parrello	1.287	my($self, $genome, $contig, $beg, $end, $pad) = @_;
3584 :			if (!defined $pad) { $pad = 10000; }
3585 :	efrank	1.1	my($x,$relational_db_response,$feature_id,$b1,$e1,@feat,@tmp,$l,$u);
3586 :
3587 :			my $rdbH = $self->db_handle;
3588 :
3589 :	parrello	1.200	my $minV = $beg - $pad;
3590 :	efrank	1.1	my $maxV = $end + $pad;
3591 :	parrello	1.287	if (($relational_db_response = $rdbH->SQL("SELECT id FROM features "
3592 :			. " WHERE ( minloc > $minV ) AND ( minloc < $maxV ) AND ( maxloc < $maxV) AND "
3593 :			. " ( genome = \'$genome\' ) AND ( contig = \'$contig\' );")) &&
3594 :			(@$relational_db_response >= 1)) {
3595 :			@tmp = sort { ($a->[1] cmp $b->[1]) or (($a->[2]+$a->[3]) <=> ($b->[2]+$b->[3])) }
3596 :			map { $feature_id = $_->[0]; $x = $self->feature_location($feature_id); $x ? [$feature_id,&boundaries_of($x)] : ()
3597 :			} @$relational_db_response;
3598 :	efrank	1.1
3599 :
3600 :	parrello	1.287	($l,$u) = (10000000000,0);
3601 :			foreach $x (@tmp)
3602 :			{
3603 :			($feature_id,undef,$b1,$e1) = @$x;
3604 :			if (&between($beg,&min($b1,$e1),$end) \|\| &between(&min($b1,$e1),$beg,&max($b1,$e1)))
3605 :			{
3606 :			if (! $self->is_deleted_fid($feature_id))
3607 :			{
3608 :			push(@feat,$feature_id);
3609 :			$l = &min($l,&min($b1,$e1));
3610 :			$u = &max($u,&max($b1,$e1));
3611 :			}
3612 :			}
3613 :			}
3614 :			(@feat <= 0) \|\| return ([@feat],$l,$u);
3615 :	efrank	1.1	}
3616 :			return ([],$l,$u);
3617 :			}
3618 :
3619 :	golsen	1.141
3620 :			#=============================================================================
3621 :			# Using the following version is better, but it brings out a very annoying
3622 :			# issue with some genomes. It already exists in the current code (above)
3623 :			# for some genes in some genomes. For example, visit fig\|70601.1.peg.1.
3624 :			# This is true for any genome that has a feature that crosses the origin.
3625 :			# The root of the problem lies in boundaries_of. I am working on a fix that
3626 :			# replaces boundaries_of with a more sophisticated function. When it is
3627 :			# all done, genes_in_retion should behave as desired. -- GJO, Aug. 22, 2004
3628 :			#=============================================================================
3629 :	parrello	1.200	#
3630 :	golsen	1.141	# =pod
3631 :	parrello	1.200	#
3632 :	parrello	1.287	# =head3 genes_in_region
3633 :	parrello	1.200	#
3634 :	golsen	1.141	# usage: ( $features_in_region, $min_coord, $max_coord )
3635 :			# = $fig->genes_in_region( $genome, $contig, $beg, $end )
3636 :	parrello	1.200	#
3637 :	golsen	1.141	# It is often important to be able to find the genes that occur in a specific
3638 :			# region on a chromosome. This routine is designed to provide this information.
3639 :			# It returns all genes that overlap the region ( $genome, $contig, $beg, $end ).
3640 :			# $min_coord is set to the minimum coordinate of the returned genes (which may
3641 :			# preceed the given region), and $max_coord the maximum coordinate. Because
3642 :			# the database is indexed by the leftmost and rightmost coordinates of each
3643 :			# feature, the function makes no assumption about the length of the feature, but
3644 :			# it can (and probably will) miss features spanning multiple contigs.
