Annotation of /FigKernelPackages/FIG.pm

Revision 1.314 - (view) (download) (as text)

1 :	efrank	1.1	package FIG;
2 :
3 :	olson	1.111	use strict;
4 :
5 :	overbeek	1.135	use Fcntl qw/:flock/; # import LOCK_* constants
6 :
7 :	olson	1.116	use POSIX;
8 :	olson	1.158	use IPC::Open2;
9 :	olson	1.116
10 :	efrank	1.1	use DBrtns;
11 :			use Sim;
12 :			use Blast;
13 :			use FIG_Config;
14 :	overbeek	1.36	use tree_utilities;
15 :	olson	1.93	use Subsystem;
16 :	olson	1.162	use SeedDas;
17 :	olson	1.183	use Construct;
18 :	parrello	1.200	use FIGRules;
19 :	parrello	1.210	use Tracer;
20 :	olson	1.297	use GenomeIDMap;
21 :	olson	1.260
22 :	olson	1.245	eval { require FigGFF; };
23 :	parrello	1.287	if ($@ and $ENV{USER} eq "olson") {
24 :	olson	1.260	warn $@;
25 :			}
26 :	olson	1.79
27 :			#
28 :			# Conditionally evaluate this in case its prerequisites are not available.
29 :			#
30 :
31 :			our $ClearinghouseOK = eval {
32 :			require Clearinghouse;
33 :			};
34 :	efrank	1.1
35 :	olson	1.10	use IO::Socket;
36 :
37 :	efrank	1.1	use FileHandle;
38 :
39 :			use Carp;
40 :			use Data::Dumper;
41 :	overbeek	1.25	use Time::Local;
42 :	olson	1.93	use File::Spec;
43 :	olson	1.123	use File::Copy;
44 :	olson	1.112	#
45 :			# Try to load the RPC stuff; it might fail on older versions of the software.
46 :			#
47 :			eval {
48 :			require FIGrpc;
49 :			};
50 :
51 :			my $xmlrpc_available = 1;
52 :	parrello	1.287	if ($@ ne "") {
53 :	olson	1.112	$xmlrpc_available = 0;
54 :			}
55 :
56 :	efrank	1.1
57 :	olson	1.111	use FIGAttributes;
58 :			use base 'FIGAttributes';
59 :
60 :			use vars qw(%_FunctionAttributes);
61 :
62 :			use Data::Dumper;
63 :
64 :	olson	1.124	#
65 :			# Force all new files to be all-writable.
66 :			#
67 :
68 :			umask 0;
69 :
70 :	parrello	1.210	=head1 FIG Genome Annotation System
71 :
72 :			=head2 Introduction
73 :
74 :			This is the main object for access to the SEED data store. The data store
75 :			itself is a combination of flat files and a database. The flat files can
76 :			be moved easily between systems and the database rebuilt as needed.
77 :
78 :			A reduced set of this object's functions are available via the B<SFXlate>
79 :			object. The SFXlate object uses a single database to represent all its
80 :			genomic information. It provides a much smaller capability for updating
81 :			the data, and eliminates all similarities except for bidirectional best
82 :			hits.
83 :
84 :			The key to making the FIG system work is proper configuration of the
85 :			C<FIG_Config.pm> file. This file contains names and URLs for the key
86 :			directories as well as the type and login information for the database.
87 :
88 :	parrello	1.287	FIG was designed to operate as a series of peer instances. Each instance is
89 :			updated independently by its owner, and the instances can be synchronized
90 :			using a process called a I<peer-to-peer update>. The terms
91 :			I<SEED instance> and I<peer> are used more-or-less interchangeably.
92 :
93 :			The POD documentation for this module is still in progress, and is provided
94 :			on an AS IS basis without warranty. If you have a correction and you're
95 :			not a developer, EMAIL the details to B<bruce@gigabarb.com> and I'll fold
96 :			it in.
97 :
98 :			B<NOTE>: The usage example for each method specifies whether it is static
99 :
100 :			FIG::something
101 :
102 :			or dynamic
103 :
104 :			$fig->something
105 :
106 :			If the method is static and has no parameters (C<FIG::something()>) it can
107 :	parrello	1.298	also be invoked dynamically. This is a general artifact of the
108 :	parrello	1.287	way PERL implements object-oriented programming.
109 :
110 :			=head2 Hiding/Caching in a FIG object
111 :
112 :			We save the DB handle, cache taxonomies, and put a few other odds and ends in the
113 :			FIG object. We expect users to invoke these services using the object $fig constructed
114 :			using:
115 :
116 :			use FIG;
117 :			my $fig = new FIG;
118 :
119 :			$fig is then used as the basic mechanism for accessing FIG services. It is, of course,
120 :			just a hash that is used to retain/cache data. The most commonly accessed item is the
121 :			DB filehandle, which is accessed via $self->db_handle.
122 :
123 :			We cache genus/species expansions, taxonomies, distances (very crudely estimated) estimated
124 :			between genomes, and a variety of other things.
125 :
126 :	parrello	1.210	=cut
127 :
128 :	parrello	1.287
129 :	parrello	1.210	#: Constructor FIG->new();
130 :
131 :			=head2 Public Methods
132 :
133 :			=head3 new
134 :
135 :			C<< my $fig = FIG->new(); >>
136 :
137 :	parrello	1.298	This is the constructor for a FIG object. It uses no parameters. If tracing
138 :			has not yet been turned on, it will be turned on here. The tracing type and
139 :			level are specified by the configuration variables C<$FIG_Config::trace_levels>
140 :	parrello	1.301	and C<$FIG_Config::trace_type>. These defaults can be overridden using the
141 :			environment variables C<Trace> and C<TraceType>, respectively.
142 :	parrello	1.210
143 :			=cut
144 :
145 :	efrank	1.1	sub new {
146 :			my($class) = @_;
147 :
148 :	olson	1.102	#
149 :			# Check to see if we have a FIG_URL environment variable set.
150 :			# If we do, don't actually create a FIG object, but rather
151 :			# create a FIGrpc and return that as the return from this constructor.
152 :			#
153 :
154 :	parrello	1.210	if ($ENV{FIG_URL} ne "" && $xmlrpc_available) {
155 :			Trace("Creating figrpc for '$ENV{FIG_URL}'") if T(0);
156 :			my $figrpc = new FIGrpc($ENV{FIG_URL});
157 :			return $figrpc;
158 :	olson	1.102	}
159 :	parrello	1.292	# Here we have the normal case. Check for default tracing. We only do this if
160 :			# the proper parameters are present and nobody else has set up tracing yet.
161 :	parrello	1.301	if (Tracer::Setups() == 0 && (defined $FIG_Config::trace_levels \|\| exists $ENV{Trace})) {
162 :			# Tracing is not active and the user has specified tracing levels, so it's safe for
163 :			# us to set it up using our own rules. First, the trace type: the default is WARN.
164 :			my $trace_type;
165 :			if (exists($ENV{TraceType})) {
166 :			$trace_type = $ENV{TraceType};
167 :			} elsif (defined($FIG_Config::trace_type)) {
168 :			$trace_type = $FIG_Config::trace_type;
169 :			} else {
170 :			$trace_type = "WARN";
171 :			}
172 :			# Now the trace levels. The environment variable wins over the FIG_Config value.
173 :			my $trace_levels = (exists($ENV{Trace}) ? $ENV{Trace} : $FIG_Config::trace_levels);
174 :			TSetup($trace_levels, $trace_type);
175 :	parrello	1.287	}
176 :			# Connect to the database, then return ourselves.
177 :	efrank	1.1	my $rdbH = new DBrtns;
178 :			bless {
179 :	parrello	1.210	_dbf => $rdbH,
180 :			}, $class;
181 :	efrank	1.1	}
182 :
183 :	parrello	1.287	=head3 db_handle
184 :
185 :			C<< my $dbh = $fig->db_handle; >>
186 :
187 :			Return the handle to the internal B<DBrtns> object. This allows direct access to
188 :			the database methods.
189 :
190 :			=cut
191 :
192 :			sub db_handle {
193 :			my($self) = @_;
194 :			return $self->{_dbf};
195 :			}
196 :
197 :	overbeek	1.293	sub table_exists {
198 :			my($self,$table) = @_;
199 :
200 :			my $rdbH = $self->db_handle;
201 :			return $rdbH->table_exists($table);
202 :			}
203 :	parrello	1.292
204 :	parrello	1.287	=head3 cached
205 :
206 :			C<< my $x = $fig->cached($name); >>
207 :
208 :			Return a reference to a hash containing transient data. If no hash exists with the
209 :			specified name, create an empty one under that name and return it.
210 :
211 :			The idea behind this method is to allow clients to cache data in the FIG object for
212 :			later use. (For example, a method might cache feature data so that it can be
213 :			retrieved later without using the database.) This facility should be used sparingly,
214 :			since different clients may destroy each other's data if they use the same name.
215 :
216 :			=over 4
217 :
218 :			=item name
219 :
220 :			Name assigned to the cached data.
221 :
222 :			=item RETURN
223 :
224 :			Returns a reference to a hash that is permanently associated with the specified name.
225 :			If no such hash exists, an empty one will be created for the purpose.
226 :
227 :			=back
228 :
229 :			=cut
230 :
231 :			sub cached {
232 :			my($self,$what) = @_;
233 :
234 :			my $x = $self->{$what};
235 :			if (! $x) {
236 :			$x = $self->{$what} = {};
237 :			}
238 :			return $x;
239 :			}
240 :	parrello	1.210
241 :			=head3 get_system_name
242 :
243 :			C<< my $name = $fig->get_system_name; >>
244 :
245 :			Returns C<seed>, indicating that this is object is using the SEED
246 :			database. The same method on an SFXlate object will return C<sprout>.
247 :
248 :			=cut
249 :			#: Return Type $;
250 :			sub get_system_name {
251 :	olson	1.207	return "seed";
252 :	olson	1.205	}
253 :	parrello	1.210
254 :	parrello	1.287	=head3 DESTROY
255 :
256 :			The destructor releases the database handle.
257 :
258 :			=cut
259 :	olson	1.205
260 :	parrello	1.287	sub DESTROY {
261 :	efrank	1.1	my($self) = @_;
262 :			my($rdbH);
263 :
264 :	parrello	1.210	if ($rdbH = $self->db_handle) {
265 :			$rdbH->DESTROY;
266 :	efrank	1.1	}
267 :			}
268 :
269 :	parrello	1.210	=head3 delete_genomes
270 :
271 :			C<< $fig->delete_genomes(\@genomes); >>
272 :
273 :			Delete the specified genomes from the data store. This requires making
274 :			system calls to move and delete files.
275 :
276 :			=cut
277 :			#: Return Type ;
278 :	overbeek	1.7	sub delete_genomes {
279 :			my($self,$genomes) = @_;
280 :			my $tmpD = "$FIG_Config::temp/tmp.deleted.$$";
281 :			my $tmp_Data = "$FIG_Config::temp/Data.$$";
282 :
283 :			my %to_del = map { $_ => 1 } @$genomes;
284 :			open(TMP,">$tmpD") \|\| die "could not open $tmpD";
285 :
286 :			my $genome;
287 :	parrello	1.287	foreach $genome ($self->genomes) {
288 :			if (! $to_del{$genome}) {
289 :			print TMP "$genome\n";
290 :			}
291 :	overbeek	1.7	}
292 :			close(TMP);
293 :
294 :			&run("extract_genomes $tmpD $FIG_Config::data $tmp_Data");
295 :	parrello	1.200
296 :	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");
297 :	parrello	1.200
298 :			&run("mv $FIG_Config::data $FIG_Config::data.deleted");
299 :	overbeek	1.47	&run("mv $tmp_Data $FIG_Config::data");
300 :			&run("fig load_all");
301 :			&run("rm -rf $FIG_Config::data.deleted");
302 :	overbeek	1.7	}
303 :	parrello	1.200
304 :	parrello	1.210	=head3 add_genome
305 :
306 :			C<< my $ok = $fig->add_genome($genomeF); >>
307 :
308 :			Add a new genome to the data store. A genome's data is kept in a directory
309 :	parrello	1.287	by itself, underneath the main organism directory. This method essentially
310 :			moves genome data from an external directory to the main directory and
311 :			performs some indexing tasks to integrate it.
312 :	parrello	1.210
313 :			=over 4
314 :
315 :			=item genomeF
316 :
317 :	parrello	1.287	Name of the directory containing the genome files. This should be a
318 :			fully-qualified directory name. The last segment of the directory
319 :			name should be the genome ID.
320 :	parrello	1.210
321 :			=item RETURN
322 :
323 :			Returns TRUE if successful, else FALSE.
324 :
325 :			=back
326 :
327 :			=cut
328 :			#: Return Type $;
329 :	efrank	1.1	sub add_genome {
330 :			my($self,$genomeF) = @_;
331 :
332 :			my $rc = 0;
333 :	olson	1.93
334 :			my(undef, $path, $genome) = File::Spec->splitpath($genomeF);
335 :
336 :	parrello	1.287	if ($genome !~ /^\d+\.\d+$/) {
337 :			warn "Invalid genome filename $genomeF\n";
338 :			return $rc;
339 :	olson	1.93	}
340 :
341 :	parrello	1.287	if (-d $FIG_Config::organisms/$genome) {
342 :			warn "Organism already exists for $genome\n";
343 :			return $rc;
344 :	olson	1.93	}
345 :	parrello	1.200
346 :	olson	1.93
347 :			#
348 :			# We're okay, it doesn't exist.
349 :			#
350 :
351 :			my @errors = `$FIG_Config::bin/verify_genome_directory $genomeF`;
352 :
353 :	parrello	1.287	if (@errors) {
354 :			warn "Errors found while verifying genome directory $genomeF:\n";
355 :			print join("", @errors);
356 :			return $rc;
357 :	olson	1.93	}
358 :	parrello	1.200
359 :	olson	1.93	&run("cp -r $genomeF $FIG_Config::organisms");
360 :			&run("chmod -R 777 $FIG_Config::organisms/$genome");
361 :
362 :			&run("index_contigs $genome");
363 :			&run("compute_genome_counts $genome");
364 :			&run("load_features $genome");
365 :
366 :			$rc = 1;
367 :	parrello	1.287	if (-s "$FIG_Config::organisms/$genome/Features/peg/fasta") {
368 :			&run("index_translations $genome");
369 :			my @tmp = `cut -f1 $FIG_Config::organisms/$genome/Features/peg/tbl`;
370 :			chomp @tmp;
371 :			&run("cat $FIG_Config::organisms/$genome/Features/peg/fasta >> $FIG_Config::data/Global/nr");
372 :			&enqueue_similarities(\@tmp);
373 :	olson	1.93	}
374 :			if ((-s "$FIG_Config::organisms/$genome/assigned_functions") \|\|
375 :	parrello	1.287	(-d "$FIG_Config::organisms/$genome/UserModels")) {
376 :			&run("add_assertions_of_function $genome");
377 :	efrank	1.1	}
378 :	parrello	1.200
379 :	efrank	1.1	return $rc;
380 :			}
381 :
382 :	parrello	1.287	=head3 parse_genome_args
383 :
384 :			C<< my ($mode, @genomes) = FIG::parse_genome_args(@args); >>
385 :
386 :			Extract a list of genome IDs from an argument list. If the argument list is empty,
387 :			return all the genomes in the data store.
388 :
389 :			This is a function that is performed by many of the FIG command-line utilities. The
390 :			user has the option of specifying a list of specific genome IDs or specifying none
391 :			in order to get all of them. If your command requires additional arguments in the
392 :			command line, you can still use this method if you shift them out of the argument list
393 :			before calling. The $mode return value will be C<all> if the user asked for all of
394 :			the genomes or C<some> if he specified a list of IDs. This is useful to know if,
395 :			for example, we are loading a table. If we're loading everything, we can delete the
396 :			entire table; if we're only loading some genomes, we must delete them individually.
397 :
398 :			This method uses the genome directory rather than the database because it may be used
399 :			before the database is ready.
400 :
401 :			=over 4
402 :
403 :			=item args1, args2, ... argsN
404 :
405 :			List of genome IDs. If all genome IDs are to be processed, then this list should be
406 :			empty.
407 :
408 :			=item RETURN
409 :
410 :			Returns a list. The first element of the list is C<all> if the user is asking for all
411 :			the genome IDs and C<some> otherwise. The remaining elements of the list are the
412 :			desired genome IDs.
413 :
414 :			=back
415 :
416 :			=cut
417 :
418 :			sub parse_genome_args {
419 :			# Get the parameters.
420 :			my @args = @_;
421 :			# Check the mode.
422 :			my $mode = (@args > 0 ? 'some' : 'all');
423 :			# Build the return list.
424 :			my @retVal = ($mode);
425 :			# Process according to the mode.
426 :			if ($mode eq 'all') {
427 :			# We want all the genomes, so we get them from the organism directory.
428 :			my $orgdir = "$FIG_Config::organisms";
429 :			opendir( GENOMES, $orgdir ) \|\| Confess("Could not open directory $orgdir");
430 :			push @retVal, grep { $_ =~ /^\d/ } readdir( GENOMES );
431 :			closedir( GENOMES );
432 :			} else {
433 :			# We want only the genomes specified by the user.
434 :			push @retVal, @args;
435 :			}
436 :			# Return the result.
437 :			return @retVal;
438 :			}
439 :
440 :			=head3 reload_table
441 :
442 :			C<< $fig->reload_table($mode, $table, $flds, $xflds, $fileName, $keyList, $keyName); >>
443 :
444 :			Reload a database table from a sequential file. If I<$mode> is C<all>, the table
445 :			will be dropped and re-created. If I<$mode> is C<some>, the data for the individual
446 :			items in I<$keyList> will be deleted before the table is loaded. Thus, the load
447 :			process is optimized for the type of reload.
448 :
449 :			=over 4
450 :
451 :			=item mode
452 :
453 :			C<all> if we are reloading the entire table, C<some> if we are only reloading
454 :			specific entries.
455 :
456 :			=item table
457 :
458 :			Name of the table to reload.
459 :
460 :			=item flds
461 :
462 :			String defining the table columns, in SQL format. In general, this is a
463 :			comma-delimited set of field specifiers, each specifier consisting of the
464 :			field name followed by the field type and any optional qualifiers (such as
465 :			C<NOT NULL> or C<DEFAULT>); however, it can be anything that would appear
466 :			between the parentheses in a C<CREATE TABLE> statement. The order in which
467 :			the fields are specified is important, since it is presumed that is the
468 :			order in which they are appearing in the load file.
469 :
470 :			=item xflds
471 :
472 :			Reference to a hash that describes the indexes. The hash is keyed by index name.
473 :			The value is the index's field list. This is a comma-delimited list of field names
474 :			in order from most significant to least significant. If a field is to be indexed
475 :			in descending order, its name should be followed by the qualifier C<DESC>. For
476 :			example, the following I<$xflds> value will create two indexes, one for name followed
477 :			by creation date in reverse chronological order, and one for ID.