3645 :	parrello	1.200	#
3646 :	golsen	1.141	# =cut
3647 :	parrello	1.200	#
3648 :			#
3649 :	golsen	1.141	# sub genes_in_region {
3650 :			# my ( $self, $genome, $contig, $beg, $end ) = @_;
3651 :			# my ( $x, $db_response, $feature_id, $b1, $e1, @tmp, @bounds );
3652 :			# my ( $min_coord, $max_coord );
3653 :	parrello	1.200	#
3654 :	golsen	1.141	# my @features = ();
3655 :			# my $rdbH = $self->db_handle;
3656 :	parrello	1.200	#
3657 :	golsen	1.141	# if ( ( $db_response = $rdbH->SQL( "SELECT id
3658 :			# FROM features
3659 :			# WHERE ( contig = '$contig' )
3660 :			# AND ( genome = '$genome' )
3661 :	parrello	1.200	# AND ( minloc <= $end )
3662 :	golsen	1.141	# AND ( maxloc >= $beg );"
3663 :			# )
3664 :			# )
3665 :			# && ( @$db_response > 0 )
3666 :			# )
3667 :			# {
3668 :			# # The sort is unnecessary, but provides a consistent ordering
3669 :	parrello	1.200	#
3670 :	golsen	1.141	# @tmp = sort { ( $a->[1] cmp $b->[1] ) # contig
3671 :			# \|\| ( ($a->[2] + $a->[3] ) <=> ( $b->[2] + $b->[3] ) ) # midpoint
3672 :			# }
3673 :			# map { $feature_id = $_->[0];
3674 :			# ( ( ! $self->is_deleted_fid( $feature_id ) ) # not deleted
3675 :			# && ( $x = $self->feature_location( $feature_id ) ) # and has location
3676 :			# && ( ( @bounds = boundaries_of( $x ) ) == 3 ) # and has bounds
3677 :	parrello	1.200	# ) ? [ $feature_id, @bounds ] : ()
3678 :	golsen	1.141	# } @$db_response;
3679 :	parrello	1.200	#
3680 :	golsen	1.141	# ( $min_coord, $max_coord ) = ( 10000000000, 0 );
3681 :	parrello	1.200	#
3682 :	golsen	1.141	# foreach $x ( @tmp )
3683 :			# {
3684 :			# ( $feature_id, undef, $b1, $e1 ) = @$x;
3685 :			# push @features, $feature_id;
3686 :			# my ( $min, $max ) = ( $b1 <= $e1 ) ? ( $b1, $e1 ) : ( $e1, $b1 );
3687 :			# ( $min_coord <= $min ) \|\| ( $min_coord = $min );
3688 :			# ( $max_coord >= $max ) \|\| ( $max_coord = $max );
3689 :			# }
3690 :			# }
3691 :	parrello	1.200	#
3692 :	golsen	1.141	# return ( @features ) ? ( [ @features ], $min_coord, $max_coord )
3693 :			# : ( [], undef, undef );
3694 :			# }
3695 :
3696 :			# These will be part of the fix to genes_in_region. -- GJO
3697 :
3698 :	parrello	1.287	=head3 regions_spanned
3699 :
3700 :			C<< my ( [ $contig, $beg, $end ], ... ) = $fig->regions_spanned( $loc ); >>
3701 :	golsen	1.141
3702 :	parrello	1.287	or
3703 :	golsen	1.141
3704 :	parrello	1.287	C<< my ( [ $contig, $beg, $end ], ... ) = FIG::regions_spanned( $loc ); >>
3705 :	golsen	1.141
3706 :			The location of a feature in a scalar context is
3707 :
3708 :	parrello	1.287	contig_b1_e1, contig_b2_e2, ... [one contig_b_e for each segment]
3709 :
3710 :			This routine takes as input a scalar location in the above form
3711 :			and reduces it to one or more regions spanned by the gene. This
3712 :			involves combining regions in the location string that are on the
3713 :			same contig and going in the same direction. Unlike L</boundaries_of>,
3714 :			which returns one region in which the entire gene can be found,
3715 :			B<regions_spanned> handles wrapping through the orgin, features
3716 :			split over contigs and exons that are not ordered nicely along
3717 :			the chromosome (ugly but true).
3718 :	golsen	1.141
3719 :	parrello	1.287	=over 4
3720 :
3721 :			=item loc
3722 :
3723 :			The location string for a feature.
3724 :
3725 :			=item RETURN
3726 :
3727 :			Returns a list of list references. Each inner list contains a contig ID, a starting
3728 :			position, and an ending position. The starting position may be numerically greater
3729 :			than the ending position (which indicates a backward-traveling gene). It is
3730 :			guaranteed that the entire feature is covered by the regions in the list.
3731 :
3732 :			=back
3733 :	golsen	1.141
3734 :			=cut
3735 :
3736 :			sub regions_spanned {
3737 :			shift if UNIVERSAL::isa( $_[0], __PACKAGE__ );
3738 :			my( $location ) = ( @_ == 1 ) ? $_[0] : $_[1];
3739 :			defined( $location ) \|\| return undef;
3740 :
3741 :			my @regions = ();
3742 :
3743 :			my ( $cur_contig, $cur_beg, $cur_end, $cur_dir );
3744 :			my ( $contig, $beg, $end, $dir );
3745 :			my @segs = split( /\s,\s/, $location ); # should not have space, but ...
3746 :			@segs \|\| return undef;
3747 :
3748 :			# Process the first segment
3749 :
3750 :			my $seg = shift @segs;
3751 :			( ( $cur_contig, $cur_beg, $cur_end ) = ( $seg =~ /^(\S+)_(\d+)_\d+$/ ) )
3752 :			\|\| return undef;
3753 :			$cur_dir = ( $cur_end >= $cur_beg ) ? 1 : -1;
3754 :
3755 :			foreach $seg ( @segs ) {
3756 :	parrello	1.298	( ( $contig, $beg, $end ) = ( $seg =~ /^(\S+)_(\d+)_\d+$/ ) ) \|\| next;
3757 :			$dir = ( $end >= $beg ) ? 1 : -1;
3758 :	golsen	1.141
3759 :	parrello	1.298	# Is this a continuation? Update end
3760 :	golsen	1.141
3761 :	parrello	1.298	if ( ( $contig eq $cur_contig )
3762 :			&& ( $dir == $cur_dir )
3763 :			&& ( ( ( $dir > 0 ) && ( $end > $cur_end ) )
3764 :			\|\| ( ( $dir < 0 ) && ( $end < $cur_end ) ) )
3765 :			)
3766 :			{
3767 :			$cur_end = $end;
3768 :			}
3769 :	golsen	1.141
3770 :	parrello	1.298	# Not a continuation. Report previous and update current.
3771 :	golsen	1.141
3772 :	parrello	1.298	else
3773 :			{
3774 :			push @regions, [ $cur_contig, $cur_beg, $cur_end ];
3775 :			( $cur_contig, $cur_beg, $cur_end, $cur_dir )
3776 :			= ( $contig, $beg, $end, $dir );
3777 :			}
3778 :	golsen	1.141	}
3779 :
3780 :			# There should alwasy be a valid, unreported region.
3781 :
3782 :			push @regions, [ $cur_contig, $cur_beg, $cur_end ];
3783 :
3784 :			return wantarray ? @regions : \@regions;
3785 :			}
3786 :
3787 :	parrello	1.287	=head3 filter_regions
3788 :
3789 :			C<< my @regions = FIG::filter_regions( $contig, $min, $max, @regions ); >>
3790 :
3791 :			or
3792 :
3793 :			C<< my \@regions = FIG::filter_regions( $contig, $min, $max, @regions ); >>
3794 :
3795 :			or
3796 :
3797 :			C<< my @regions = FIG::filter_regions( $contig, $min, $max, \@regions ); >>
3798 :
3799 :			or
3800 :
3801 :			C<< my \@regions = FIG::filter_regions( $contig, $min, $max, \@regions ); >>
3802 :
3803 :			Filter a list of regions to those that overlap a specified section of a
3804 :			particular contig. Region definitions correspond to those produced
3805 :			by L</regions_spanned>. That is, C<[>I<contig>C<,>I<beg>C<,>I<end>C<]>.