478 :
479 :			{ name_index => "name, createDate DESC", id_index => "id" }
480 :
481 :			=item fileName
482 :
483 :			Fully-qualified name of the file containing the data to load. Each line of the
484 :			file must correspond to a record, and the fields must be arranged in order and
485 :	parrello	1.298	tab-delimited. If the file name is omitted, the table is dropped and re-created
486 :			but not loaded.
487 :	parrello	1.287
488 :			=item keyList
489 :
490 :			Reference to a list of the IDs for the objects being reloaded. This parameter is
491 :			only used if I<$mode> is C<some>.
492 :
493 :			=item keyName (optional)
494 :
495 :			Name of the key field containing the IDs in the keylist. If omitted, C<genome> is
496 :			assumed.
497 :
498 :			=back
499 :
500 :			=cut
501 :
502 :			sub reload_table {
503 :	parrello	1.298	# Get the parameters.
504 :			my ($self, $mode, $table, $flds, $xflds, $fileName, $keyList, $keyName) = @_;
505 :	parrello	1.287	if (!defined $keyName) {
506 :			$keyName = 'genome';
507 :			}
508 :			# Get the database handler.
509 :			my $dbf = $self->{_dbf};
510 :	parrello	1.298	# Call the DBKernel method.
511 :			$dbf->reload_table($mode, $table, $flds, $xflds, $fileName, $keyList, $keyName);
512 :	parrello	1.287	}
513 :
514 :	parrello	1.210	=head3 enqueue_similarities
515 :	olson	1.93
516 :	parrello	1.287	C<< FIG::enqueue_similarities(\@fids); >>
517 :
518 :			Queue the passed Feature IDs for similarity computation. The actual
519 :			computation is performed by L</create_sim_askfor_pool>. The queue is a
520 :			persistent text file in the global data directory, and this method
521 :			essentially writes new IDs on the end of it.
522 :
523 :			=over 4
524 :
525 :			=item fids
526 :
527 :			Reference to a list of feature IDs.
528 :	olson	1.93
529 :	parrello	1.287	=back
530 :	olson	1.93
531 :			=cut
532 :	parrello	1.210	#: Return Type ;
533 :	olson	1.93	sub enqueue_similarities {
534 :	efrank	1.1	my($fids) = @_;
535 :			my $fid;
536 :
537 :	olson	1.93	my $sim_q = "$FIG_Config::global/queued_similarities";
538 :
539 :			open(TMP,">>$sim_q")
540 :	parrello	1.287	\|\| die "could not open $sim_q";
541 :	olson	1.93
542 :			#
543 :			# We need to lock here so that if a computation is creating a snapshot of the
544 :			# queue, we block until it's done.
545 :			#
546 :
547 :			flock(TMP, LOCK_EX) or die "Cannot lock $sim_q\n";
548 :
549 :	parrello	1.287	foreach $fid (@$fids) {
550 :			print TMP "$fid\n";
551 :	efrank	1.1	}
552 :			close(TMP);
553 :	olson	1.10	}
554 :
555 :	olson	1.281	=head3 export_similarity_request
556 :
557 :			Creates a similarity computation request from the queued similarities and
558 :	parrello	1.287	the current NR.
559 :	olson	1.281
560 :			We keep track of the exported requests in case one gets lost.
561 :
562 :			=cut
563 :
564 :	parrello	1.287	sub export_similarity_request {
565 :	olson	1.281	my($self, $nr_file, $fasta_file) = @_;
566 :
567 :			my $req_dir = "$FIG_Config::fig/var/sim_requests";
568 :			&verify_dir("$FIG_Config::fig/var");
569 :			&verify_dir($req_dir);
570 :
571 :			$req_dir = "$req_dir/" . time;
572 :			&verify_dir($req_dir);
573 :
574 :			#
575 :			# Open all of our output files before zeroing out the sim queue, in case
576 :			# there is a problem.
577 :			#
578 :
579 :			open(my $user_fasta_fh, ">$fasta_file") or confess "Cannot open $fasta_file for writing: $!";
580 :			open(my $fasta_fh, ">$req_dir/fasta.in");
581 :
582 :			open(my $user_nr_fh, ">$nr_file") or confess "Cannot open $nr_file for writing: $!";
583 :			open(my $nr_fh, ">$req_dir/nr") or confess "Cannot open $req_dir/nr for writing: $!";
584 :
585 :			open(my $nr_read_fh, "<$FIG_Config::data/Global/nr") or die "Cannot open $FIG_Config::data/Global/nr for reading: $!";
586 :	parrello	1.287
587 :	olson	1.281	my $sim_q = "$FIG_Config::global/queued_similarities";
588 :
589 :			#
590 :			# We need to lock here so that if a computation is creating a snapshot of the
591 :			# queue, we block until it's done.
592 :			#
593 :
594 :			open(my $sim_q_lock, ">>$sim_q") or confess "could not open $sim_q";
595 :			flock($sim_q_lock, LOCK_EX) or confess "Cannot lock $sim_q\n";
596 :
597 :			#
598 :			# Everything open & locked, start copying.
599 :			#
600 :	parrello	1.287
601 :	olson	1.281	copy("$sim_q", "$req_dir/q") or confess "Copy $sim_q $req_dir/q failed: $!";
602 :	parrello	1.287
603 :	olson	1.281	my($buf);
604 :	parrello	1.287	while (1) {
605 :			my $n = read($nr_read_fh, $buf, 4096);
606 :			defined($n) or confess "Error reading nr: $!";
607 :			last unless $n;
608 :			syswrite($user_nr_fh, $buf) or confess "Error writing $nr_file: $!";
609 :			syswrite($nr_fh, $buf) or confess "Error writing $req_dir/nr: $!";
610 :	olson	1.281	}
611 :
612 :			close($nr_read_fh);
613 :			close($nr_fh);
614 :			close($user_nr_fh);
615 :
616 :			#
617 :			# We can zero out the queue and unlock now.
618 :			#
619 :
620 :			open(F, ">$sim_q") or die "Cannot open $sim_q to truncate it: $!\n";
621 :			close(F);
622 :	parrello	1.287
623 :	olson	1.281	close($sim_q_lock);
624 :
625 :			#
626 :			# Generate the fasta input from the queued ids.
627 :			#
628 :
629 :			open(my $q_fh, "<$req_dir/q");
630 :	parrello	1.287	while (my $id = <$q_fh>) {
631 :			chomp $id;
632 :	olson	1.281
633 :	parrello	1.287	my $seq = $self->get_translation($id);
634 :	olson	1.281
635 :	parrello	1.287	display_id_and_seq($id, \$seq, $user_fasta_fh);
636 :			display_id_and_seq($id, \$seq, $fasta_fh);
637 :	olson	1.281	}
638 :			close($q_fh);
639 :
640 :			close($user_fasta_fh);
641 :			close($fasta_fh);
642 :			}
643 :
644 :	parrello	1.210	=head3 create_sim_askfor_pool
645 :	olson	1.93
646 :	parrello	1.287	C<< $fig->create_sim_askfor_pool($chunk_size); >>
647 :	olson	1.93
648 :	parrello	1.287	Creates an askfor pool, which a snapshot of the current NR and similarity
649 :			queue. This process clears the old queue.
650 :	olson	1.123
651 :			The askfor pool needs to keep track of which sequences need to be
652 :			calculated, which have been handed out, etc. To simplify this task we
653 :	olson	1.279	chunk the sequences into fairly small numbers (20k characters) and
654 :	olson	1.123	allocate work on a per-chunk basis. We make use of the relational
655 :			database to keep track of chunk status as well as the seek locations
656 :			into the file of sequence data. The initial creation of the pool
657 :			involves indexing the sequence data with seek offsets and lengths and
658 :			populating the sim_askfor_index table with this information and with
659 :			initial status information.
660 :	olson	1.93
661 :	parrello	1.287	=over 4
662 :
663 :			=item chunk_size
664 :
665 :			Number of features to put into a processing chunk. The default is 15.
666 :
667 :			=back
668 :
669 :	parrello	1.200	=cut
670 :	parrello	1.210	#: Return Type $;
671 :	parrello	1.287	sub create_sim_askfor_pool {
672 :	olson	1.123	my($self, $chunk_size) = @_;
673 :
674 :	olson	1.279	$chunk_size = 20000 unless $chunk_size =~ /^\d+$/;
675 :	olson	1.93
676 :	olson	1.279	my $pool_dir = "$FIG_Config::fig/var/sim_pools";
677 :	olson	1.93	&verify_dir($pool_dir);
678 :
679 :			#
680 :			# Lock the pool directory.
681 :			#
682 :			open(my $lock, ">$pool_dir/lockfile");
683 :
684 :			flock($lock, LOCK_EX);
685 :
686 :			my $num = 0;
687 :	parrello	1.287	if (open(my $toc, "<$pool_dir/TOC")) {
688 :			while (<$toc>) {
689 :			chomp;
690 :			# print STDERR "Have toc entry $_\n";
691 :			my ($idx, $time, $str) = split(/\s+/, $_, 3);
692 :	olson	1.93
693 :	parrello	1.287	$num = max($num, $idx);
694 :			}
695 :			close($toc);
696 :	olson	1.93	}
697 :			$num++;
698 :			open(my $toc, ">>$pool_dir/TOC") or die "Cannot write $pool_dir/TOC: $!\n";
699 :
700 :			print $toc "$num ", time(), " New toc entry\n";
701 :			close($toc);
702 :
703 :	olson	1.123	my $cpool_id = sprintf "%04d", $num;
704 :			my $cpool_dir = "$pool_dir/$cpool_id";
705 :	olson	1.93
706 :			#
707 :			# All set, create the directory for this pool.
708 :			#
709 :
710 :			&verify_dir($cpool_dir);
711 :
712 :			#
713 :			# Now we can copy the nr and sim queue here.
714 :			# Do this stuff inside an eval so we can clean up
715 :			# the lockfile.
716 :			#
717 :
718 :			eval {
719 :	parrello	1.287	my $sim_q = "$FIG_Config::global/queued_similarities";
720 :	olson	1.93
721 :	parrello	1.287	copy("$sim_q", "$cpool_dir/q");
722 :			copy("$FIG_Config::data/Global/nr", "$cpool_dir/nr");
723 :	olson	1.93
724 :	parrello	1.287	open(F, ">$sim_q") or die "Cannot open $sim_q to truncate it: $!\n";
725 :			close(F);
726 :	olson	1.93	};
727 :	parrello	1.200
728 :	olson	1.93	unlink("$pool_dir/lockfile");
729 :			close($lock);
730 :	olson	1.123
731 :			#
732 :			# We've created our pool; we can now run the formatdb and
733 :			# extract the sequences for the blast run.
734 :			#
735 :	parrello	1.287	my $child_pid = $self->run_in_background(
736 :			sub {
737 :			#
738 :			# Need to close db or there's all sorts of trouble.
739 :			#
740 :
741 :			my $cmd = "$FIG_Config::ext_bin/formatdb -i $cpool_dir/nr -p T -l $cpool_dir/formatdb.log";
742 :			print "Will run '$cmd'\n";
743 :			&run($cmd);
744 :			print "finished. Logfile:\n";
745 :			print &FIG::file_read("$cpool_dir/formatdb.log");
746 :			unlink("$cpool_dir/formatdb.pid");
747 :			});
748 :	olson	1.279	warn "Running formatdb in background job $child_pid\n";
749 :	olson	1.123	open(FPID, ">$cpool_dir/formatdb.pid");
750 :			print FPID "$child_pid\n";
751 :			close(FPID);
752 :
753 :			my $db = $self->db_handle();
754 :	parrello	1.287	if (!$db->table_exists("sim_queue")) {
755 :			$db->create_table(tbl => "sim_queue",
756 :			flds => "qid varchar(32), chunk_id INTEGER, seek INTEGER, len INTEGER, " .
757 :			"assigned BOOL, finished BOOL, output_file varchar(255), " .
758 :			"assignment_expires INTEGER, worker_info varchar(255)"
759 :			);
760 :	olson	1.123	}
761 :
762 :			#
763 :			# Write the fasta input file. Keep track of how many have been written,
764 :			# and write seek info into the database as appropriate.
765 :			#
766 :
767 :			open(my $seq_fh, ">$cpool_dir/fasta.in");
768 :
769 :			my($chunk_idx, $chunk_begin, $seq_idx);
770 :
771 :	olson	1.279	my $cur_size = 0;
772 :
773 :	olson	1.123	$chunk_idx = 0;
774 :			$chunk_begin = 0;
775 :			$seq_idx = 0;
776 :
777 :			my(@seeks);
778 :
779 :	olson	1.279	my $tmpfile = "$FIG_Config::temp/simseek.$$";
780 :			open(my $tmpfh, ">$tmpfile") or confess "Cannot open tmpfile $tmpfile: $!";
781 :
782 :	olson	1.123	open(my $q_fh, "<$cpool_dir/q");
783 :	parrello	1.287	while (my $id = <$q_fh>) {
784 :			chomp $id;
785 :	olson	1.123
786 :	parrello	1.287	my $seq = $self->get_translation($id);
787 :	olson	1.123
788 :	parrello	1.287	#
789 :			# check if we're at the beginning of a chunk
790 :			#
791 :
792 :			print $seq_fh ">$id\n$seq\n";
793 :
794 :			#
795 :			# Check if we're at the end of a chunk
796 :			#
797 :
798 :			$cur_size += length($seq);
799 :			if ($cur_size >= $chunk_size) {
800 :			my $chunk_end = tell($seq_fh);
801 :			my $chunk_len = $chunk_end - $chunk_begin;
802 :
803 :			push(@seeks, [$cpool_id, $chunk_idx, $chunk_begin, $chunk_len]);
804 :			print $tmpfh join("\t", $cpool_id, $chunk_idx, $chunk_begin, $chunk_len, 'FALSE', 'FALSE'), "\n";
805 :			$chunk_idx++;
806 :			$chunk_begin = $chunk_end;
807 :			$cur_size = 0;
808 :			}
809 :			$seq_idx++;
810 :	olson	1.123	}
811 :
812 :	parrello	1.287	if ($cur_size > 0) {
813 :			my $chunk_end = tell($seq_fh);
814 :			my $chunk_len = $chunk_end - $chunk_begin;
815 :	olson	1.123
816 :	parrello	1.287	print $tmpfh join("\t", $cpool_id, $chunk_idx, $chunk_begin, $chunk_len, 'FALSE', 'FALSE'), "\n";
817 :			push(@seeks, [$cpool_id, $chunk_idx, $chunk_begin, $chunk_len]);
818 :	olson	1.123	}
819 :
820 :			close($q_fh);
821 :			close($seq_fh);
822 :	olson	1.279	close($tmpfh);
823 :	olson	1.123
824 :	olson	1.279	warn "Write seqs from $tmpfile\n";
825 :	olson	1.123
826 :	olson	1.279	$self->db_handle->load_table(tbl => 'sim_queue',
827 :	parrello	1.298	file => $tmpfile);
828 :	parrello	1.200
829 :	olson	1.279	unlink($tmpfile);
830 :	parrello	1.287
831 :	olson	1.279	# for my $seek (@seeks)
832 :			# {
833 :	parrello	1.298	# my($cpool_id, $chunk_idx, $chunk_begin, $chunk_len) = @$seek;
834 :	olson	1.279
835 :	parrello	1.298	# $db->SQL("insert into sim_queue (qid, chunk_id, seek, len, assigned, finished) " .
836 :			# "values('$cpool_id', $chunk_idx, $chunk_begin, $chunk_len, FALSE, FALSE)");
837 :	olson	1.279	# }
838 :	parrello	1.200
839 :	olson	1.123	return $cpool_id;
840 :			}
841 :
842 :	parrello	1.210	#=head3 get_sim_queue
843 :			#
844 :			#usage: get_sim_queue($pool_id, $all_sims)
845 :			#
846 :			#Returns the sims in the given pool. If $all_sims is true, return the entire queue. Otherwise,
847 :			#just return the sims awaiting processing.
848 :			#
849 :			#=cut
850 :	olson	1.123
851 :	parrello	1.287	sub get_sim_queue {
852 :	olson	1.123	my($self, $pool_id, $all_sims) = @_;
853 :	olson	1.279	}
854 :
855 :	parrello	1.287	=head3 get_sim_work
856 :	olson	1.279
857 :	parrello	1.287	C<< my ($nrPath, $fasta) = $fig->get_sim_work(); >>
858 :	olson	1.279
859 :			Get the next piece of sim computation work to be performed. Returned are
860 :			the path to the NR and a string containing the fasta data.
861 :
862 :			=cut
863 :
864 :	parrello	1.287	sub get_sim_work {
865 :
866 :			my ($self) = @_;
867 :	olson	1.279
868 :			#
869 :			# For now, just don't care about order of data that we get back.
870 :			#
871 :
872 :			my $db = $self->db_handle();
873 :			my $lock = FIG::SimLock->new;
874 :
875 :			my $work = $db->SQL(qq(SELECT qid, chunk_id, seek, len
876 :	parrello	1.298	FROM sim_queue
877 :			WHERE not finished
878 :			LIMIT 1));
879 :	olson	1.279	print "Got work ", Dumper($work), "\n";
880 :
881 :	parrello	1.287	if (not $work or @$work == 0) {
882 :			return undef;
883 :	olson	1.279	}
884 :
885 :			my($cpool_id, $chunk_id, $seek, $len) = @{$work->[0]};
886 :	parrello	1.287
887 :	olson	1.279	my $pool_dir = "$FIG_Config::fig/var/sim_pools";
888 :			my $cpool_dir = "$pool_dir/$cpool_id";
889 :
890 :			my $nr = "$cpool_dir/nr";
891 :			open(my $fh, "<$cpool_dir/fasta.in");
892 :			seek($fh, $seek, 0);
893 :			my $fasta;
894 :			read($fh, $fasta, $len);
895 :
896 :			return($cpool_id, $chunk_id, $nr, $fasta, "$cpool_dir/out.$chunk_id");
897 :			}
898 :
899 :			=head3 sim_work_done
900 :
901 :	parrello	1.287	C<< $fig->sim_work_done($pool_id, $chunk_id, $out_file); >>
902 :
903 :	olson	1.279	Declare that the work in pool_id/chunk_id has been completed, and output written
904 :			to the pool directory (get_sim_work gave it the path).
905 :
906 :	parrello	1.287	=over 4
907 :
908 :			=item pool_id
909 :
910 :			The ID number of the pool containing the work that just completed.
911 :
912 :			=item chunk_id
913 :
914 :			The ID number of the chunk completed.
915 :
916 :			=item out_file
917 :
918 :			The file into which the work was placed.
919 :
920 :			=back
921 :
922 :	olson	1.279	=cut
923 :
924 :	parrello	1.287	sub sim_work_done {
925 :			my ($self, $pool_id, $chunk_id, $out_file) = @_;
926 :	olson	1.279
927 :	parrello	1.287	if (! -f $out_file) {
928 :			Confess("sim_work_done: output file $out_file does not exist");
929 :	olson	1.279	}
930 :
931 :			my $db = $self->db_handle();
932 :			my $lock = FIG::SimLock->new;
933 :
934 :			my $dbh = $db->{_dbh};
935 :
936 :			my $rows = $dbh->do(qq(UPDATE sim_queue
937 :	parrello	1.298	SET finished = TRUE, output_file = ?