3806 :			In the function call, either I<$contig> or I<$min> and I<$max> can be
3807 :			undefined (permitting anything). So, for example,
3808 :
3809 :			my @regions = FIG::filter_regions(undef, 1, 5000, $regionList);
3810 :
3811 :			would return all regions in C<$regionList> that overlap the first
3812 :			5000 base pairs in any contig. Conversely,
3813 :
3814 :			my @regions = FIG::filter_regions('NC_003904', undef, undef, $regionList);
3815 :	golsen	1.141
3816 :	parrello	1.287	would return all regions on the contig C<NC_003904>.
3817 :	golsen	1.141
3818 :	parrello	1.287	=over 4
3819 :
3820 :			=item contig
3821 :
3822 :			ID of the contig whose regions are to be passed by the filter, or C<undef>
3823 :			if the contig doesn't matter.
3824 :
3825 :			=item min
3826 :
3827 :			Leftmost position of the region used for filtering. Only regions which contain
3828 :			at least one base pair at or beyond this position will be passed. A value
3829 :			of C<undef> is equivalent to zero.
3830 :
3831 :			=item max
3832 :
3833 :			Rightmost position of the region used for filtering. Only regions which contain
3834 :			at least one base pair on or before this position will be passed. A value
3835 :			of C<undef> is equivalent to the length of the contig.
3836 :
3837 :			=item regionList
3838 :	golsen	1.141
3839 :	parrello	1.287	A list of regions, or a reference to a list of regions. Each region is a
3840 :			reference to a three-element list, the first element of which is a contig
3841 :			ID, the second element of which is the start position, and the third
3842 :			element of which is the ending position. (The ending position can be
3843 :			before the starting position if the region is backward-traveling.)
3844 :
3845 :			=item RETURN
3846 :
3847 :			In a scalar context, returns a reference to a list of the filtered regions.
3848 :			In a list context, returns the list itself.
3849 :
3850 :			=back
3851 :	golsen	1.141
3852 :			=cut
3853 :
3854 :			sub filter_regions {
3855 :			my ( $contig, $min, $max, @regions ) = @_;
3856 :
3857 :			@regions \|\| return ();
3858 :			( ref( $regions[0] ) eq "ARRAY" ) \|\| return undef;
3859 :
3860 :			# Is it a region list, or a reference to a region list?
3861 :
3862 :			if ( ref( $regions[0]->[0] ) eq "ARRAY" ) { @regions = @{ $regions[0] } }
3863 :
3864 :			if ( ! defined( $contig ) )
3865 :			{
3866 :			( defined( $min ) && defined( $max ) ) \|\| return undef;
3867 :			}
3868 :			else # with a defined contig name, allow undefined range
3869 :			{
3870 :			defined( $min ) \|\| ( $min = 1 );
3871 :			defined( $max ) \|\| ( $max = 1000000000 );
3872 :			}
3873 :			( $min <= $max ) \|\| return ();
3874 :
3875 :			my ( $c, $b, $e );
3876 :			my @filtered = grep { ( @$_ >= 3 ) # Allow extra fields?
3877 :			&& ( ( $c, $b, $e ) = @$_ )
3878 :			&& ( ( ! defined( $contig ) ) \|\| ( $c eq $contig ) )
3879 :			&& ( ( $e >= $b ) \|\| ( ( $b, $e ) = ( $e, $b ) ) )
3880 :			&& ( ( $b <= $max ) && ( $e >= $min ) )
3881 :			} @regions;
3882 :
3883 :			return wantarray ? @filtered : \@filtered;
3884 :			}
3885 :
3886 :	parrello	1.287	=head3 close_genes
3887 :
3888 :			C<< my @features = $fig->close_genes($fid, $dist); >>
3889 :
3890 :			Return all features within a certain distance of a specified other feature.