938 :			WHERE qid = ? and chunk_id = ?), undef, $out_file, $pool_id, $chunk_id);
939 :	parrello	1.287	if ($rows != 1) {
940 :			if ($dbh->errstr) {
941 :			Confess("Update not able to set finished=TRUE: ", $dbh->errstr);
942 :			} else {
943 :			Confess("Update not able to set finished=TRUE");
944 :			}
945 :	olson	1.279	}
946 :			#
947 :			# Determine if this was the last piece of work for this pool. If so, we can
948 :	parrello	1.287	# schedule the postprocessing work.
949 :	olson	1.279	#
950 :			# Note we're still holding the lock.
951 :			#
952 :
953 :			my $out = $db->SQL(qq(SELECT chunk_id
954 :	parrello	1.298	FROM sim_queue
955 :			WHERE qid = ? AND not finished), undef, $pool_id);
956 :	parrello	1.287	if (@$out == 0) {
957 :			#
958 :			# Pool is done.
959 :			#
960 :			$self->schedule_sim_pool_postprocessing($pool_id);
961 :	olson	1.279	}
962 :	olson	1.123	}
963 :
964 :	olson	1.279	=head3 schedule_sim_pool_postprocessing
965 :
966 :	parrello	1.287	C<< $fig->schedule_sim_pool_postprocessing($pool_id); >>
967 :
968 :			Schedule a job to do the similarity postprocessing for the specified pool.
969 :
970 :			=over 4
971 :
972 :			=item pool_id
973 :
974 :			ID of the pool whose similarity postprocessing needs to be scheduled.
975 :	olson	1.279
976 :	parrello	1.287	=back
977 :	olson	1.279
978 :			=cut
979 :
980 :	parrello	1.287	sub schedule_sim_pool_postprocessing {
981 :
982 :	olson	1.279	my($self, $pool_id) = @_;
983 :
984 :			my $pool_dir = "$FIG_Config::fig/var/sim_pools";
985 :			my $cpool_dir = "$pool_dir/$pool_id";
986 :
987 :			my $js = JobScheduler->new();
988 :			my $job = $js->job_create();
989 :
990 :			my $spath = $job->get_script_path();
991 :			open(my $sfh, ">$spath");
992 :			print $sfh <<END;
993 :			#!/bin/sh
994 :			. $FIG_Config::fig_disk/config/fig-user-env.sh
995 :			$FIG_Config::bin/postprocess_computed_sims $pool_id
996 :			END
997 :
998 :			close($sfh);
999 :			chmod(0775, $spath);
1000 :
1001 :			#
1002 :			# Write the job ID to the subsystem queue dir.
1003 :			#
1004 :
1005 :			open(J, ">$cpool_dir/postprocess_jobid");
1006 :			print J $job->get_id(), "\n";
1007 :			close(J);
1008 :
1009 :			$job->enqueue();
1010 :			}
1011 :
1012 :			=head3 postprocess_computed_sims
1013 :
1014 :	parrello	1.287	C<< $fig->postprocess_computed_sims($pool_id); >>
1015 :
1016 :			Set up to reduce, reformat, and split the similarities in a given pool. We build
1017 :			a pipe to this pipeline:
1018 :	olson	1.279
1019 :			reduce_sims peg.synonyms 300 \| reformat_sims nr \| split_sims dest prefix
1020 :
1021 :	parrello	1.287	Then we put the new sims in the pool directory, and then copy to NewSims.
1022 :
1023 :			=over 4
1024 :
1025 :			=item pool_id
1026 :
1027 :			ID of the pool whose similarities are to be post-processed.
1028 :
1029 :			=back
1030 :	olson	1.279
1031 :			=cut
1032 :
1033 :	parrello	1.287	sub postprocess_computed_sims {
1034 :	olson	1.279	my($self, $pool_id) = @_;
1035 :
1036 :			#
1037 :			# We don't lock here because the job is already done, and we
1038 :			# shouldn't (ha, ha) ever postprocess twice.
1039 :			#
1040 :
1041 :			my $pool_dir = "$FIG_Config::fig/var/sim_pools";
1042 :			my $cpool_dir = "$pool_dir/$pool_id";
1043 :
1044 :			my $sim_dir = "$cpool_dir/NewSims";
1045 :			&verify_dir($sim_dir);
1046 :
1047 :			#
1048 :			# Open the processing pipeline.
1049 :			#
1050 :
1051 :			my $reduce = "$FIG_Config::bin/reduce_sims $FIG_Config::global/peg.synonyms 300";
1052 :			my $reformat = "$FIG_Config::bin/reformat_sims $cpool_dir/nr";
1053 :			my $split = "$FIG_Config::bin/split_sims $sim_dir sims.$pool_id";
1054 :			open(my $process, "\| $reduce \| $reformat \| $split");
1055 :
1056 :			#
1057 :			# Iterate over all the sims files, taken from the database.
1058 :			#
1059 :
1060 :			my $dbh = $self->db_handle()->{_dbh};
1061 :			my $files = $dbh->selectcol_arrayref(qq(SELECT output_file
1062 :	parrello	1.298	FROM sim_queue
1063 :			WHERE qid = ? and output_file IS NOT NULL
1064 :			ORDER BY chunk_id), undef, $pool_id);
1065 :	parrello	1.287	for my $file (@$files) {
1066 :			my $buf;
1067 :			open(my $fh, "<$file") or confess "Cannot sim input file $file: $!";
1068 :			while (read($fh, $buf, 4096)) {
1069 :			print $process $buf;
1070 :			}
1071 :			close($fh);
1072 :	olson	1.279	}
1073 :			my $res = close($process);
1074 :	parrello	1.287	if (!$res) {
1075 :			if ($!) {
1076 :			confess "Error closing process pipeline: $!";
1077 :			} else {
1078 :			confess "Process pipeline exited with status $?";
1079 :			}
1080 :	olson	1.279	}
1081 :
1082 :			#
1083 :			# If we got here, it worked. Copy the new sims files over to NewSims.
1084 :			#
1085 :
1086 :			opendir(my $simdh, $sim_dir) or confess "Cannot open $sim_dir: $!";
1087 :			my @new_sims = grep { $_ !~ /^\./ } readdir($simdh);
1088 :			closedir($simdh);
1089 :
1090 :			&verify_dir("$FIG_Config::data/NewSims");
1091 :
1092 :	parrello	1.287	for my $sim_file (@new_sims) {
1093 :			my $target = "$FIG_Config::data/NewSims/$sim_file";
1094 :			if (-s $target) {
1095 :			Confess("$target already exists");
1096 :			}
1097 :			print "copying sim file $sim_file\n";
1098 :			&FIG::run("cp $sim_dir/$sim_file $target");
1099 :			&FIG::run("$FIG_Config::bin/index_sims $target");
1100 :	olson	1.279	}
1101 :			}
1102 :
1103 :	parrello	1.210	=head3 get_active_sim_pools
1104 :	olson	1.123
1105 :	parrello	1.287	C<< @pools = $fig->get_active_sim_pools(); >>
1106 :	olson	1.123
1107 :	parrello	1.287	Return a list of the pool IDs for the sim processing queues that have
1108 :			entries awaiting computation.
1109 :	olson	1.123
1110 :			=cut
1111 :	parrello	1.210	#: Return Type @;
1112 :	parrello	1.287	sub get_active_sim_pools {
1113 :	olson	1.123	my($self) = @_;
1114 :
1115 :			my $dbh = $self->db_handle();
1116 :
1117 :			my $res = $dbh->SQL("select distinct qid from sim_queue where not finished");
1118 :			return undef unless $res;
1119 :
1120 :			return map { $_->[0] } @$res;
1121 :			}
1122 :
1123 :	parrello	1.210	=head3 get_sim_pool_info
1124 :	olson	1.123
1125 :	parrello	1.287	C<< my ($total_entries, $n_finished, $n_assigned, $n_unassigned) = $fig->get_sim_pool_info($pool_id); >>
1126 :
1127 :			Return information about the given sim pool.
1128 :
1129 :			=over 4
1130 :
1131 :			=item pool_id
1132 :
1133 :			Pool ID of the similarity processing queue whose information is desired.
1134 :
1135 :			=item RETURN
1136 :
1137 :			Returns a four-element list. The first is the number of features in the
1138 :			queue; the second is the number of features that have been processed; the
1139 :			third is the number of features that have been assigned to a
1140 :			processor, and the fourth is the number of features left over.
1141 :	olson	1.123
1142 :	parrello	1.287	=back
1143 :	olson	1.123
1144 :			=cut
1145 :	parrello	1.210	#: Return Type @;
1146 :	parrello	1.287	sub get_sim_pool_info {
1147 :
1148 :	olson	1.123	my($self, $pool_id) = @_;
1149 :			my($dbh, $res, $total_entries, $n_finished, $n_assigned, $n_unassigned);
1150 :
1151 :			$dbh = $self->db_handle();
1152 :
1153 :			$res = $dbh->SQL("select count(chunk_id) from sim_queue where qid = '$pool_id'");
1154 :	parrello	1.200	$total_entries = $res->[0]->[0];
1155 :	olson	1.123
1156 :			$res = $dbh->SQL("select count(chunk_id) from sim_queue where qid = '$pool_id' and finished");
1157 :			$n_finished = $res->[0]->[0];
1158 :
1159 :			$res = $dbh->SQL("select count(chunk_id) from sim_queue where qid = '$pool_id' and assigned and not finished");
1160 :			$n_assigned = $res->[0]->[0];
1161 :
1162 :			$res = $dbh->SQL("select count(chunk_id) from sim_queue where qid = '$pool_id' and not finished and not assigned");
1163 :			$n_unassigned = $res->[0]->[0];
1164 :
1165 :			return ($total_entries, $n_finished, $n_assigned, $n_unassigned);
1166 :	olson	1.93	}
1167 :
1168 :	parrello	1.210	#=head3 get_sim_chunk
1169 :			#
1170 :			#usage: get_sim_chunk($n_seqs, $worker_id)
1171 :			#
1172 :			#Returns a chunk of $n_seqs of work.
1173 :			#
1174 :			#From Ross, about how sims are processed:
1175 :			#
1176 :			#Here is how I process them:
1177 :			#
1178 :			#
1179 :			# bash$ cd /Volumes/seed/olson/Sims/June22.out
1180 :			# bash$ for i in really*
1181 :			# > do
1182 :			# > cat < $i >> /Volumes/laptop/new.sims
1183 :			# > done
1184 :			#
1185 :			#
1186 :			#Then, I need to "reformat" them by adding to columns to each one
1187 :			# and split the result into files of about 3M each This I do using
1188 :			#
1189 :			#reduce_sims /Volumes/laptop/NR/NewNR/peg.synonyms.june21 300 < /Volumes/laptop/new.sims \|
1190 :			# reformat_sims /Volumes/laptop/NR/NewNR/checked.nr.june21 > /Volumes/laptop/reformated.sims
1191 :			#rm /Volumes/laptop/new.sims
1192 :			#split_sims /Volumes/laptop/NewSims sims.june24 reformated.sims
1193 :			#rm reformatted.sims
1194 :			#
1195 :			#=cut
1196 :	olson	1.93
1197 :	parrello	1.287	sub get_sim_chunk {
1198 :	parrello	1.210	my($self, $n_seqs, $worker_id) = @_;
1199 :			}
1200 :	olson	1.123
1201 :	parrello	1.210	=head3 get_local_hostname
1202 :	parrello	1.200
1203 :	parrello	1.287	C<< my $result = FIG::get_local_hostname(); >>
1204 :
1205 :			Return the local host name for the current processor. The name may be
1206 :			stored in a configuration file, or we may have to get it from the
1207 :			operating system.
1208 :	olson	1.123
1209 :	olson	1.93	=cut
1210 :	parrello	1.213	#: Return Type $;
1211 :	olson	1.10	sub get_local_hostname {
1212 :	olson	1.52
1213 :			#
1214 :			# See if there is a FIGdisk/config/hostname file. If there
1215 :			# is, force the hostname to be that.
1216 :			#
1217 :
1218 :			my $hostfile = "$FIG_Config::fig_disk/config/hostname";
1219 :	parrello	1.287	if (-f $hostfile) {
1220 :			my $fh;
1221 :			if (open($fh, $hostfile)) {
1222 :			my $hostname = <$fh>;
1223 :			chomp($hostname);
1224 :			return $hostname;
1225 :			}
1226 :	olson	1.52	}
1227 :	parrello	1.200
1228 :	olson	1.10	#
1229 :			# First check to see if we our hostname is correct.
1230 :			#
1231 :			# Map it to an IP address, and try to bind to that ip.
1232 :			#
1233 :
1234 :			my $tcp = getprotobyname('tcp');
1235 :	parrello	1.200
1236 :	olson	1.10	my $hostname = `hostname`;
1237 :	golsen	1.44	chomp($hostname);
1238 :	olson	1.10
1239 :			my @hostent = gethostbyname($hostname);
1240 :
1241 :	parrello	1.287	if (@hostent > 0) {
1242 :			my $sock;
1243 :			my $ip = $hostent[4];
1244 :
1245 :			socket($sock, PF_INET, SOCK_STREAM, $tcp);
1246 :			if (bind($sock, sockaddr_in(0, $ip))) {
1247 :			#
1248 :			# It worked. Reverse-map back to a hopefully fqdn.
1249 :			#
1250 :
1251 :			my @rev = gethostbyaddr($ip, AF_INET);
1252 :			if (@rev > 0) {
1253 :			my $host = $rev[0];
1254 :			#
1255 :			# Check to see if we have a FQDN.
1256 :			#
1257 :
1258 :			if ($host =~ /\./) {
1259 :			#
1260 :			# Good.
1261 :			#
1262 :			return $host;
1263 :			} else {
1264 :			#
1265 :			# We didn't get a fqdn; bail and return the IP address.
1266 :			#
1267 :			return get_hostname_by_adapter()
1268 :			}
1269 :			} else {
1270 :			return inet_ntoa($ip);
1271 :			}
1272 :			} else {
1273 :			#
1274 :			# Our hostname must be wrong; we can't bind to the IP
1275 :			# address it maps to.
1276 :			# Return the name associated with the adapter.
1277 :			#
1278 :			return get_hostname_by_adapter()
1279 :			}
1280 :			} else {
1281 :			#
1282 :			# Our hostname isn't known to DNS. This isn't good.
1283 :			# Return the name associated with the adapter.
1284 :			#
1285 :			return get_hostname_by_adapter()
1286 :			}
1287 :			}
1288 :
1289 :			=head3 get_hostname_by_adapter
1290 :	parrello	1.200
1291 :	parrello	1.287	C<< my $name = FIG::get_hostname_by_adapter(); >>
1292 :	olson	1.10
1293 :	parrello	1.287	Return the local host name for the current network environment.
1294 :	parrello	1.213
1295 :			=cut
1296 :			#: Return Type $;
1297 :	olson	1.10	sub get_hostname_by_adapter {
1298 :			#
1299 :			# Attempt to determine our local hostname based on the
1300 :			# network environment.
1301 :			#
1302 :			# This implementation reads the routing table for the default route.
1303 :			# We then look at the interface config for the interface that holds the default.
1304 :			#
1305 :			#
1306 :			# Linux routing table:
1307 :			# [olson@yips 0.0.0]$ netstat -rn
1308 :			# Kernel IP routing table
1309 :			# Destination Gateway Genmask Flags MSS Window irtt Iface
1310 :			# 140.221.34.32 0.0.0.0 255.255.255.224 U 0 0 0 eth0
1311 :			# 169.254.0.0 0.0.0.0 255.255.0.0 U 0 0 0 eth0
1312 :			# 127.0.0.0 0.0.0.0 255.0.0.0 U 0 0 0 lo
1313 :			# 0.0.0.0 140.221.34.61 0.0.0.0 UG 0 0 0 eth0
1314 :	parrello	1.200	#
1315 :	olson	1.10	# Mac routing table:
1316 :	parrello	1.200	#
1317 :	olson	1.10	# bash-2.05a$ netstat -rn
1318 :			# Routing tables
1319 :	parrello	1.200	#
1320 :	olson	1.10	# Internet:
1321 :			# Destination Gateway Flags Refs Use Netif Expire
1322 :			# default 140.221.11.253 UGSc 12 120 en0
1323 :			# 127.0.0.1 127.0.0.1 UH 16 8415486 lo0
1324 :			# 140.221.8/22 link#4 UCS 12 0 en0
1325 :			# 140.221.8.78 0:6:5b:f:51:c4 UHLW 0 183 en0 408
1326 :			# 140.221.8.191 0:3:93:84:ab:e8 UHLW 0 92 en0 622
1327 :			# 140.221.8.198 0:e0:98:8e:36:e2 UHLW 0 5 en0 691
1328 :			# 140.221.9.6 0:6:5b:f:51:d6 UHLW 1 63 en0 1197
1329 :			# 140.221.10.135 0:d0:59:34:26:34 UHLW 2 2134 en0 1199
1330 :			# 140.221.10.152 0:30:1b:b0:ec:dd UHLW 1 137 en0 1122
1331 :			# 140.221.10.153 127.0.0.1 UHS 0 0 lo0
1332 :			# 140.221.11.37 0:9:6b:53:4e:4b UHLW 1 624 en0 1136
1333 :			# 140.221.11.103 0:30:48:22:59:e6 UHLW 3 973 en0 1016
1334 :			# 140.221.11.224 0:a:95:6f:7:10 UHLW 1 1 en0 605
1335 :			# 140.221.11.237 0:1:30:b8:80:c0 UHLW 0 0 en0 1158
1336 :			# 140.221.11.250 0:1:30:3:1:0 UHLW 0 0 en0 1141
1337 :			# 140.221.11.253 0:d0:3:e:70:a UHLW 13 0 en0 1199
1338 :			# 169.254 link#4 UCS 0 0 en0
1339 :	parrello	1.200	#
1340 :	olson	1.10	# Internet6:
1341 :			# Destination Gateway Flags Netif Expire
1342 :			# UH lo0
1343 :			# fe80::%lo0/64 Uc lo0
1344 :			# link#1 UHL lo0
1345 :			# fe80::%en0/64 link#4 UC en0
1346 :			# 0:a:95:a8:26:68 UHL lo0
1347 :			# ff01::/32 U lo0
1348 :			# ff02::%lo0/32 UC lo0
1349 :			# ff02::%en0/32 link#4 UC en0
1350 :
1351 :			my($fh);
1352 :
1353 :	parrello	1.287	if (!open($fh, "netstat -rn \|")) {
1354 :			warn "Cannot run netstat to determine local IP address\n";
1355 :			return "localhost";
1356 :	olson	1.10	}
1357 :
1358 :			my $interface_name;
1359 :	parrello	1.200
1360 :	parrello	1.287	while (<$fh>) {
1361 :			my @cols = split();
1362 :	olson	1.10
1363 :	parrello	1.287	if ($cols[0] eq "default" \|\| $cols[0] eq "0.0.0.0") {
1364 :			$interface_name = $cols[$#cols];
1365 :			}
1366 :	olson	1.10	}
1367 :			close($fh);
1368 :	parrello	1.200
1369 :	olson	1.11	# print "Default route on $interface_name\n";
1370 :	olson	1.10
1371 :			#
1372 :			# Find ifconfig.
1373 :			#
1374 :
1375 :			my $ifconfig;
1376 :
1377 :	parrello	1.287	for my $dir ((split(":", $ENV{PATH}), "/sbin", "/usr/sbin")) {
1378 :			if (-x "$dir/ifconfig") {
1379 :			$ifconfig = "$dir/ifconfig";
1380 :			last;
1381 :			}
1382 :	olson	1.10	}
1383 :
1384 :	parrello	1.287	if ($ifconfig eq "") {
1385 :			warn "Ifconfig not found\n";
1386 :			return "localhost";
1387 :	olson	1.10	}
1388 :	olson	1.11	# print "Foudn $ifconfig\n";
1389 :	olson	1.10
1390 :	parrello	1.287	if (!open($fh, "$ifconfig $interface_name \|")) {
1391 :			warn "Could not run $ifconfig: $!\n";
1392 :			return "localhost";
1393 :	olson	1.10	}
1394 :
1395 :			my $ip;
1396 :	parrello	1.287	while (<$fh>) {
1397 :			#
1398 :			# Mac:
1399 :			# inet 140.221.10.153 netmask 0xfffffc00 broadcast 140.221.11.255
1400 :			# Linux:
1401 :			# inet addr:140.221.34.37 Bcast:140.221.34.63 Mask:255.255.255.224
1402 :			#
1403 :
1404 :			chomp;
1405 :			s/^\s*//;
1406 :
1407 :			# print "Have '$_'\n";
1408 :			if (/inet\s+addr:(\d+\.\d+\.\d+\.\d+)\s+/) {
1409 :			#
1410 :			# Linux hit.
1411 :			#
1412 :			$ip = $1;
1413 :			# print "Got linux $ip\n";
1414 :			last;
1415 :			} elsif (/inet\s+(\d+\.\d+\.\d+\.\d+)\s+/) {
1416 :			#
1417 :			# Mac hit.
1418 :			#
1419 :			$ip = $1;
1420 :			# print "Got mac $ip\n";
1421 :			last;
1422 :			}
1423 :	olson	1.10	}
1424 :			close($fh);
1425 :
1426 :	parrello	1.287	if ($ip eq "") {
1427 :			warn "Didn't find an IP\n";
1428 :			return "localhost";
1429 :	olson	1.10	}
1430 :
1431 :			return $ip;
1432 :	efrank	1.1	}
1433 :
1434 :	parrello	1.213	=head3 get_seed_id
1435 :
1436 :	parrello	1.287	C<< my $id = FIG::get_seed_id(); >>
1437 :
1438 :			Return the Universally Unique ID for this SEED instance. If one
1439 :			does not exist, it will be created.
1440 :	parrello	1.213
1441 :			=cut
1442 :			#: Return type $;
1443 :	olson	1.38	sub get_seed_id {
1444 :			#
1445 :			# Retrieve the seed identifer from FIGdisk/config/seed_id.
1446 :			#
1447 :			# If it's not there, create one, and make it readonly.
1448 :			#
1449 :			my $id;
1450 :			my $id_file = "$FIG_Config::fig_disk/config/seed_id";
1451 :	parrello	1.287	if (! -f $id_file) {
1452 :			my $newid = `uuidgen`;
1453 :			if (!$newid) {
1454 :			die "Cannot run uuidgen: $!";
1455 :			}
1456 :	olson	1.38
1457 :	parrello	1.287	chomp($newid);
1458 :			my $fh = new FileHandle(">$id_file");
1459 :			if (!$fh) {
1460 :			die "error creating $id_file: $!";
1461 :			}
1462 :			print $fh "$newid\n";
1463 :			$fh->close();
1464 :			chmod(0444, $id_file);
1465 :	olson	1.38	}
1466 :			my $fh = new FileHandle("<$id_file");
1467 :			$id = <$fh>;
1468 :			chomp($id);
1469 :			return $id;
1470 :			}
1471 :
1472 :	parrello	1.287	=head3 get_release_info
1473 :	olson	1.155
1474 :	parrello	1.287	C<< my ($name, $id, $inst, $email, $parent_id, $description) = FIG::get_release_info(); >>
1475 :	olson	1.155
1476 :	parrello	1.287	Return the current data release information..
1477 :	olson	1.195
1478 :			The release info comes from the file FIG/Data/RELEASE. It is formatted as:
1479 :
1480 :	parrello	1.287	<release-name>
1481 :			<unique id>
1482 :			<institution>
1483 :			<contact email>
1484 :			<unique id of data release this release derived from>
1485 :			<description>
1486 :	olson	1.195
1487 :			For instance:
1488 :
1489 :	parrello	1.287	-----
1490 :			SEED Data Release, 09/15/2004.
1491 :			4148208C-1DF2-11D9-8417-000A95D52EF6
1492 :			ANL/FIG
1493 :			olson@mcs.anl.gov
1494 :
1495 :			Test release.
1496 :			-----
1497 :	olson	1.195
1498 :			If no RELEASE file exists, this routine will create one with a new unique ID. This
1499 :			lets a peer optimize the data transfer by being able to cache ID translations
1500 :			from this instance.
1501 :	olson	1.155
1502 :			=cut
1503 :	parrello	1.213	#: Return Type @;
1504 :	parrello	1.287	sub get_release_info {
1505 :	olson	1.196	my($fig, $no_create) = @_;
1506 :	olson	1.195
1507 :			my $rel_file = "$FIG_Config::data/RELEASE";
1508 :
1509 :	parrello	1.287	if (! -f $rel_file and !$no_create) {
1510 :	parrello	1.298	#
1511 :			# Create a new one.
1512 :			#
1513 :	olson	1.195
1514 :	parrello	1.287	my $newid = `uuidgen`;
1515 :			if (!$newid) {
1516 :			die "Cannot run uuidgen: $!";
1517 :			}
1518 :	olson	1.195
1519 :	parrello	1.287	chomp($newid);
1520 :	olson	1.195
1521 :	parrello	1.287	my $relinfo = "Automatically generated release info " . localtime();
1522 :			my $inst = "Unknown";
1523 :			my $contact = "Unknown";
1524 :			my $parent = "";
1525 :			my( $a, $b, $e, $v, $env ) = $fig->genome_counts;
1526 :			my $description = "Automatically generated release info\n";
1527 :			$description .= "Contains $a archaeal, $b bacterial, $e eukaryal, $v viral and $env environmental genomes.\n";
1528 :
1529 :			my $fh = new FileHandle(">$rel_file");
1530 :			if (!$fh) {
1531 :			warn "error creating $rel_file: $!";
1532 :			return undef;
1533 :			}
1534 :			print $fh "$relinfo\n";
1535 :			print $fh "$newid\n";
1536 :			print $fh "$inst\n";
1537 :			print $fh "$contact\n";
1538 :			print $fh "$parent\n";
1539 :			print $fh $description;
1540 :			$fh->close();
1541 :			chmod(0444, $rel_file);
1542 :	olson	1.195	}
1543 :
1544 :	parrello	1.287	if (open(my $fh, $rel_file)) {
1545 :			my(@lines) = <$fh>;
1546 :			close($fh);
1547 :	parrello	1.200
1548 :	parrello	1.287	chomp(@lines);
1549 :	parrello	1.200
1550 :	parrello	1.287	my($info, $id, $inst, $contact, $parent, @desc) = @lines;
1551 :	olson	1.195
1552 :	parrello	1.287	return ($info, $id, $inst, $contact, $parent, join("\n", @desc));
1553 :	olson	1.195	}
1554 :	olson	1.155
1555 :			return undef;
1556 :			}
1557 :
1558 :	parrello	1.287	=head3 get_peer_last_update
1559 :	olson	1.155
1560 :	parrello	1.287	C<< my $date = $fig->get_peer_last_update($peer_id); >>
1561 :	parrello	1.213
1562 :	olson	1.155	Return the timestamp from the last successful peer-to-peer update with
1563 :	parrello	1.287	the given peer. If the specified peer has made updates, comparing this
1564 :			timestamp to the timestamp of the updates can tell you whether or not
1565 :			the updates have been integrated into your SEED data store.
1566 :	olson	1.155
1567 :			We store this information in FIG/Data/Global/Peers/<peer-id>.
1568 :
1569 :	parrello	1.287	=over 4
1570 :
1571 :			=item peer_id
1572 :
1573 :			Universally Unique ID for the desired peer.
1574 :
1575 :			=item RETURN
1576 :
1577 :			Returns the date/time stamp for the last peer-to-peer updated performed
1578 :			with the identified SEED instance.
1579 :
1580 :			=back
1581 :
1582 :	olson	1.155	=cut
1583 :	parrello	1.213	#: Return Type $;
1584 :	parrello	1.287	sub get_peer_last_update {
1585 :	olson	1.155	my($self, $peer_id) = @_;
1586 :
1587 :			my $dir = "$FIG_Config::data/Global/Peers";
1588 :			&verify_dir($dir);
1589 :			$dir .= "/$peer_id";
1590 :			&verify_dir($dir);
1591 :
1592 :			my $update_file = "$dir/last_update";
1593 :	parrello	1.287	if (-f $update_file) {
1594 :			my $time = file_head($update_file, 1);
1595 :			chomp $time;
1596 :			return $time;
1597 :			} else {
1598 :			return undef;
1599 :	olson	1.155	}
1600 :			}
1601 :
1602 :	parrello	1.287	=head3 set_peer_last_update
1603 :	parrello	1.213
1604 :	parrello	1.287	C<< $fig->set_peer_last_update($peer_id, $time); >>
1605 :	parrello	1.213
1606 :	parrello	1.287	Manually set the update timestamp for a specified peer. This informs
1607 :			the SEED that you have all of the assignments and updates from a
1608 :			particular SEED instance as of a certain date.
1609 :	parrello	1.213
1610 :			=cut
1611 :			#: Return Type ;
1612 :
1613 :	parrello	1.287	sub set_peer_last_update {
1614 :	olson	1.155	my($self, $peer_id, $time) = @_;
1615 :
1616 :			my $dir = "$FIG_Config::data/Global/Peers";
1617 :			&verify_dir($dir);
1618 :			$dir .= "/$peer_id";
1619 :			&verify_dir($dir);
1620 :
1621 :			my $update_file = "$dir/last_update";
1622 :			open(F, ">$update_file");
1623 :			print F "$time\n";
1624 :			close(F);
1625 :			}
1626 :
1627 :	redwards	1.302	=head3 clean_spaces
1628 :
1629 :			Remove any extra spaces from input fields. This will (currently) remove ^\s, \s$, and concatenate multiple spaces into one.
1630 :
1631 :			my $input=$fig->clean_spaces($cgi->param('input'));
1632 :
1633 :			=cut
1634 :
1635 :			sub clean_spaces
1636 :			{
1637 :			my ($self, $s)=@_;
1638 :			# note at the moment I do not use \s because that recognizes \t and \n too. This should only remove multiple spaces.
1639 :			$s =~ s/^ +//;
1640 :			$s =~ s/ +$//;
1641 :			$s =~ s/ +/ /g;
1642 :			return $s;
1643 :			}
1644 :
1645 :
1646 :
1647 :	parrello	1.213	=head3 cgi_url
1648 :
1649 :	parrello	1.287	C<< my $url = FIG::$fig->cgi_url(); >>
1650 :
1651 :			Return the URL for the CGI script directory.
1652 :	parrello	1.213
1653 :			=cut
1654 :			#: Return Type $;
1655 :	efrank	1.1	sub cgi_url {
1656 :			return &plug_url($FIG_Config::cgi_url);
1657 :			}
1658 :	parrello	1.200
1659 :	parrello	1.213	=head3 temp_url
1660 :
1661 :	parrello	1.287	C<< my $url = FIG::temp_url(); >>
1662 :
1663 :			Return the URL of the temporary file directory.
1664 :	parrello	1.213
1665 :			=cut
1666 :			#: Return Type $;
1667 :	efrank	1.1	sub temp_url {
1668 :			return &plug_url($FIG_Config::temp_url);
1669 :			}
1670 :	parrello	1.200
1671 :	parrello	1.213	=head3 plug_url
1672 :
1673 :	parrello	1.287	C<< my $url2 = $fig->plug_url($url); >>
1674 :
1675 :			or
1676 :
1677 :			C<< my $url2 = $fig->plug_url($url); >>
1678 :
1679 :			Change the domain portion of a URL to point to the current domain. This essentially
1680 :			relocates URLs into the current environment.
1681 :
1682 :			=over 4
1683 :
1684 :			=item url
1685 :
1686 :			URL to relocate.
1687 :
1688 :			=item RETURN
1689 :
1690 :			Returns a new URL with the base portion converted to the current operating host.
1691 :			If the URL does not begin with C<http://>, the URL will be returned unmodified.
1692 :
1693 :			=back
1694 :	parrello	1.213
1695 :			=cut
1696 :			#: Return Type $;
1697 :	efrank	1.1	sub plug_url {
1698 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1699 :	efrank	1.1	my($url) = @_;
1700 :
1701 :	golsen	1.44	my $name;
1702 :
1703 :			# Revised by GJO
1704 :			# First try to get url from the current http request
1705 :
1706 :			if ( defined( $ENV{ 'HTTP_HOST' } ) # This is where $cgi->url gets its value
1707 :			&& ( $name = $ENV{ 'HTTP_HOST' } )
1708 :			&& ( $url =~ s~^http://[^/]*~http://$name~ ) # ~ is delimiter
1709 :			) {}
1710 :
1711 :			# Otherwise resort to alternative sources
1712 :
1713 :			elsif ( ( $name = &get_local_hostname )
1714 :			&& ( $url =~ s~^http://[^/]*~http://$name~ ) # ~ is delimiter
1715 :			) {}
1716 :
1717 :	efrank	1.1	return $url;
1718 :			}
1719 :
1720 :	parrello	1.213	=head3 file_read
1721 :
1722 :	parrello	1.287	C<< my $text = $fig->file_read($fileName); >>
1723 :
1724 :			or
1725 :
1726 :			C<< my @lines = $fig->file_read($fileName); >>
1727 :
1728 :			or
1729 :
1730 :			C<< my $text = FIG::file_read($fileName); >>
1731 :
1732 :			or
1733 :
1734 :			C<< my @lines = FIG::file_read($fileName); >>
1735 :
1736 :			Read an entire file into memory. In a scalar context, the file is returned
1737 :			as a single text string with line delimiters included. In a list context, the
1738 :			file is returned as a list of lines, each line terminated by a line
1739 :			delimiter. (For a method that automatically strips the line delimiters,
1740 :			use C<Tracer::GetFile>.)
1741 :
1742 :			=over 4
1743 :
1744 :			=item fileName
1745 :
1746 :			Fully-qualified name of the file to read.
1747 :
1748 :			=item RETURN
1749 :
1750 :			In a list context, returns a list of the file lines. In a scalar context, returns
1751 :			a string containing all the lines of the file with delimiters included.
1752 :	parrello	1.213
1753 :	parrello	1.287	=back
1754 :	parrello	1.213
1755 :			=cut
1756 :			#: Return Type $;
1757 :			#: Return Type @;
1758 :	parrello	1.287	sub file_read {
1759 :
1760 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1761 :	parrello	1.287	my($fileName) = @_;
1762 :			return file_head($fileName, '*');
1763 :	olson	1.90
1764 :			}
1765 :
1766 :
1767 :	parrello	1.213	=head3 file_head
1768 :
1769 :	parrello	1.287	C<< my $text = $fig->file_head($fileName, $count); >>
1770 :
1771 :			or
1772 :
1773 :			C<< my @lines = $fig->file_head($fileName, $count); >>
1774 :	parrello	1.213
1775 :	parrello	1.287	or
1776 :	parrello	1.213
1777 :	parrello	1.287	C<< my $text = FIG::file_head($fileName, $count); >>
1778 :	olson	1.90
1779 :	parrello	1.287	or
1780 :	olson	1.90
1781 :	parrello	1.287	C<< my @lines = FIG::file_head($fileName, $count); >>
1782 :	olson	1.90
1783 :	parrello	1.287	Read a portion of a file into memory. In a scalar context, the file portion is
1784 :			returned as a single text string with line delimiters included. In a list
1785 :			context, the file portion is returned as a list of lines, each line terminated
1786 :			by a line delimiter.
1787 :	olson	1.155
1788 :	parrello	1.287	=over 4
1789 :	olson	1.90
1790 :	parrello	1.287	=item fileName
1791 :	olson	1.90
1792 :	parrello	1.287	Fully-qualified name of the file to read.
1793 :	efrank	1.1
1794 :	parrello	1.287	=item count (optional)
1795 :	efrank	1.1
1796 :	parrello	1.287	Number of lines to read from the file. If omitted, C<1> is assumed. If the
1797 :			non-numeric string C<*> is specified, the entire file will be read.
1798 :	efrank	1.1
1799 :	parrello	1.287	=item RETURN
1800 :	efrank	1.1
1801 :	parrello	1.287	In a list context, returns a list of the desired file lines. In a scalar context, returns
1802 :			a string containing the desired lines of the file with delimiters included.
1803 :	efrank	1.1
1804 :	parrello	1.287	=back
1805 :	efrank	1.1
1806 :			=cut
1807 :	parrello	1.287	#: Return Type $;
1808 :			#: Return Type @;
1809 :			sub file_head {
1810 :	efrank	1.1
1811 :	parrello	1.287	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1812 :			my($file, $count) = @_;
1813 :	efrank	1.1
1814 :	parrello	1.287	my ($n, $allFlag);
1815 :			if ($count eq '*') {
1816 :	olson	1.304	Trace("Full file read for \"$file\".") if T(3);
1817 :	parrello	1.287	$allFlag = 1;
1818 :			$n = 0;
1819 :			} else {
1820 :			$allFlag = 0;
1821 :			$n = (!$count ? 1 : $count);
1822 :	olson	1.304	Trace("Reading $n record(s) from \"$file\".") if T(3);
1823 :	parrello	1.287	}
1824 :	efrank	1.1
1825 :	parrello	1.287	if (open(my $fh, "<$file")) {
1826 :	parrello	1.298	my(@ret, $i);
1827 :	parrello	1.287	$i = 0;
1828 :			while (<$fh>) {
1829 :			push(@ret, $_);
1830 :			$i++;
1831 :			last if !$allFlag && $i >= $n;
1832 :			}
1833 :			close($fh);
1834 :			if (wantarray) {
1835 :			return @ret;
1836 :			} else {
1837 :			return join("", @ret);
1838 :			}
1839 :	efrank	1.1	}
1840 :			}
1841 :
1842 :			################ Basic Routines [ existed since WIT ] ##########################
1843 :
1844 :	parrello	1.287	=head3 min
1845 :
1846 :			C<< my $min = FIG::min(@x); >>
1847 :
1848 :			or
1849 :
1850 :			C<< my $min = $fig->min(@x); >>
1851 :
1852 :			Return the minimum numeric value from a list.