3891 :
3892 :			This method is a quick way to get genes that are near another gene. It calls
3893 :			L</boundaries_of> to get the boundaries of the incoming gene, then passes
3894 :			the region computed to L</genes_in_region>.
3895 :
3896 :			So, for example, if the specified I<$dist> is 500, the method would select
3897 :			a region that extends 500 base pairs to either side of the boundaries for
3898 :			the gene I<$fid>, and pass it to C<genes_in_region> for analysis. The
3899 :			features returned would be those that overlap the selected region. Note
3900 :			that the flaws inherent in C<genes_in_region> are also inherent in this
3901 :			method: if a feature is more than 10000 base pairs long, it may not
3902 :			be caught even though it has an overlap in the specified region.
3903 :
3904 :			=over 4
3905 :
3906 :			=item fid
3907 :
3908 :			ID of the relevant feature.
3909 :
3910 :			=item dist
3911 :
3912 :			Desired maximum distance.
3913 :
3914 :			=item RETURN
3915 :
3916 :			Returns a list of feature IDs for genes that overlap or are close to the boundaries
3917 :			for the specified incoming feature.
3918 :
3919 :			=back
3920 :
3921 :			=cut
3922 :	golsen	1.141
3923 :	efrank	1.1	sub close_genes {
3924 :			my($self,$fid,$dist) = @_;
3925 :	parrello	1.200
3926 :	mkubal	1.147	# warn "In close_genes, self=$self, fid=$fid";
3927 :	parrello	1.200
3928 :	efrank	1.1	my $loc = $self->feature_location($fid);
3929 :			if ($loc)
3930 :			{
3931 :	parrello	1.298	my($contig,$beg,$end) = &FIG::boundaries_of($loc);
3932 :			if ($contig && $beg && $end)
3933 :			{
3934 :			my $min = &min($beg,$end) - $dist;
3935 :			my $max = &max($beg,$end) + $dist;
3936 :			my $feat;
3937 :			($feat,undef,undef) = $self->genes_in_region(&FIG::genome_of($fid),$contig,$min,$max);
3938 :			return @$feat;
3939 :			}
3940 :	efrank	1.1	}
3941 :			return ();
3942 :			}
3943 :
3944 :	parrello	1.287	=head3 adjacent_genes
3945 :
3946 :			C<< my ($left_fid, $right_fid) = $fig->adjacent_genes($fid, $dist); >>
3947 :
3948 :			Return the IDs of the genes immediately to the left and right of a specified
3949 :			feature.
3950 :
3951 :			This method gets a list of the features within the specified distance of
3952 :			the incoming feature (using L</close_genes>), and then chooses the two
3953 :			closest to the feature found. If the incoming feature is on the + strand,
3954 :			these are features to the left and the right. If the incoming feature is
3955 :			on the - strand, the features will be returned in reverse order.
3956 :
3957 :			=over 4
3958 :
3959 :			=item fid
3960 :
3961 :			ID of the feature whose neighbors are desired.
3962 :
3963 :			=item dist
3964 :
3965 :			Maximum permissible distance to the neighbors.
3966 :
3967 :			=item RETURN
3968 :
3969 :			Returns a two-element list containing the IDs of the features on either side
3970 :			of the incoming feature.
3971 :
3972 :			=back
3973 :
3974 :			=cut
3975 :
3976 :	mkubal	1.147	sub adjacent_genes
3977 :			{
3978 :			my ($self, $fid, $dist) = @_;
3979 :			my (@close, $strand, $i);
3980 :	parrello	1.200
3981 :	mkubal	1.147	# warn "In adjacent_genes, self=$self, fid=$fid";
3982 :	parrello	1.200
3983 :
3984 :	mkubal	1.147	$strand = $self->strand_of($fid);
3985 :	parrello	1.200
3986 :	mkubal	1.147	$dist = $dist \|\| 2000;
3987 :			@close = $self->close_genes($fid, $dist);
3988 :			for ($i=0; $i < @close; ++$i) { last if ($close[$i] eq $fid); }
3989 :	parrello	1.200
3990 :	redwards	1.157	# RAE note that if $self->strand_of($close[$i-1]) ne $strand then left/right neighbors
3991 :			# were never set! oops!
3992 :	parrello	1.200
3993 :	redwards	1.157	# I think the concept of Left and right is confused here. In my mind, left and right
3994 :			# are independent of strand ?? E.g. take a look at PEG fig\|196600.1.peg.1806
3995 :			# this is something like
3996 :			#
3997 :			# ---> <--1805--- --1806--> <--1807-- <----
3998 :			#
3999 :			# 1805 is always the left neighbor, no?
4000 :
4001 :			my ($left_neighbor, $right_neighbor) = ($close[$i-1], $close[$i+1]);
4002 :	parrello	1.200
4003 :	parrello	1.287	# if (0) # this was if ($i > 0) I just skip this whole section!
4004 :			# {
4005 :	parrello	1.298	# if ($self->strand_of($close[$i-1]) eq $strand) { $left_neighbor = $close[$i-1]; }
4006 :	parrello	1.287	# }
4007 :
4008 :			if ($i < $#close)
4009 :	mkubal	1.147	{
4010 :	parrello	1.298	if ($self->strand_of($close[$i+1]) eq $strand) { $right_neighbor = $close[$i+1]; }
4011 :	mkubal	1.147	}
4012 :	parrello	1.200
4013 :	parrello	1.287	# ...return genes in transcription order...
4014 :			if ($strand eq '-')
4015 :	mkubal	1.147	{
4016 :	parrello	1.298	($left_neighbor, $right_neighbor) = ($right_neighbor, $left_neighbor);
4017 :	mkubal	1.147	}
4018 :	parrello	1.200
4019 :	parrello	1.287	return ($left_neighbor, $right_neighbor) ;
4020 :			}
4021 :
4022 :			=head3 feature_location
4023 :
4024 :			C<< my $loc = $fig->feature_location($fid); >>
4025 :
4026 :			or
4027 :
4028 :			C<< my @loc = $fig->feature_location($fid);; >>
4029 :
4030 :			Return the location of a feature. The location consists
4031 :			of a list of (contigID, begin, end) triples encoded
4032 :			as strings with an underscore delimiter. So, for example,
4033 :			C<NC_002755_100_199> indicates a location starting at position
4034 :			100 and extending through 199 on the contig C<NC_002755>. If
4035 :			the location goes backward, the start location will be higher
4036 :			than the end location (e.g. C<NC_002755_199_100>).
4037 :
4038 :			In a scalar context, this method returns the locations as a
4039 :			comma-delimited string
4040 :	parrello	1.200
4041 :	parrello	1.287	NC_002755_100_199,NC_002755_210_498
4042 :	mkubal	1.147
4043 :	parrello	1.287	In a list context, the locations are returned as a list
4044 :	efrank	1.1
4045 :	parrello	1.287	(NC_002755_100_199, NC_002755_210_498)
4046 :	efrank	1.1
4047 :	parrello	1.287	=over 4
4048 :	efrank	1.1
4049 :	parrello	1.287	=item fid
4050 :	efrank	1.1
4051 :	parrello	1.287	ID of the feature whose location is desired.
4052 :	efrank	1.1
4053 :	parrello	1.287	=item RETURN
4054 :	efrank	1.1
4055 :	parrello	1.287	Returns the locations of a feature, either as a comma-delimited
4056 :			string or a list.