1853 :
1854 :			=over 4
1855 :
1856 :			=item x1, x2, ... xN
1857 :	efrank	1.1
1858 :	parrello	1.287	List of numbers to process.
1859 :	efrank	1.1
1860 :	parrello	1.287	=item RETURN
1861 :	efrank	1.1
1862 :	parrello	1.287	Returns the numeric value of the list entry possessing the lowest value. Returns
1863 :			C<undef> if the list is empty.
1864 :	efrank	1.1
1865 :	parrello	1.287	=back
1866 :	efrank	1.1
1867 :			=cut
1868 :	parrello	1.213	#: Return Type $;
1869 :	efrank	1.1	sub min {
1870 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1871 :	efrank	1.1	my(@x) = @_;
1872 :			my($min,$i);
1873 :
1874 :			(@x > 0) \|\| return undef;
1875 :			$min = $x[0];
1876 :	parrello	1.287	for ($i=1; ($i < @x); $i++) {
1877 :			$min = ($min > $x[$i]) ? $x[$i] : $min;
1878 :	efrank	1.1	}
1879 :			return $min;
1880 :			}
1881 :
1882 :	parrello	1.287	=head3 max
1883 :
1884 :			C<< my $max = FIG::max(@x); >>
1885 :
1886 :			or
1887 :
1888 :			C<< my $max = $fig->max(@x); >>
1889 :	efrank	1.1
1890 :	parrello	1.287	Return the maximum numeric value from a list.
1891 :	efrank	1.1
1892 :	parrello	1.287	=over 4
1893 :
1894 :			=item x1, x2, ... xN
1895 :
1896 :			List of numbers to process.
1897 :
1898 :			=item RETURN
1899 :
1900 :			Returns the numeric value of t/he list entry possessing the highest value. Returns
1901 :			C<undef> if the list is empty.
1902 :	efrank	1.1
1903 :	parrello	1.287	=back
1904 :	efrank	1.1
1905 :			=cut
1906 :	parrello	1.213	#: Return Type $;
1907 :	efrank	1.1	sub max {
1908 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1909 :	efrank	1.1	my(@x) = @_;
1910 :			my($max,$i);
1911 :
1912 :			(@x > 0) \|\| return undef;
1913 :			$max = $x[0];
1914 :	parrello	1.287	for ($i=1; ($i < @x); $i++) {
1915 :			$max = ($max < $x[$i]) ? $x[$i] : $max;
1916 :	efrank	1.1	}
1917 :			return $max;
1918 :			}
1919 :
1920 :	parrello	1.287	=head3 between
1921 :	efrank	1.1
1922 :	parrello	1.287	C<< my $flag = FIG::between($x, $y, $z); >>
1923 :	efrank	1.1
1924 :	parrello	1.287	or
1925 :
1926 :			C<< my $flag = $fig->between($x, $y, $z); >>
1927 :
1928 :			Determine whether or not $y is between $x and $z.
1929 :
1930 :			=over 4
1931 :
1932 :			=item x
1933 :
1934 :			First edge number.
1935 :
1936 :			=item y
1937 :	efrank	1.1
1938 :	parrello	1.287	Number to examine.
1939 :
1940 :			=item z
1941 :
1942 :			Second edge number.
1943 :
1944 :			=item RETURN
1945 :
1946 :			Return TRUE if the number I<$y> is between the numbers I<$x> and I<$z>. The check
1947 :			is inclusive (that is, if I<$y> is equal to I<$x> or I<$z> the function returns
1948 :			TRUE), and the order of I<$x> and I<$z> does not matter. If I<$x> is lower than
1949 :			I<$z>, then the return is TRUE if I<$x> <= I<$y> <= I<$z>. If I<$z> is lower,
1950 :			then the return is TRUE if I<$x> >= I$<$y> >= I<$z>.
1951 :
1952 :			=back
1953 :	efrank	1.1
1954 :			=cut
1955 :	parrello	1.213	#: Return Type $;
1956 :	efrank	1.1	sub between {
1957 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1958 :	efrank	1.1	my($x,$y,$z) = @_;
1959 :
1960 :	parrello	1.287	if ($x < $z) {
1961 :			return (($x <= $y) && ($y <= $z));
1962 :			} else {
1963 :			return (($x >= $y) && ($y >= $z));
1964 :	efrank	1.1	}
1965 :			}
1966 :
1967 :	parrello	1.287	=head3 standard_genetic_code
1968 :	efrank	1.1
1969 :	parrello	1.287	C<< my $code = FIG::standard_genetic_code(); >>
1970 :	efrank	1.1
1971 :	parrello	1.287	Return a hash containing the standard translation of nucleotide triples to proteins.
1972 :			Methods such as L</translate> can take a translation scheme as a parameter. This method
1973 :			returns the default translation scheme. The scheme is implemented as a reference to a
1974 :			hash that contains nucleotide triplets as keys and has protein letters as values.
1975 :	efrank	1.1
1976 :			=cut
1977 :	parrello	1.213	#: Return Type $;
1978 :	efrank	1.1	sub standard_genetic_code {
1979 :	parrello	1.200
1980 :	efrank	1.1	my $code = {};
1981 :
1982 :			$code->{"AAA"} = "K";
1983 :			$code->{"AAC"} = "N";
1984 :			$code->{"AAG"} = "K";
1985 :			$code->{"AAT"} = "N";
1986 :			$code->{"ACA"} = "T";
1987 :			$code->{"ACC"} = "T";
1988 :			$code->{"ACG"} = "T";
1989 :			$code->{"ACT"} = "T";
1990 :			$code->{"AGA"} = "R";
1991 :			$code->{"AGC"} = "S";
1992 :			$code->{"AGG"} = "R";
1993 :			$code->{"AGT"} = "S";
1994 :			$code->{"ATA"} = "I";
1995 :			$code->{"ATC"} = "I";
1996 :			$code->{"ATG"} = "M";
1997 :			$code->{"ATT"} = "I";
1998 :			$code->{"CAA"} = "Q";
1999 :			$code->{"CAC"} = "H";
2000 :			$code->{"CAG"} = "Q";
2001 :			$code->{"CAT"} = "H";
2002 :			$code->{"CCA"} = "P";
2003 :			$code->{"CCC"} = "P";
2004 :			$code->{"CCG"} = "P";
2005 :			$code->{"CCT"} = "P";
2006 :			$code->{"CGA"} = "R";
2007 :			$code->{"CGC"} = "R";
2008 :			$code->{"CGG"} = "R";
2009 :			$code->{"CGT"} = "R";
2010 :			$code->{"CTA"} = "L";
2011 :			$code->{"CTC"} = "L";
2012 :			$code->{"CTG"} = "L";
2013 :			$code->{"CTT"} = "L";
2014 :			$code->{"GAA"} = "E";
2015 :			$code->{"GAC"} = "D";
2016 :			$code->{"GAG"} = "E";
2017 :			$code->{"GAT"} = "D";
2018 :			$code->{"GCA"} = "A";
2019 :			$code->{"GCC"} = "A";
2020 :			$code->{"GCG"} = "A";
2021 :			$code->{"GCT"} = "A";
2022 :			$code->{"GGA"} = "G";
2023 :			$code->{"GGC"} = "G";
2024 :			$code->{"GGG"} = "G";
2025 :			$code->{"GGT"} = "G";
2026 :			$code->{"GTA"} = "V";
2027 :			$code->{"GTC"} = "V";
2028 :			$code->{"GTG"} = "V";
2029 :			$code->{"GTT"} = "V";
2030 :			$code->{"TAA"} = "*";
2031 :			$code->{"TAC"} = "Y";
2032 :			$code->{"TAG"} = "*";
2033 :			$code->{"TAT"} = "Y";
2034 :			$code->{"TCA"} = "S";
2035 :			$code->{"TCC"} = "S";
2036 :			$code->{"TCG"} = "S";
2037 :			$code->{"TCT"} = "S";
2038 :			$code->{"TGA"} = "*";
2039 :			$code->{"TGC"} = "C";
2040 :			$code->{"TGG"} = "W";
2041 :			$code->{"TGT"} = "C";
2042 :			$code->{"TTA"} = "L";
2043 :			$code->{"TTC"} = "F";
2044 :			$code->{"TTG"} = "L";
2045 :			$code->{"TTT"} = "F";
2046 :	parrello	1.200
2047 :	efrank	1.1	return $code;
2048 :			}
2049 :
2050 :	parrello	1.287	=head3 translate
2051 :
2052 :			C<< my $aa_seq = &FIG::translate($dna_seq, $code, $fix_start); >>
2053 :
2054 :			Translate a DNA sequence to a protein sequence using the specified genetic code.
2055 :			If I<$fix_start> is TRUE, will translate an initial C<TTG> or C<GTG> code to
2056 :			C<M>. (In the standard genetic code, these two combinations normally translate
2057 :			to C<V> and C<L>, respectively.)
2058 :
2059 :			=over 4
2060 :	efrank	1.1
2061 :	parrello	1.287	=item dna_seq
2062 :	efrank	1.1
2063 :	parrello	1.287	DNA sequence to translate. Note that the DNA sequence can only contain
2064 :			known nucleotides.
2065 :	efrank	1.1
2066 :	parrello	1.287	=item code
2067 :	efrank	1.1
2068 :	parrello	1.287	Reference to a hash specifying the translation code. The hash is keyed by
2069 :			nucleotide triples, and the value for each key is the corresponding protein
2070 :			letter. If this parameter is omitted, the L</standard_genetic_code> will be
2071 :			used.
2072 :	efrank	1.1
2073 :	parrello	1.287	=item fix_start
2074 :
2075 :			TRUE if the first triple is to get special treatment, else FALSE. If TRUE,
2076 :			then a value of C<TTG> or C<GTG> in the first position will be translated to
2077 :			C<M> instead of the value specified in the translation code.
2078 :
2079 :			=item RETURN
2080 :
2081 :			Returns a string resulting from translating each nucleotide triple into a
2082 :			protein letter.
2083 :
2084 :			=back
2085 :
2086 :			=cut
2087 :			#: Return Type $;
2088 :			sub translate {
2089 :			shift if UNIVERSAL::isa($_[0],__PACKAGE__);
2090 :
2091 :			my( $dna,$code,$start ) = @_;
2092 :			my( $i,$j,$ln );
2093 :			my( $x,$y );
2094 :			my( $prot );
2095 :
2096 :			if (! defined($code)) {
2097 :			$code = &FIG::standard_genetic_code;
2098 :	efrank	1.1	}
2099 :			$ln = length($dna);
2100 :			$prot = "X" x ($ln/3);
2101 :			$dna =~ tr/a-z/A-Z/;
2102 :
2103 :	parrello	1.287	for ($i=0,$j=0; ($i < ($ln-2)); $i += 3,$j++) {
2104 :			$x = substr($dna,$i,3);
2105 :			if ($y = $code->{$x}) {
2106 :			substr($prot,$j,1) = $y;
2107 :	efrank	1.1	}
2108 :			}
2109 :	parrello	1.200
2110 :	parrello	1.287	if (($start) && ($ln >= 3) && (substr($dna,0,3) =~ /^[GT]TG$/)) {
2111 :			substr($prot,0,1) = 'M';
2112 :	efrank	1.1	}
2113 :			return $prot;
2114 :			}
2115 :
2116 :	parrello	1.287	=head3 reverse_comp
2117 :
2118 :			C<< my $dnaR = FIG::reverse_comp($dna); >>
2119 :
2120 :			or
2121 :
2122 :			C<< my $dnaR = $fig->reverse_comp($dna); >>
2123 :
2124 :			Return the reverse complement os the specified DNA sequence.
2125 :	efrank	1.1
2126 :	parrello	1.287	NOTE: for extremely long DNA strings, use L</rev_comp>, which allows you to
2127 :			pass the strings around in the form of pointers.
2128 :	efrank	1.1
2129 :	parrello	1.287	=over 4
2130 :
2131 :			=item dna
2132 :	efrank	1.1
2133 :	parrello	1.287	DNA sequence whose reverse complement is desired.
2134 :
2135 :			=item RETURN
2136 :
2137 :			Returns the reverse complement of the incoming DNA sequence.
2138 :
2139 :			=back
2140 :	efrank	1.1
2141 :			=cut
2142 :	parrello	1.213	#: Return Type $;
2143 :	efrank	1.1	sub reverse_comp {
2144 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
2145 :	efrank	1.1	my($seq) = @_;
2146 :
2147 :			return ${&rev_comp(\$seq)};
2148 :			}
2149 :
2150 :	parrello	1.287	=head3 rev_comp
2151 :
2152 :			C<< my $dnaRP = FIG::rev_comp(\$dna); >>
2153 :
2154 :			or
2155 :
2156 :			C<< my $dnaRP = $fig->rev_comp(\$dna); >>
2157 :
2158 :			Return the reverse complement of the specified DNA sequence. The DNA sequence
2159 :			is passed in as a string reference rather than a raw string for performance
2160 :			reasons. If this is unnecessary, use L</reverse_comp>, which processes strings
2161 :			instead of references to strings.
2162 :
2163 :			=over 4
2164 :
2165 :			=item dna
2166 :
2167 :			Reference to the DNA sequence whose reverse complement is desired.
2168 :
2169 :			=item RETURN
2170 :
2171 :			Returns a reference to the reverse complement of the incoming DNA sequence.
2172 :
2173 :			=back
2174 :	parrello	1.213
2175 :			=cut
2176 :			#: Return Type $;
2177 :	efrank	1.1	sub rev_comp {
2178 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
2179 :	efrank	1.1	my( $seqP ) = @_;
2180 :			my( $rev );
2181 :
2182 :			$rev = reverse( $$seqP );
2183 :			$rev =~ tr/a-z/A-Z/;
2184 :			$rev =~ tr/ACGTUMRWSYKBDHV/TGCAAKYWSRMVHDB/;
2185 :			return \$rev;
2186 :			}
2187 :
2188 :	parrello	1.287	=head3 verify_dir
2189 :
2190 :			C<< FIG::verify_dir($dir); >>
2191 :	efrank	1.1
2192 :	parrello	1.287	or
2193 :	efrank	1.1
2194 :	parrello	1.287	C<< $fig->verify_dir($dir); >>
2195 :	efrank	1.1
2196 :	parrello	1.287	Insure that the specified directory exists. If it must be created, the permissions will
2197 :			be set to C<0777>.
2198 :	efrank	1.1
2199 :			=cut
2200 :
2201 :			sub verify_dir {
2202 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
2203 :	efrank	1.1	my($dir) = @_;
2204 :
2205 :	parrello	1.287	if (-d $dir) {
2206 :			return
2207 :			}
2208 :			if ($dir =~ /^(.*)\/[^\/]+$/) {
2209 :			&verify_dir($1);
2210 :	efrank	1.1	}
2211 :	parrello	1.287	mkdir($dir,0777) \|\| Confess("Could not make directory $dir: $!");
2212 :	efrank	1.1	}
2213 :
2214 :	parrello	1.287	=head3 run
2215 :	efrank	1.1
2216 :	parrello	1.287	C<< FIG::run($cmd); >>
2217 :	overbeek	1.283
2218 :	parrello	1.287	or
2219 :
2220 :			C<< $fig->run($cmd); >>
2221 :	overbeek	1.283
2222 :	parrello	1.287	Run a command. If the command fails, the error will be traced.
2223 :	overbeek	1.283
2224 :			=cut
2225 :
2226 :	parrello	1.287	sub run {
2227 :			shift if UNIVERSAL::isa($_[0],__PACKAGE__);
2228 :			my($cmd) = @_;
2229 :
2230 :			if ($ENV{VERBOSE}) {
2231 :			my @tmp = `date`;
2232 :			chomp @tmp;
2233 :			print STDERR "$tmp[0]: running $cmd\n";
2234 :			}
2235 :			Trace("Running command: $cmd") if T(3);
2236 :			(system($cmd) == 0) \|\| Confess("FAILED: $cmd");
2237 :			}
2238 :
2239 :			=head3 augment_path
2240 :
2241 :			C<< FIG::augment_path($dirName); >>
2242 :	overbeek	1.283
2243 :	parrello	1.287	Add a directory to the system path.
2244 :	overbeek	1.283
2245 :	parrello	1.287	This method adds a new directory to the front of the system path. It looks in the
2246 :			configuration file to determine whether this is Windows or Unix, and uses the
2247 :			appropriate separator.
2248 :	efrank	1.1
2249 :	parrello	1.287	=over 4
2250 :	efrank	1.1
2251 :	parrello	1.287	=item dirName
2252 :
2253 :			Name of the directory to add to the path.
2254 :
2255 :			=back
2256 :	efrank	1.1
2257 :			=cut
2258 :
2259 :	parrello	1.287	sub augment_path {
2260 :			my ($dirName) = @_;
2261 :			if ($FIG_Config::win_mode) {
2262 :			$ENV{PATH} = "$dirName;$ENV{PATH}";
2263 :			} else {
2264 :			$ENV{PATH} = "$dirName:$ENV{PATH}";
2265 :	overbeek	1.278	}
2266 :	efrank	1.1	}
2267 :
2268 :	parrello	1.287	=head3 read_fasta_record
2269 :	gdpusch	1.45
2270 :	parrello	1.287	C<< my ($seq_id, $seq_pointer, $comment) = FIG::read_fasta_record(\*FILEHANDLE); >>
2271 :	gdpusch	1.45
2272 :	parrello	1.287	or
2273 :	gdpusch	1.45
2274 :	parrello	1.287	C<< my ($seq_id, $seq_pointer, $comment) = $fig->read_fasta_record(\*FILEHANDLE); >>
2275 :	gdpusch	1.45
2276 :	parrello	1.287	Read and parse the next logical record of a FASTA file. A FASTA logical record
2277 :			consists of multiple lines of text. The first line begins with a C<< > >> symbol
2278 :			and contains the sequence ID followed by an optional comment. (NOTE: comments
2279 :			are currently deprecated, because not all tools handle them properly.) The
2280 :			remaining lines contain the sequence data.
2281 :
2282 :			This method uses a trick to smooth its operation: the line terminator character
2283 :			is temporarily changed to C<< \n> >> so that a single read operation brings in
2284 :			the entire logical record.
2285 :	gdpusch	1.45
2286 :	parrello	1.287	=over 4
2287 :	gdpusch	1.45
2288 :	parrello	1.287	=item FILEHANDLE
2289 :	gdpusch	1.45
2290 :	parrello	1.287	Open handle of the FASTA file. If not specified, C<STDIN> is assumed.
2291 :
2292 :			=item RETURN
2293 :
2294 :			If we are at the end of the file, returns C<undef>. Otherwise, returns a
2295 :			three-element list. The first element is the sequence ID, the second is
2296 :			a pointer to the sequence data (that is, a string reference as opposed to
2297 :			as string), and the third is the comment.
2298 :
2299 :			=back
2300 :	gdpusch	1.45
2301 :			=cut
2302 :	parrello	1.213	#: Return Type @;
2303 :	parrello	1.287	sub read_fasta_record {
2304 :
2305 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
2306 :	gdpusch	1.45	my ($file_handle) = @_;
2307 :	parrello	1.287	my ($old_end_of_record, $fasta_record, @lines, $head, $sequence, $seq_id, $comment, @parsed_fasta_record);
2308 :	parrello	1.200
2309 :	gdpusch	1.45	if (not defined($file_handle)) { $file_handle = \*STDIN; }
2310 :	parrello	1.200
2311 :	gdpusch	1.45	$old_end_of_record = $/;
2312 :			$/ = "\n>";
2313 :	parrello	1.200
2314 :	parrello	1.287	if (defined($fasta_record = <$file_handle>)) {
2315 :			chomp $fasta_record;
2316 :			@lines = split( /\n/, $fasta_record );
2317 :			$head = shift @lines;
2318 :			$head =~ s/^>?//;
2319 :			$head =~ m/^(\S+)/;
2320 :			$seq_id = $1;
2321 :			if ($head =~ m/^\S+\s+(.*)$/) { $comment = $1; } else { $comment = ""; }
2322 :			$sequence = join( "", @lines );
2323 :			@parsed_fasta_record = ( $seq_id, \$sequence, $comment );
2324 :			} else {
2325 :			@parsed_fasta_record = ();
2326 :	gdpusch	1.45	}
2327 :	parrello	1.200
2328 :	gdpusch	1.45	$/ = $old_end_of_record;
2329 :	parrello	1.200
2330 :	gdpusch	1.45	return @parsed_fasta_record;
2331 :			}
2332 :
2333 :	parrello	1.287	=head3 display_id_and_seq
2334 :
2335 :			C<< FIG::display_id_and_seq($id_and_comment, $seqP, $fh); >>
2336 :
2337 :			or
2338 :
2339 :			C<< $fig->display_id_and_seq($id_and_comment, $seqP, $fh); >>
2340 :
2341 :			Display a fasta ID and sequence to the specified open file. This method is designed
2342 :			to work well with L</read_fasta_sequence> and L</rev_comp>, because it takes as
2343 :			input a string pointer rather than a string. If the file handle is omitted it
2344 :			defaults to STDOUT.
2345 :
2346 :			The output is formatted into a FASTA record. The first line of the output is
2347 :			preceded by a C<< > >> symbol, and the sequence is split into 60-character
2348 :			chunks displayed one per line. Thus, this method can be used to produce
2349 :			FASTA files from data gathered by the rest of the system.
2350 :
2351 :			=over 4
2352 :
2353 :			=item id_and_comment
2354 :
2355 :			The sequence ID and (optionally) the comment from the sequence's FASTA record.
2356 :			The ID
2357 :	gdpusch	1.45
2358 :	parrello	1.287	=item seqP
2359 :	efrank	1.1
2360 :	parrello	1.287	Reference to a string containing the sequence. The sequence is automatically
2361 :			formatted into 60-character chunks displayed one per line.
2362 :	efrank	1.1
2363 :	parrello	1.287	=item fh
2364 :	efrank	1.1
2365 :	parrello	1.287	Open file handle to which the ID and sequence should be output. If omitted,
2366 :			C<STDOUT> is assumed.
2367 :
2368 :			=back
2369 :	efrank	1.1
2370 :			=cut
2371 :
2372 :	parrello	1.287	sub display_id_and_seq {
2373 :	mkubal	1.53
2374 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
2375 :	parrello	1.287
2376 :	efrank	1.1	my( $id, $seq, $fh ) = @_;
2377 :	parrello	1.200
2378 :	efrank	1.1	if (! defined($fh) ) { $fh = \*STDOUT; }
2379 :	parrello	1.200
2380 :	efrank	1.1	print $fh ">$id\n";
2381 :			&display_seq($seq, $fh);
2382 :			}
2383 :
2384 :	parrello	1.287	=head3 display_id_and_seq
2385 :
2386 :			C<< FIG::display_seq($seqP, $fh); >>
2387 :
2388 :			or
2389 :
2390 :			C<< $fig->display_seq($seqP, $fh); >>
2391 :
2392 :			Display a fasta sequence to the specified open file. This method is designed
2393 :			to work well with L</read_fasta_sequence> and L</rev_comp>, because it takes as
2394 :			input a string pointer rather than a string. If the file handle is omitted it
2395 :			defaults to STDOUT.
2396 :
2397 :			The sequence is split into 60-character chunks displayed one per line for
2398 :			readability.
2399 :
2400 :			=over 4
2401 :
2402 :			=item seqP
2403 :
2404 :			Reference to a string containing the sequence.
2405 :
2406 :			=item fh
2407 :
2408 :			Open file handle to which the sequence should be output. If omitted,
2409 :			C<STDOUT> is assumed.
2410 :
2411 :			=back
2412 :
2413 :			=cut
2414 :
2415 :	efrank	1.1	sub display_seq {
2416 :	parrello	1.287
2417 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
2418 :	parrello	1.287
2419 :	efrank	1.1	my ( $seq, $fh ) = @_;
2420 :			my ( $i, $n, $ln );
2421 :	parrello	1.200
2422 :	efrank	1.1	if (! defined($fh) ) { $fh = \*STDOUT; }
2423 :
2424 :			$n = length($$seq);
2425 :			# confess "zero-length sequence ???" if ( (! defined($n)) \|\| ($n == 0) );
2426 :	parrello	1.287	for ($i=0; ($i < $n); $i += 60) {
2427 :			if (($i + 60) <= $n) {
2428 :			$ln = substr($$seq,$i,60);
2429 :			} else {
2430 :			$ln = substr($$seq,$i,($n-$i));
2431 :			}
2432 :			print $fh "$ln\n";
2433 :	efrank	1.1	}
2434 :			}
2435 :
2436 :			########## I commented the pods on the following routines out, since they should not
2437 :			########## be part of the SOAP/WSTL interface
2438 :			#=pod
2439 :			#
2440 :	parrello	1.287	#=head3 file2N
2441 :	efrank	1.1	#
2442 :			#usage: $n = $fig->file2N($file)
2443 :			#
2444 :			#In some of the databases I need to store filenames, which can waste a lot of
2445 :			#space. Hence, I maintain a database for converting filenames to/from integers.
2446 :			#
2447 :			#=cut
2448 :			#
2449 :	olson	1.111	sub file2N :scalar {
2450 :	efrank	1.1	my($self,$file) = @_;
2451 :			my($relational_db_response);
2452 :
2453 :			my $rdbH = $self->db_handle;
2454 :
2455 :			if (($relational_db_response = $rdbH->SQL("SELECT fileno FROM file_table WHERE ( file = \'$file\')")) &&
2456 :	parrello	1.298	(@$relational_db_response == 1)) {
2457 :	parrello	1.287	return $relational_db_response->[0]->[0];
2458 :			} elsif (($relational_db_response = $rdbH->SQL("SELECT MAX(fileno) FROM file_table ")) && (@$relational_db_response == 1) && ($relational_db_response->[0]->[0])) {
2459 :			my $fileno = $relational_db_response->[0]->[0] + 1;
2460 :			if ($rdbH->SQL("INSERT INTO file_table ( file, fileno ) VALUES ( \'$file\', $fileno )")) {
2461 :			return $fileno;
2462 :			}
2463 :			} elsif ($rdbH->SQL("INSERT INTO file_table ( file, fileno ) VALUES ( \'$file\', 1 )")) {
2464 :			return 1;
2465 :	efrank	1.1	}
2466 :			return undef;
2467 :			}
2468 :
2469 :			#=pod
2470 :			#
2471 :	parrello	1.287	#=head3 N2file
2472 :	efrank	1.1	#
2473 :			#usage: $filename = $fig->N2file($n)
2474 :			#
2475 :			#In some of the databases I need to store filenames, which can waste a lot of
2476 :			#space. Hence, I maintain a database for converting filenames to/from integers.
2477 :			#
2478 :			#=cut
2479 :			#
2480 :	olson	1.111	sub N2file :scalar {
2481 :	efrank	1.1	my($self,$fileno) = @_;
2482 :			my($relational_db_response);
2483 :
2484 :			my $rdbH = $self->db_handle;
2485 :
2486 :			if (($relational_db_response = $rdbH->SQL("SELECT file FROM file_table WHERE ( fileno = $fileno )")) &&
2487 :	parrello	1.298	(@$relational_db_response == 1)) {
2488 :	parrello	1.287	return $relational_db_response->[0]->[0];
2489 :	efrank	1.1	}
2490 :			return undef;
2491 :			}
2492 :
2493 :
2494 :			#=pod
2495 :			#
2496 :	parrello	1.287	#=head3 openF
2497 :	efrank	1.1	#
2498 :			#usage: $fig->openF($filename)
2499 :			#
2500 :			#Parts of the system rely on accessing numerous different files. The most obvious case is
2501 :			#the situation with similarities. It is important that the system be able to run in cases in
2502 :			#which an arbitrary number of files cannot be open simultaneously. This routine (with closeF) is
2503 :			#a hack to handle this. I should probably just pitch them and insist that the OS handle several
2504 :			#hundred open filehandles.
2505 :			#
2506 :			#=cut
2507 :			#
2508 :			sub openF {
2509 :			my($self,$file) = @_;
2510 :			my($fxs,$x,@fxs,$fh);
2511 :
2512 :			$fxs = $self->cached('_openF');
2513 :	parrello	1.287	if ($x = $fxs->{$file}) {
2514 :			$x->[1] = time();
2515 :			return $x->[0];
2516 :	efrank	1.1	}
2517 :	parrello	1.200
2518 :	efrank	1.1	@fxs = keys(%$fxs);
2519 :	parrello	1.287	if (defined($fh = new FileHandle "<$file")) {
2520 :			if (@fxs >= 50) {
2521 :			@fxs = sort { $fxs->{$a}->[1] <=> $fxs->{$b}->[1] } @fxs;
2522 :			$x = $fxs->{$fxs[0]};
2523 :			undef $x->[0];
2524 :			delete $fxs->{$fxs[0]};
2525 :			}
2526 :			$fxs->{$file} = [$fh,time()];
2527 :			return $fh;
2528 :	efrank	1.1	}
2529 :			return undef;
2530 :			}
2531 :
2532 :			#=pod
2533 :			#
2534 :	parrello	1.287	#=head3 closeF
2535 :	efrank	1.1	#
2536 :			#usage: $fig->closeF($filename)
2537 :			#
2538 :			#Parts of the system rely on accessing numerous different files. The most obvious case is
2539 :			#the situation with similarities. It is important that the system be able to run in cases in
2540 :			#which an arbitrary number of files cannot be open simultaneously. This routine (with openF) is
2541 :			#a hack to handle this. I should probably just pitch them and insist that the OS handle several
2542 :			#hundred open filehandles.
2543 :			#
2544 :			#=cut
2545 :			#
2546 :			sub closeF {
2547 :			my($self,$file) = @_;
2548 :			my($fxs,$x);
2549 :
2550 :	parrello	1.287	if (($fxs = $self->{_openF}) && ($x = $fxs->{$file})) {
2551 :			undef $x->[0];
2552 :			delete $fxs->{$file};
2553 :	efrank	1.1	}
2554 :			}
2555 :
2556 :	parrello	1.287	=head3 ec_name
2557 :
2558 :			C<< my $enzymatic_function = $fig->ec_name($ec); >>
2559 :	efrank	1.1
2560 :	parrello	1.287	Returns the enzymatic name corresponding to the specified enzyme code.
2561 :	efrank	1.1
2562 :	parrello	1.287	=over 4
2563 :
2564 :			=item ec
2565 :	efrank	1.1
2566 :	parrello	1.287	Code number for the enzyme whose name is desired. The code number is actually
2567 :			a string of digits and periods (e.g. C<1.2.50.6>).
2568 :
2569 :			=item RETURN
2570 :
2571 :			Returns the name of the enzyme specified by the indicated code, or a null string
2572 :			if the code is not found in the database.
2573 :
2574 :			=back
2575 :	efrank	1.1
2576 :			=cut
2577 :
2578 :			sub ec_name {
2579 :			my($self,$ec) = @_;
2580 :
2581 :			($ec =~ /^\d+\.\d+\.\d+\.\d+$/) \|\| return "";
2582 :			my $rdbH = $self->db_handle;
2583 :			my $relational_db_response = $rdbH->SQL("SELECT name FROM ec_names WHERE ( ec = \'$ec\' )");
2584 :
2585 :			return (@$relational_db_response == 1) ? $relational_db_response->[0]->[0] : "";
2586 :			return "";
2587 :			}
2588 :
2589 :	parrello	1.287	=head3 all_roles
2590 :	efrank	1.1
2591 :	parrello	1.287	C<< my @roles = $fig->all_roles; >>
2592 :	efrank	1.1
2593 :	parrello	1.287	Return a list of the known roles. Currently, this is a list of the enzyme codes and names.
2594 :	efrank	1.1
2595 :	parrello	1.287	The return value is a list of list references. Each element of the big list contains an
2596 :			enzyme code (EC) followed by the enzymatic name.
2597 :	efrank	1.1
2598 :			=cut
2599 :
2600 :			sub all_roles {
2601 :			my($self) = @_;
2602 :
2603 :			my $rdbH = $self->db_handle;
2604 :			my $relational_db_response = $rdbH->SQL("SELECT ec,name FROM ec_names");
2605 :
2606 :			return @$relational_db_response;
2607 :			}
2608 :
2609 :	parrello	1.287	=head3 expand_ec
2610 :	efrank	1.1
2611 :	parrello	1.287	C<< my $expanded_ec = $fig->expand_ec($ec); >>
2612 :	efrank	1.1
2613 :			Expands "1.1.1.1" to "1.1.1.1 - alcohol dehydrogenase" or something like that.
2614 :
2615 :			=cut
2616 :
2617 :			sub expand_ec {
2618 :			my($self,$ec) = @_;
2619 :			my($name);
2620 :
2621 :			return ($name = $self->ec_name($ec)) ? "$ec - $name" : $ec;
2622 :			}
2623 :
2624 :	parrello	1.287	=head3 clean_tmp
2625 :	efrank	1.1
2626 :	parrello	1.287	C<< FIG::clean_tmp(); >>
2627 :	efrank	1.1
2628 :	parrello	1.287	Delete temporary files more than two days old.
2629 :	efrank	1.1
2630 :			We store temporary files in $FIG_Config::temp. There are specific classes of files
2631 :			that are created and should be saved for at least a few days. This routine can be
2632 :			invoked to clean out those that are over two days old.
2633 :
2634 :			=cut
2635 :
2636 :			sub clean_tmp {
2637 :
2638 :			my($file);
2639 :	parrello	1.287	if (opendir(TMP,"$FIG_Config::temp")) {
2640 :			# change the pattern to pick up other files that need to be cleaned up
2641 :			my @temp = grep { $_ =~ /^(Geno\|tmp)/ } readdir(TMP);
2642 :			foreach $file (@temp) {
2643 :			if (-M "$FIG_Config::temp/$file" > 2) {
2644 :			unlink("$FIG_Config::temp/$file");
2645 :			}
2646 :			}
2647 :	efrank	1.1	}
2648 :			}
2649 :
2650 :			################ Routines to process genomes and genome IDs ##########################
2651 :
2652 :
2653 :	parrello	1.287	=head3 genomes
2654 :	efrank	1.1
2655 :	parrello	1.287	C<< my @genome_ids = $fig->genomes($complete, $restrictions, $domain); >>
2656 :	efrank	1.1
2657 :	parrello	1.287	Return a list of genome IDs. If called with no parameters, all genome IDs
2658 :			in the database will be returned.
2659 :	efrank	1.1
2660 :			Genomes are assigned ids of the form X.Y where X is the taxonomic id maintained by
2661 :			NCBI for the species (not the specific strain), and Y is a sequence digit assigned to
2662 :			this particular genome (as one of a set with the same genus/species). Genomes also
2663 :			have versions, but that is a separate issue.
2664 :
2665 :	parrello	1.287	=over 4
2666 :
2667 :			=item complete
2668 :
2669 :			TRUE if only complete genomes should be returned, else FALSE.
2670 :
2671 :			=item restrictions
2672 :
2673 :			TRUE if only restriction genomes should be returned, else FALSE.
2674 :
2675 :			=item domain
2676 :
2677 :			Name of the domain from which the genomes should be returned. Possible values are
2678 :			C<Bacteria>, C<Virus>, C<Eukaryota>, C<unknown>, C<Archaea>, and
2679 :			C<Environmental Sample>. If no domain is specified, all domains will be
2680 :			eligible.
2681 :
2682 :			=item RETURN
2683 :
2684 :			Returns a list of all the genome IDs with the specified characteristics.
2685 :
2686 :			=back
2687 :
2688 :	efrank	1.1	=cut
2689 :
2690 :	olson	1.111	sub genomes :remote :list {
2691 :	golsen	1.150	my( $self, $complete, $restrictions, $domain ) = @_;
2692 :	overbeek	1.13
2693 :			my $rdbH = $self->db_handle;
2694 :
2695 :			my @where = ();
2696 :	parrello	1.287	if ($complete) {
2697 :			push(@where, "( complete = \'1\' )")
2698 :	overbeek	1.13	}
2699 :
2700 :	parrello	1.287	if ($restrictions) {
2701 :			push(@where, "( restrictions = \'1\' )")
2702 :	overbeek	1.13	}
2703 :	golsen	1.150
2704 :	parrello	1.287	if ($domain) {
2705 :			push( @where, "( maindomain = '$domain' )" )
2706 :	golsen	1.150	}
2707 :
2708 :	overbeek	1.13	my $relational_db_response;
2709 :	parrello	1.287	if (@where > 0) {
2710 :			my $where = join(" AND ",@where);
2711 :			$relational_db_response = $rdbH->SQL("SELECT genome FROM genome where $where");
2712 :			} else {
2713 :			$relational_db_response = $rdbH->SQL("SELECT genome FROM genome");
2714 :	overbeek	1.13	}
2715 :			my @genomes = sort { $a <=> $b } map { $_->[0] } @$relational_db_response;
2716 :	efrank	1.1	return @genomes;
2717 :			}
2718 :
2719 :	parrello	1.287	=head3 is_complete
2720 :
2721 :			C<< my $flag = $fig->is_complete($genome); >>
2722 :
2723 :			Return TRUE if the genome with the specified ID is complete, else FALSE.
2724 :
2725 :			=over 4
2726 :
2727 :			=item genome
2728 :
2729 :			ID of the relevant genome.