4057 :	efrank	1.1
4058 :	parrello	1.287	=back
4059 :	efrank	1.1
4060 :			=cut
4061 :
4062 :	olson	1.111	sub feature_location :scalar :list {
4063 :	efrank	1.1	my($self,$feature_id) = @_;
4064 :			my($relational_db_response,$locations,$location);
4065 :	parrello	1.200
4066 :	mkubal	1.147	# warn "In feature_location, self=$self, fid=$feature_id";
4067 :	parrello	1.200
4068 :	overbeek	1.136	if ($self->is_deleted_fid($feature_id)) { return undef }
4069 :
4070 :	efrank	1.1	$locations = $self->cached('_location');
4071 :	parrello	1.287	if (! ($location = $locations->{$feature_id})) {
4072 :			my $rdbH = $self->db_handle;
4073 :			if (($relational_db_response = $rdbH->SQL("SELECT location FROM features WHERE ( id = \'$feature_id\' )")) &&
4074 :			(@$relational_db_response == 1)) {
4075 :			$locations->{$feature_id} = $location = $relational_db_response->[0]->[0];
4076 :			}
4077 :	efrank	1.1	}
4078 :
4079 :	parrello	1.287	if ($location) {
4080 :			return wantarray() ? split(/,/,$location) : $location;
4081 :	efrank	1.1	}
4082 :			return undef;
4083 :			}
4084 :
4085 :	parrello	1.298	=head3 contig_of
4086 :
4087 :			C<< my $contigID = $fig->contig_of($location); >>
4088 :
4089 :			Return the ID of the contig containing a location.
4090 :
4091 :			This method only works with SEED-style locations (I<contigID>C<_>I<beg>C<_>I<end>).
4092 :			For more comprehensive location parsing, use the B<Location> object.
4093 :
4094 :			=over 4
4095 :
4096 :			=item location
4097 :
4098 :			A SEED-style location (I<contigID>C<_>I<beg>C<_>I<end>), or a comma-delimited list
4099 :			of SEED-style locations. In the latter case, only the first location in the list will
4100 :			be processed.
4101 :
4102 :			=item RETURN
4103 :
4104 :			Returns the contig ID from the first location in the incoming string.
4105 :
4106 :			=back
4107 :
4108 :			=cut
4109 :	parrello	1.287
4110 :	mkubal	1.147	sub contig_of
4111 :			{
4112 :			my ($self, $locus) = @_;
4113 :	parrello	1.200
4114 :	olson	1.159	$locus =~ m/^([^,]+)_\d+_\d+/;
4115 :	parrello	1.200
4116 :	mkubal	1.147	return $1;
4117 :			}
4118 :
4119 :	parrello	1.298	=head3 beg_of
4120 :
4121 :			C<< my $beg = $fig->beg_of($location); >>
4122 :
4123 :			Return the beginning point of a location.
4124 :
4125 :			This method only works with SEED-style locations (I<contigID>C<_>I<beg>C<_>I<end>).
4126 :			For more comprehensive location parsing, use the B<Location> object.
4127 :
4128 :			=over 4
4129 :
4130 :			=item location
4131 :
4132 :			A SEED-style location (I<contigID>C<_>I<beg>C<_>I<end>), or a comma-delimited list
4133 :			of SEED-style locations. In the latter case, only the first location in the list will
4134 :			be processed.
4135 :
4136 :			=item RETURN
4137 :
4138 :			Returns the beginning point from the first location in the incoming string.
4139 :
4140 :			=back
4141 :
4142 :			=cut
4143 :
4144 :	mkubal	1.147	sub beg_of
4145 :			{
4146 :			my ($self, $locus) = @_;
4147 :	parrello	1.200
4148 :	olson	1.159	$locus =~ m/^[^,]+_(\d+)_\d+/;
4149 :	parrello	1.200
4150 :	mkubal	1.147	return $1;
4151 :			}
4152 :
4153 :	parrello	1.298	=head3 end_of
4154 :
4155 :			C<< my $end = $fig->end_of($location); >>
4156 :
4157 :			Return the ending point of a location.
4158 :
4159 :			This method only works with SEED-style locations (I<contigID>C<_>I<beg>C<_>I<end>).
4160 :			For more comprehensive location parsing, use the B<Location> object.
4161 :
4162 :			=over 4
4163 :
4164 :			=item location
4165 :
4166 :			A SEED-style location (I<contigID>C<_>I<beg>C<_>I<end>), or a comma-delimited list
4167 :			of SEED-style locations. In the latter case, only the first location in the list will
4168 :			be processed.
4169 :
4170 :			=item RETURN
4171 :
4172 :			Returns the contig ID from the first location in the incoming string.