2730 :
2731 :			=item RETURN
2732 :
2733 :			Returns TRUE if there is a complete genome in the database with the specified ID,
2734 :			else FALSE.
2735 :
2736 :			=back
2737 :
2738 :			=cut
2739 :
2740 :	overbeek	1.180	sub is_complete {
2741 :			my($self,$genome) = @_;
2742 :
2743 :			my $rdbH = $self->db_handle;
2744 :			my $relational_db_response = $rdbH->SQL("SELECT genome FROM genome where (genome = '$genome') AND (complete = '1')");
2745 :			return (@$relational_db_response == 1)
2746 :	parrello	1.287	}
2747 :
2748 :			=head3 genome_counts
2749 :
2750 :			C<< my ($arch, $bact, $euk, $vir, $env, $unk) = $fig->genome_counts($complete); >>
2751 :
2752 :			Count the number of genomes in each domain. If I<$complete> is TRUE, only complete
2753 :			genomes will be included in the counts.
2754 :
2755 :			=over 4
2756 :
2757 :			=item complete
2758 :
2759 :			TRUE if only complete genomes are to be counted, FALSE if all genomes are to be
2760 :			counted
2761 :
2762 :			=item RETURN
2763 :
2764 :			A six-element list containing the number of genomes in each of six categories--
2765 :			Archaea, Bacteria, Eukaryota, Viral, Environmental, and Unknown, respectively.
2766 :
2767 :			=back
2768 :
2769 :			=cut
2770 :	golsen	1.150
2771 :	efrank	1.2	sub genome_counts {
2772 :	overbeek	1.13	my($self,$complete) = @_;
2773 :			my($x,$relational_db_response);
2774 :	efrank	1.2
2775 :	overbeek	1.13	my $rdbH = $self->db_handle;
2776 :
2777 :	parrello	1.287	if ($complete) {
2778 :			$relational_db_response = $rdbH->SQL("SELECT genome, maindomain FROM genome where complete = '1'");
2779 :			} else {
2780 :			$relational_db_response = $rdbH->SQL("SELECT genome,maindomain FROM genome");
2781 :	overbeek	1.13	}
2782 :
2783 :	gdpusch	1.107	my ($arch, $bact, $euk, $vir, $env, $unk) = (0, 0, 0, 0, 0, 0);
2784 :	parrello	1.287	if (@$relational_db_response > 0) {
2785 :			foreach $x (@$relational_db_response) {
2786 :			if ($x->[1] =~ /^archaea/i) { ++$arch }
2787 :			elsif ($x->[1] =~ /^bacter/i) { ++$bact }
2788 :			elsif ($x->[1] =~ /^eukar/i) { ++$euk }
2789 :			elsif ($x->[1] =~ /^vir/i) { ++$vir }
2790 :			elsif ($x->[1] =~ /^env/i) { ++$env }
2791 :			else { ++$unk }
2792 :	parrello	1.298	}
2793 :	efrank	1.2	}
2794 :	parrello	1.200
2795 :	gdpusch	1.107	return ($arch, $bact, $euk, $vir, $env, $unk);
2796 :			}
2797 :
2798 :
2799 :	parrello	1.287	=head3 genome_domain
2800 :
2801 :			C<< my $domain = $fig->genome_domain($genome_id); >>
2802 :
2803 :			Find the domain of a genome.
2804 :	gdpusch	1.107
2805 :	parrello	1.287	=over 4
2806 :
2807 :			=item genome_id
2808 :	gdpusch	1.107
2809 :	parrello	1.287	ID of the genome whose domain is desired.
2810 :	gdpusch	1.107
2811 :	parrello	1.287	=item RETURN
2812 :
2813 :			Returns the name of the genome's domain (archaea, bacteria, etc.), or C<undef> if
2814 :			the genome is not in the database.
2815 :	gdpusch	1.107
2816 :	parrello	1.292	=back
2817 :
2818 :	gdpusch	1.107	=cut
2819 :
2820 :			sub genome_domain {
2821 :			my($self,$genome) = @_;
2822 :			my $relational_db_response;
2823 :			my $rdbH = $self->db_handle;
2824 :	parrello	1.200
2825 :	parrello	1.287	if ($genome) {
2826 :			if (($relational_db_response = $rdbH->SQL("SELECT genome,maindomain FROM genome WHERE ( genome = \'$genome\' )"))
2827 :			&& (@$relational_db_response == 1)) {
2828 :			# die Dumper($relational_db_response);
2829 :			return $relational_db_response->[0]->[1];
2830 :			}
2831 :	gdpusch	1.107	}
2832 :			return undef;
2833 :	efrank	1.2	}
2834 :
2835 :	gdpusch	1.92
2836 :	parrello	1.287	=head3 genome_pegs
2837 :	gdpusch	1.92
2838 :	parrello	1.287	C<< my $num_pegs = $fig->genome_pegs($genome_id); >>
2839 :	gdpusch	1.92
2840 :	parrello	1.287	Return the number of protein-encoding genes (PEGs) for a specified
2841 :			genome.
2842 :	gdpusch	1.92
2843 :	parrello	1.287	=over 4
2844 :
2845 :			=item genome_id
2846 :
2847 :			ID of the genome whose PEG count is desired.
2848 :
2849 :			=item RETURN
2850 :
2851 :			Returns the number of PEGs for the specified genome, or C<undef> if the genome
2852 :			is not indexed in the database.
2853 :
2854 :			=back
2855 :	gdpusch	1.92
2856 :			=cut
2857 :
2858 :			sub genome_pegs {
2859 :			my($self,$genome) = @_;
2860 :			my $relational_db_response;
2861 :			my $rdbH = $self->db_handle;
2862 :	parrello	1.200
2863 :	parrello	1.287	if ($genome) {
2864 :			if (($relational_db_response = $rdbH->SQL("SELECT pegs FROM genome WHERE ( genome = \'$genome\' )"))
2865 :			&& (@$relational_db_response == 1)) {
2866 :			return $relational_db_response->[0]->[0];
2867 :			}
2868 :	gdpusch	1.92	}
2869 :			return undef;
2870 :			}
2871 :
2872 :
2873 :	parrello	1.287	=head3 genome_rnas
2874 :
2875 :			C<< my $num_rnas = $fig->genome_rnas($genome_id); >>
2876 :
2877 :			Return the number of RNA-encoding genes for a genome.
2878 :			"$genome_id" is indexed in the "genome" database, and 'undef' otherwise.
2879 :	efrank	1.1
2880 :	parrello	1.287	=over 4
2881 :
2882 :			=item genome_id
2883 :
2884 :			ID of the genome whose RNA count is desired.
2885 :
2886 :			=item RETURN
2887 :	gdpusch	1.92
2888 :	parrello	1.287	Returns the number of RNAs for the specified genome, or C<undef> if the genome
2889 :			is not indexed in the database.
2890 :	gdpusch	1.92
2891 :	parrello	1.287	=back
2892 :	gdpusch	1.92
2893 :			=cut
2894 :
2895 :			sub genome_rnas {
2896 :			my($self,$genome) = @_;
2897 :			my $relational_db_response;
2898 :			my $rdbH = $self->db_handle;
2899 :	parrello	1.200
2900 :	parrello	1.287	if ($genome) {
2901 :			if (($relational_db_response = $rdbH->SQL("SELECT rnas FROM genome WHERE ( genome = \'$genome\' )"))
2902 :			&& (@$relational_db_response == 1)) {
2903 :			return $relational_db_response->[0]->[0];
2904 :			}
2905 :	gdpusch	1.92	}
2906 :			return undef;
2907 :			}
2908 :
2909 :
2910 :	parrello	1.287	=head3 genome_szdna
2911 :
2912 :			usage: $szdna = $fig->genome_szdna($genome_id);
2913 :
2914 :			Return the number of DNA base-pairs in a genome's contigs.
2915 :
2916 :			=over 4
2917 :
2918 :			=item genome_id
2919 :
2920 :			ID of the genome whose base-pair count is desired.
2921 :	gdpusch	1.92
2922 :	parrello	1.287	=item RETURN
2923 :	efrank	1.1
2924 :	parrello	1.287	Returns the number of base pairs in the specified genome's contigs, or C<undef>
2925 :			if the genome is not indexed in the database.
2926 :	gdpusch	1.91
2927 :	parrello	1.287	=back
2928 :	gdpusch	1.91
2929 :			=cut
2930 :
2931 :	gdpusch	1.92	sub genome_szdna {
2932 :	gdpusch	1.91	my($self,$genome) = @_;
2933 :			my $relational_db_response;
2934 :			my $rdbH = $self->db_handle;
2935 :	parrello	1.200
2936 :	parrello	1.287	if ($genome) {
2937 :			if (($relational_db_response =
2938 :			$rdbH->SQL("SELECT szdna FROM genome WHERE ( genome = \'$genome\' )"))
2939 :			&& (@$relational_db_response == 1)) {
2940 :
2941 :			return $relational_db_response->[0]->[0];
2942 :
2943 :			}
2944 :	gdpusch	1.91	}
2945 :			return undef;
2946 :			}
2947 :
2948 :	parrello	1.287	=head3 genome_version
2949 :	gdpusch	1.91
2950 :	parrello	1.287	C<< my $version = $fig->genome_version($genome_id); >>
2951 :	gdpusch	1.91
2952 :	parrello	1.287	Return the version number of the specified genome.
2953 :	efrank	1.1
2954 :			Versions are incremented for major updates. They are put in as major
2955 :			updates of the form 1.0, 2.0, ...
2956 :
2957 :			Users may do local "editing" of the DNA for a genome, but when they do,
2958 :			they increment the digits to the right of the decimal. Two genomes remain
2959 :	parrello	1.200	comparable only if the versions match identically. Hence, minor updating should be
2960 :	efrank	1.1	committed only by the person/group responsible for updating that genome.
2961 :
2962 :			We can, of course, identify which genes are identical between any two genomes (by matching
2963 :			the DNA or amino acid sequences). However, the basic intent of the system is to
2964 :			support editing by the main group issuing periodic major updates.
2965 :
2966 :	parrello	1.287	=over 4
2967 :
2968 :			=item genome_id
2969 :
2970 :			ID of the genome whose version is desired.
2971 :
2972 :			=item RETURN
2973 :
2974 :			Returns the version number of the specified genome, or C<undef> if the genome is not in
2975 :			the data store or no version number has been assigned.
2976 :
2977 :			=back
2978 :
2979 :	efrank	1.1	=cut
2980 :
2981 :	olson	1.113	sub genome_version :scalar {
2982 :	efrank	1.1	my($self,$genome) = @_;
2983 :
2984 :			my(@tmp);
2985 :			if ((-s "$FIG_Config::organisms/$genome/VERSION") &&
2986 :	parrello	1.298	(@tmp = `cat $FIG_Config::organisms/$genome/VERSION`) &&
2987 :			($tmp[0] =~ /^(\S+)$/)) {
2988 :			return $1;
2989 :	efrank	1.1	}
2990 :			return undef;
2991 :			}
2992 :
2993 :	parrello	1.287	=head3 genome_md5sum
2994 :	olson	1.236
2995 :	parrello	1.287	C<< my $md5sum = $fig->genome_md5sum($genome_id); >>
2996 :	olson	1.236
2997 :	parrello	1.287	Returns the MD5 checksum of the specified genome.
2998 :	olson	1.236
2999 :			The checksum of a genome is defined as the checksum of its signature file. The signature
3000 :			file consists of tab-separated lines, one for each contig, ordered by the contig id.
3001 :	parrello	1.287	Each line contains the contig ID, the length of the contig in nucleotides, and the
3002 :	olson	1.236	MD5 checksum of the nucleotide data, with uppercase letters forced to lower case.
3003 :
3004 :	parrello	1.287	The checksum is indexed in the database. If you know a genome's checksum, you can use
3005 :			the L</genome_with_md5sum> method to find its ID in the database.
3006 :
3007 :			=over 4
3008 :
3009 :			=item genome
3010 :
3011 :			ID of the genome whose checksum is desired.
3012 :
3013 :			=item RETURN
3014 :
3015 :			Returns the specified genome's checksum, or C<undef> if the genome is not in the
3016 :			database.
3017 :
3018 :			=back
3019 :	olson	1.236
3020 :			=cut
3021 :
3022 :	olson	1.237	sub genome_md5sum :scalar {
3023 :	olson	1.236	my($self,$genome) = @_;
3024 :			my $relational_db_response;
3025 :			my $rdbH = $self->db_handle;
3026 :
3027 :	parrello	1.287	if ($genome) {
3028 :			if (($relational_db_response =
3029 :			$rdbH->SQL("SELECT md5sum FROM genome_md5sum WHERE ( genome = \'$genome\' )"))
3030 :			&& (@$relational_db_response == 1)) {
3031 :			return $relational_db_response->[0]->[0];
3032 :			}
3033 :	olson	1.236	}
3034 :			return undef;
3035 :			}
3036 :
3037 :	parrello	1.287	=head3 genome_with_md5sum
3038 :
3039 :			C<< my $genome = $fig->genome_with_md5sum($cksum); >>
3040 :
3041 :			Find a genome with the specified checksum.
3042 :
3043 :			The MD5 checksum is computed from the content of the genome (see L</genome_md5sum>). This method
3044 :			can be used to determine if a genome already exists for a specified content.
3045 :
3046 :			=over 4
3047 :
3048 :			=item cksum
3049 :
3050 :			Checksum to use for searching the genome table.
3051 :	olson	1.260
3052 :	parrello	1.287	=item RETURN
3053 :
3054 :			The ID of a genome with the specified checksum, or C<undef> if no such genome exists.
3055 :	olson	1.260
3056 :	parrello	1.287	=back
3057 :	olson	1.260
3058 :			=cut
3059 :
3060 :			sub genome_with_md5sum :scalar {
3061 :			my($self,$cksum) = @_;
3062 :			my $relational_db_response;
3063 :			my $rdbH = $self->db_handle;
3064 :
3065 :	parrello	1.287	if (($relational_db_response =
3066 :			$rdbH->SQL("SELECT genome FROM genome_md5sum WHERE ( md5sum = \'$cksum\' )"))
3067 :	parrello	1.298	&& (@$relational_db_response == 1)) {
3068 :			return $relational_db_response->[0]->[0];
3069 :	olson	1.260	}
3070 :
3071 :			return undef;
3072 :			}
3073 :
3074 :	parrello	1.287	=head3 contig_md5sum
3075 :
3076 :			C<< my $cksum = $fig->contig_md5sum($genome, $contig); >>
3077 :
3078 :			Return the MD5 checksum for a contig. The MD5 checksum is computed from the content
3079 :			of the contig. This method retrieves the checksum stored in the database. The checksum
3080 :			can be compared to the checksum of an external contig as a cheap way of seeing if they
3081 :			match.
3082 :
3083 :			=over 4
3084 :
3085 :			=item genome
3086 :
3087 :			ID of the genome containing the contig.
3088 :
3089 :			=item contig
3090 :
3091 :			ID of the relevant contig.
3092 :
3093 :			=item RETURN
3094 :
3095 :			Returns the checksum of the specified contig, or C<undef> if the contig is not in the
3096 :			database.
3097 :
3098 :			=back
3099 :
3100 :			=cut
3101 :
3102 :	olson	1.237	sub contig_md5sum :scalar {
3103 :			my($self, $genome, $contig) = @_;
3104 :			my $relational_db_response;
3105 :			my $rdbH = $self->db_handle;
3106 :
3107 :	parrello	1.287	if ($genome) {
3108 :			if (($relational_db_response =
3109 :			$rdbH->SQL(qq(SELECT md5 FROM contig_md5sums WHERE (genome = ? AND contig = ?)), undef, $genome, $contig))
3110 :			&& (@$relational_db_response == 1)) {
3111 :			return $relational_db_response->[0]->[0];
3112 :			}
3113 :	olson	1.237	}
3114 :			return undef;
3115 :			}
3116 :
3117 :	parrello	1.287	=head3 genus_species
3118 :
3119 :			C<< my $gs = $fig->genus_species($genome_id); >>
3120 :
3121 :			Return the genus, species, and possibly also the strain of a specified genome.
3122 :
3123 :			This method converts a genome ID into a more recognizble species name. The species name
3124 :			is stored directly in the genome table of the database. Essentially, if the strain is
3125 :			present in the database, it will be returned by this method, and if it's not present,
3126 :			it won't.
3127 :	efrank	1.1
3128 :	parrello	1.287	=over 4
3129 :
3130 :			=item genome_id
3131 :
3132 :			ID of the genome whose name is desired.
3133 :	efrank	1.1
3134 :	parrello	1.287	=item RETURN
3135 :
3136 :			Returns the scientific species name associated with the specified ID, or C<undef> if the
3137 :			ID is not in the database.
3138 :	efrank	1.1
3139 :	parrello	1.287	=back
3140 :	efrank	1.1
3141 :			=cut
3142 :
3143 :	olson	1.111	sub genus_species :scalar {
3144 :	efrank	1.1	my ($self,$genome) = @_;
3145 :	overbeek	1.13	my $ans;
3146 :	efrank	1.1
3147 :			my $genus_species = $self->cached('_genus_species');
3148 :	parrello	1.287	if (! ($ans = $genus_species->{$genome})) {
3149 :			my $rdbH = $self->db_handle;
3150 :			my $relational_db_response = $rdbH->SQL("SELECT genome,gname FROM genome");
3151 :			my $pair;
3152 :			foreach $pair (@$relational_db_response) {
3153 :			$genus_species->{$pair->[0]} = $pair->[1];
3154 :			}
3155 :			$ans = $genus_species->{$genome};
3156 :	efrank	1.1	}
3157 :			return $ans;
3158 :			}
3159 :
3160 :	parrello	1.287	=head3 org_of
3161 :
3162 :			C<< my $org = $fig->org_of($prot_id); >>
3163 :
3164 :			Return the genus/species name of the organism containing a protein. Note that in this context
3165 :			I<protein> is not a certain string of amino acids but a protein encoding region on a specific
3166 :			contig.
3167 :
3168 :			For a FIG protein ID (e.g. C<fig\|134537.1.peg.123>), the organism and strain
3169 :			information is always available. In the case of external proteins, we can usually
3170 :			determine an organism, but not anything more precise than genus/species (and
3171 :			often not that). When the organism name is not present, a null string is returned.
3172 :
3173 :			=over 4
3174 :
3175 :			=item prot_id
3176 :	efrank	1.1
3177 :	parrello	1.287	Protein or feature ID.
3178 :	efrank	1.1
3179 :	parrello	1.287	=item RETURN
3180 :
3181 :			Returns the displayable scientific name (genus, species, and strain) of the organism containing
3182 :			the identified PEG. If the name is not available, returns a null string. If the PEG is not found,
3183 :			returns C<undef>.