4173 :
4174 :			=back
4175 :
4176 :			=cut
4177 :
4178 :	mkubal	1.147	sub end_of
4179 :			{
4180 :			my ($self, $locus) = @_;
4181 :	parrello	1.200
4182 :	mkubal	1.147	$locus =~ m/\S+_\d+_(\d+)$/;
4183 :	parrello	1.200
4184 :	mkubal	1.147	return $1;
4185 :			}
4186 :
4187 :	parrello	1.320	=head3 upstream_of
4188 :
4189 :			C<< my $dna = $fig->upstream_of($peg, $upstream, $coding); >>
4190 :
4191 :			Return the DNA immediately upstream of a feature. This method contains code lifted from
4192 :			the C<upstream.pl> script.
4193 :
4194 :			=over 4
4195 :
4196 :			=item peg
4197 :
4198 :			ID of the feature whose upstream DNA is desired.
4199 :
4200 :			=item upstream
4201 :
4202 :			Number of base pairs considered upstream.
4203 :
4204 :			=item coding
4205 :
4206 :			Number of base pairs inside the feature to be included in the upstream region.
4207 :
4208 :			=item RETURN
4209 :
4210 :			Returns the DNA sequence upstream of the feature's begin point and extending into the coding
4211 :			region. Letters inside a feature are in upper case and inter-genic letters are in lower case.
4212 :			A hyphen separates the true upstream letters from the coding region.
4213 :
4214 :			=back
4215 :
4216 :			=cut
4217 :			#: Return Type $;
4218 :			sub upstream_of {
4219 :			# Get the parameters.
4220 :			my ($self, $peg, $upstream, $coding) = @_;
4221 :			# Declare the work variables.
4222 :			my ($gene_before, $inter_genic, $c_seq) = ("", "", "");
4223 :			# Declare the return variable.
4224 :			my $retVal;
4225 :			# Compute the upstream.
4226 :			my($contig,$beg,$end) = $self->boundaries_of(scalar $self->feature_location($peg));
4227 :			my $genome = $self->genome_of($peg);
4228 :			if (defined($contig) && (my $contig_ln = $self->contig_ln($genome,$contig)))
4229 :			{
4230 :			if ($beg < $end)
4231 :			{
4232 :			# Here the feature goes from left to right. Set "b" and "e" to the start and
4233 :			# end of the upstream region, which precedes the feature.
4234 :			my $b = max(1,$beg-$upstream);
4235 :			my $e = max(1,$beg-1);
4236 :			if ($e > $b)
4237 :			{
4238 :			# Here an upstream region exists. We put it in u_seq.
4239 :			my $u_seq = lc $self->dna_seq($genome,join("_",($contig,$b,$e)));
4240 :			# Now we look for a coding region inside the feature. It would go from
4241 :			# "$beg" to "$end1".
4242 :			my $end1 = min($end,$beg+$coding-1);
4243 :			# If a coding region exists, we put it in c_seq.
4244 :			$c_seq = ($end1 > $beg) ?
4245 :			uc $self->dna_seq($genome,join("_",($contig,$beg,$end1))) : "";
4246 :			# Now we look for a gene in the upstream region. If one exists, we put its
4247 :			# rightmost point in "$e_ov".
4248 :			my (undef,undef,$e_ov) = $self->genes_in_region($genome,$contig,$b,$e);
4249 :			if ($e_ov && ($e_ov >= $b))
4250 :			{
4251 :			# Get the length of the upstream region that overlaps the preceding gene.
4252 :			# We need to be careful here, because it might actually extend into the
4253 :			# coding region.
4254 :			my $ov_ln = min($e_ov - $b + 1, length $u_seq);
4255 :			$gene_before = uc substr($u_seq,0,$ov_ln);
4256 :			$inter_genic = substr($u_seq,$ov_ln);
4257 :			}
4258 :			else
4259 :			{
4260 :			# No overlap. The entire upstream is considered inter-genic.
4261 :			$gene_before = "";
4262 :