3184 :	efrank	1.1
3185 :	parrello	1.287	=back
3186 :	efrank	1.1
3187 :			=cut
3188 :
3189 :			sub org_of {
3190 :			my($self,$prot_id) = @_;
3191 :			my $relational_db_response;
3192 :			my $rdbH = $self->db_handle;
3193 :
3194 :	parrello	1.287	if ($prot_id =~ /^fig\\|/) {
3195 :			return $self->is_deleted_fid( $prot_id) ? undef
3196 :			: $self->genus_species( $self->genome_of( $prot_id ) ) \|\| "";
3197 :	efrank	1.1	}
3198 :
3199 :	parrello	1.287	if (($relational_db_response =
3200 :			$rdbH->SQL("SELECT org FROM external_orgs WHERE ( prot = \'$prot_id\' )")) &&
3201 :			(@$relational_db_response >= 1)) {
3202 :			$relational_db_response->[0]->[0] =~ s/^\d+://;
3203 :			return $relational_db_response->[0]->[0];
3204 :	efrank	1.1	}
3205 :			return "";
3206 :			}
3207 :
3208 :	parrello	1.287	=head3 genus_species_domain
3209 :
3210 :			C<< my ($gs, $domain) = $fig->genus_species_domain($genome_id); >>
3211 :
3212 :			Returns a genome's genus and species (and strain if that has been properly
3213 :			recorded) in a printable form, along with its domain. This method is similar
3214 :			to L</genus_species>, except it also returns the domain name (archaea,
3215 :			bacteria, etc.).
3216 :
3217 :			=over 4
3218 :
3219 :			=item genome_id
3220 :
3221 :			ID of the genome whose species and domain information is desired.
3222 :	golsen	1.130
3223 :	parrello	1.287	=item RETURN
3224 :	golsen	1.130
3225 :	parrello	1.287	Returns a two-element list. The first element is the species name and the
3226 :			second is the domain name.
3227 :	golsen	1.130
3228 :	parrello	1.287	=back
3229 :	golsen	1.130
3230 :			=cut
3231 :
3232 :			sub genus_species_domain {
3233 :			my ($self, $genome) = @_;
3234 :
3235 :			my $genus_species_domain = $self->cached('_genus_species_domain');
3236 :	parrello	1.287	if ( ! $genus_species_domain->{ $genome } ) {
3237 :			my $rdbH = $self->db_handle;
3238 :			my $relational_db_response = $rdbH->SQL("SELECT genome,gname,maindomain FROM genome");
3239 :			my $triple;
3240 :			foreach $triple ( @$relational_db_response ) {
3241 :			$genus_species_domain->{ $triple->[0] } = [ $triple->[1], $triple->[2] ];
3242 :			}
3243 :	golsen	1.130	}
3244 :			my $gsdref = $genus_species_domain->{ $genome };
3245 :			return $gsdref ? @$gsdref : ( "", "" );
3246 :			}
3247 :
3248 :	parrello	1.287	=head3 domain_color
3249 :
3250 :			C<< my $web_color = FIG::domain_color($domain); >>
3251 :
3252 :			Return the web color string associated with a specified domain. The colors are
3253 :			extremely subtle (86% luminance), so they absolutely require a black background.
3254 :			Archaea are slightly cyan, bacteria are slightly magenta, eukaryota are slightly
3255 :			yellow, viruses are slightly silver, environmental samples are slightly gray,
3256 :			and unknown or invalid domains are pure white.
3257 :
3258 :			=over 4
3259 :
3260 :			=item domain
3261 :
3262 :			Name of the domain whose color is desired.
3263 :
3264 :			=item RETURN
3265 :
3266 :			Returns a web color string for the specified domain (e.g. C<#FFDDFF> for
3267 :			bacteria).
3268 :
3269 :			=back
3270 :
3271 :			=cut
3272 :	golsen	1.130
3273 :			my %domain_color = ( AR => "#DDFFFF", BA => "#FFDDFF", EU => "#FFFFDD",
3274 :			VI => "#DDDDDD", EN => "#BBBBBB" );
3275 :
3276 :			sub domain_color {
3277 :			my ($domain) = @_;
3278 :			defined $domain \|\| return "#FFFFFF";
3279 :			return $domain_color{ uc substr($domain, 0, 2) } \|\| "#FFFFFF";
3280 :			}
3281 :
3282 :	parrello	1.287	=head3 org_and_color_of
3283 :	golsen	1.130
3284 :	parrello	1.287	C<< my ($org, $color) = $fig->org_and_domain_of($prot_id); >>
3285 :	golsen	1.130
3286 :	parrello	1.287	Return the best guess organism and domain html color string of an organism.
3287 :			In the case of external proteins, we can usually determine an organism, but not
3288 :			anything more precise than genus/species (and often not that).
3289 :
3290 :			=over 4
3291 :
3292 :			=item prot_id
3293 :
3294 :			Relevant protein or feature ID.
3295 :
3296 :			=item RETURN
3297 :	golsen	1.130
3298 :	parrello	1.287	Returns a two-element list. The first element is the displayable organism name, and the second
3299 :			is an HTML color string based on the domain (see L</domain_color>).
3300 :	golsen	1.130
3301 :	parrello	1.287	=back
3302 :	golsen	1.130
3303 :			=cut
3304 :
3305 :			sub org_and_color_of {
3306 :			my($self,$prot_id) = @_;
3307 :			my $relational_db_response;
3308 :			my $rdbH = $self->db_handle;
3309 :
3310 :	parrello	1.287	if ($prot_id =~ /^fig\\|/) {
3311 :			my( $gs, $domain ) = $self->genus_species_domain($self->genome_of($prot_id));
3312 :			return ( $gs, domain_color( $domain ) );
3313 :	golsen	1.130	}
3314 :
3315 :	parrello	1.287	if (($relational_db_response =
3316 :			$rdbH->SQL("SELECT org FROM external_orgs WHERE ( prot = \'$prot_id\' )")) &&
3317 :			(@$relational_db_response >= 1)) {
3318 :			return ($relational_db_response->[0]->[0], "#FFFFFF");
3319 :	golsen	1.130	}
3320 :			return ("", "#FFFFFF");
3321 :			}
3322 :
3323 :	redwards	1.310	=head3 partial_genus_matching
3324 :
3325 :			Return a list of genome IDs that match a partial genus.
3326 :
3327 :	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)
3328 :	redwards	1.310
3329 :			=cut
3330 :
3331 :			sub partial_genus_matching {
3332 :	redwards	1.311	my ($self, $gen, $complete)=@_;
3333 :			return grep {$self->genus_species($_) =~ /$gen/i} $self->genomes($complete);
3334 :	redwards	1.310	}
3335 :
3336 :
3337 :	parrello	1.287	=head3 abbrev
3338 :
3339 :			C<< my $abbreviated_name = FIG::abbrev($genome_name); >>
3340 :	golsen	1.130
3341 :	parrello	1.287	or
3342 :	efrank	1.1
3343 :	parrello	1.287	C<< my $abbreviated_name = $fig->abbrev($genome_name); >>
3344 :	efrank	1.1
3345 :	parrello	1.287	Abbreviate a genome name to 10 characters or less.
3346 :	efrank	1.1
3347 :			For alignments and such, it is very useful to be able to produce an abbreviation of genus/species.
3348 :			That's what this does. Note that multiple genus/species might reduce to the same abbreviation, so
3349 :			be careful (disambiguate them, if you must).
3350 :
3351 :	parrello	1.287	The abbreviation is formed from the first three letters of the species name followed by the
3352 :			first three letters of the genus name followed by the first three letters of the species name and
3353 :			then the next four nonblank characters.
3354 :
3355 :			=over 4
3356 :
3357 :			=item genome_name
3358 :
3359 :			The name to abbreviate.
3360 :
3361 :			=item RETURN
3362 :
3363 :			An abbreviated version of the specified name.
3364 :
3365 :			=back
3366 :
3367 :	efrank	1.1	=cut
3368 :
3369 :	olson	1.111	sub abbrev :scalar {
3370 :			shift if UNIVERSAL::isa($_[0],__PACKAGE__);
3371 :	efrank	1.1	my($genome_name) = @_;
3372 :
3373 :			$genome_name =~ s/^(\S{3})\S+/$1./;
3374 :	overbeek	1.198	$genome_name =~ s/^(\S+)\s+(\S{3})\S+/$1$2./;
3375 :	overbeek	1.257	$genome_name =~ s/ //g;
3376 :	parrello	1.287	if (length($genome_name) > 10) {
3377 :	parrello	1.298	$genome_name = substr($genome_name,0,10);
3378 :	efrank	1.1	}
3379 :			return $genome_name;
3380 :			}
3381 :
3382 :			################ Routines to process Features and Feature IDs ##########################
3383 :
3384 :	parrello	1.287	=head3 ftype
3385 :
3386 :			C<< my $type = FIG::ftype($fid); >>
3387 :	efrank	1.1
3388 :	parrello	1.287	or
3389 :	efrank	1.1
3390 :	parrello	1.287	C<< my $type = $fig->ftype($fid); >>
3391 :	efrank	1.1
3392 :			Returns the type of a feature, given the feature ID. This just amounts
3393 :	parrello	1.287	to lifting it out of the feature ID, since features have IDs of the form
3394 :	efrank	1.1
3395 :	parrello	1.287	fig\|x.y.f.n
3396 :	efrank	1.1
3397 :			where
3398 :			x.y is the genome ID
3399 :	parrello	1.287	f is the type of feature
3400 :	efrank	1.1	n is an integer that is unique within the genome/type
3401 :
3402 :	parrello	1.287	=over 4
3403 :
3404 :			=item fid
3405 :
3406 :			FIG ID of the feature whose type is desired.
3407 :
3408 :			=item RETURN
3409 :
3410 :			Returns the feature type (e.g. C<peg>, C<rna>, C<pi>, or C<pp>), or C<undef> if the
3411 :			feature ID is not a FIG ID.
3412 :
3413 :			=back
3414 :
3415 :	efrank	1.1	=cut
3416 :
3417 :			sub ftype {
3418 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
3419 :	efrank	1.1	my($feature_id) = @_;
3420 :
3421 :	parrello	1.287	if ($feature_id =~ /^fig\\|\d+\.\d+\.([^\.]+)/) {
3422 :			return $1;
3423 :	efrank	1.1	}
3424 :			return undef;
3425 :			}
3426 :
3427 :	parrello	1.287	=head3 genome_of
3428 :
3429 :			C<< my $genome_id = $fig->genome_of($fid); >>
3430 :
3431 :			or
3432 :
3433 :			C<< my $genome_id = FIG::genome_of($fid); >>
3434 :
3435 :			Return the genome ID from a feature ID.
3436 :	efrank	1.1
3437 :	parrello	1.287	=over 4
3438 :
3439 :			=item fid
3440 :
3441 :			ID of the feature whose genome ID is desired.
3442 :
3443 :			=item RETURN
3444 :	efrank	1.1
3445 :	parrello	1.287	If the feature ID is a FIG ID, returns the genome ID embedded inside it; otherwise, it
3446 :			returns C<undef>.
3447 :	efrank	1.1
3448 :	parrello	1.287	=back
3449 :	efrank	1.1
3450 :			=cut
3451 :
3452 :
3453 :	olson	1.113	sub genome_of :scalar {
3454 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
3455 :	parrello	1.200	my $prot_id = (@_ == 1) ? $_[0] : $_[1];
3456 :	efrank	1.1
3457 :			if ($prot_id =~ /^fig\\|(\d+\.\d+)/) { return $1; }
3458 :			return undef;
3459 :			}
3460 :
3461 :	parrello	1.287	=head3 genome_and_peg_of
3462 :
3463 :			C<< my ($genome_id, $peg_number = FIG::genome_and_peg_of($fid); >>
3464 :
3465 :			C<< my ($genome_id, $peg_number = $fig->genome_and_peg_of($fid); >>
3466 :	olson	1.96
3467 :	parrello	1.287	Return the genome ID and peg number from a feature ID.
3468 :	olson	1.96
3469 :	parrello	1.287	=over 4
3470 :
3471 :			=item prot_id
3472 :
3473 :			ID of the feature whose genome and PEG number as desired.
3474 :
3475 :			=item RETURN
3476 :
3477 :			Returns the genome ID and peg number associated with a feature if the feature
3478 :			is represented by a FIG ID, else C<undef>.
3479 :
3480 :			=back
3481 :	olson	1.96
3482 :			=cut
3483 :
3484 :			sub genome_and_peg_of {
3485 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
3486 :	parrello	1.200	my $prot_id = (@_ == 1) ? $_[0] : $_[1];
3487 :	olson	1.96
3488 :	parrello	1.287	if ($prot_id =~ /^fig\\|(\d+\.\d+)\.peg\.(\d+)/) {
3489 :	parrello	1.298	return ($1, $2);
3490 :	olson	1.96	}
3491 :			return undef;
3492 :			}
3493 :
3494 :	parrello	1.287	=head3 by_fig_id
3495 :
3496 :			C<< my @sorted_by_fig_id = sort { FIG::by_fig_id($a,$b) } @fig_ids; >>
3497 :
3498 :			Compare two feature IDs.
3499 :
3500 :			This function is designed to assist in sorting features by ID. The sort is by
3501 :			genome ID followed by feature type and then feature number.
3502 :
3503 :			=over 4
3504 :
3505 :			=item a
3506 :	efrank	1.1
3507 :	parrello	1.287	First feature ID.
3508 :	efrank	1.1
3509 :	parrello	1.287	=item b
3510 :	efrank	1.1
3511 :	parrello	1.287	Second feature ID.
3512 :
3513 :			=item RETURN
3514 :
3515 :			Returns a negative number if the first parameter is smaller, zero if both parameters
3516 :			are equal, and a positive number if the first parameter is greater.
3517 :
3518 :			=back
3519 :	efrank	1.1
3520 :			=cut
3521 :
3522 :			sub by_fig_id {
3523 :			my($a,$b) = @_;
3524 :			my($g1,$g2,$t1,$t2,$n1,$n2);
3525 :			if (($a =~ /^fig\\|(\d+\.\d+).([^\.]+)\.(\d+)$/) && (($g1,$t1,$n1) = ($1,$2,$3)) &&
3526 :	parrello	1.298	($b =~ /^fig\\|(\d+\.\d+).([^\.]+)\.(\d+)$/) && (($g2,$t2,$n2) = ($1,$2,$3))) {
3527 :			($g1 <=> $g2) or ($t1 cmp $t2) or ($n1 <=> $n2);
3528 :	parrello	1.287	} else {
3529 :	parrello	1.298	$a cmp $b;
3530 :	efrank	1.1	}
3531 :			}
3532 :
3533 :	parrello	1.287	=head3 genes_in_region
3534 :	efrank	1.1
3535 :	parrello	1.287	C<< my ($features_in_region, $beg1, $end1) = $fig->genes_in_region($genome, $contig, $beg, $end, size_limit); >>
3536 :	efrank	1.1
3537 :	parrello	1.287	Locate features that overlap a specified region of a contig. This includes features that begin or end
3538 :			outside that region, just so long as some part of the feature can be found in the region of interest.
3539 :	efrank	1.1
3540 :			It is often important to be able to find the genes that occur in a specific region on
3541 :			a chromosome. This routine is designed to provide this information. It returns all genes
3542 :	parrello	1.287	that overlap positions from I<$beg> through I<$end> in the specified contig.
3543 :
3544 :			The I<$size_limit> parameter limits the search process. It is presumed that no features are longer than the
3545 :			specified size limit. A shorter size limit means you'll miss some features; a longer size limit significantly
3546 :			slows the search process. For prokaryotes, a value of C<10000> (the default) seems to work best.
3547 :
3548 :			=over 4
3549 :
3550 :			=item genome
3551 :
3552 :			ID of the genome containing the relevant contig.
3553 :
3554 :			=item contig
3555 :
3556 :			ID of the relevant contig.
3557 :
3558 :			=item beg
3559 :
3560 :			Position of the first base pair in the region of interest.
3561 :
3562 :			=item end
3563 :
3564 :			Position of the last base pair in the region of interest.
3565 :
3566 :			=item size_limit
3567 :
3568 :			Maximum allowable size for a feature. If omitted, C<10000> is assumed.
3569 :
3570 :			=item RETURN
3571 :	efrank	1.1
3572 :	parrello	1.287	Returns a three-element list. The first element is a reference to a list of the feature IDs found. The second
3573 :			element is the position of the leftmost base pair in any feature found. This may be well before the region of
3574 :			interest begins or it could be somewhere inside. The third element is the position of the rightmost base pair
3575 :			in any feature found. Again, this can be somewhere inside the region or it could be well to the right of it.
3576 :
3577 :			=back
3578 :	efrank	1.1
3579 :			=cut
3580 :	parrello	1.213	#: Return Type @;
3581 :	efrank	1.1	sub genes_in_region {
3582 :	parrello	1.287	my($self, $genome, $contig, $beg, $end, $pad) = @_;
3583 :			if (!defined $pad) { $pad = 10000; }
3584 :	efrank	1.1	my($x,$relational_db_response,$feature_id,$b1,$e1,@feat,@tmp,$l,$u);
3585 :
3586 :			my $rdbH = $self->db_handle;
3587 :
3588 :	parrello	1.200	my $minV = $beg - $pad;
3589 :	efrank	1.1	my $maxV = $end + $pad;
3590 :	parrello	1.287	if (($relational_db_response = $rdbH->SQL("SELECT id FROM features "
3591 :			. " WHERE ( minloc > $minV ) AND ( minloc < $maxV ) AND ( maxloc < $maxV) AND "
3592 :			. " ( genome = \'$genome\' ) AND ( contig = \'$contig\' );")) &&
3593 :			(@$relational_db_response >= 1)) {
3594 :			@tmp = sort { ($a->[1] cmp $b->[1]) or (($a->[2]+$a->[3]) <=> ($b->[2]+$b->[3])) }
3595 :			map { $feature_id = $_->[0]; $x = $self->feature_location($feature_id); $x ? [$feature_id,&boundaries_of($x)] : ()
3596 :			} @$relational_db_response;
3597 :	efrank	1.1
3598 :
3599 :	parrello	1.287	($l,$u) = (10000000000,0);
3600 :			foreach $x (@tmp)
3601 :			{
3602 :			($feature_id,undef,$b1,$e1) = @$x;
3603 :			if (&between($beg,&min($b1,$e1),$end) \|\| &between(&min($b1,$e1),$beg,&max($b1,$e1)))
3604 :			{
3605 :			if (! $self->is_deleted_fid($feature_id))
3606 :			{
3607 :			push(@feat,$feature_id);
3608 :			$l = &min($l,&min($b1,$e1));
3609 :			$u = &max($u,&max($b1,$e1));
3610 :			}
3611 :			}
3612 :			}
3613 :			(@feat <= 0) \|\| return ([@feat],$l,$u);
3614 :	efrank	1.1	}
3615 :			return ([],$l,$u);
3616 :			}
3617 :
3618 :	golsen	1.141
3619 :			#=============================================================================
3620 :			# Using the following version is better, but it brings out a very annoying
3621 :			# issue with some genomes. It already exists in the current code (above)
3622 :			# for some genes in some genomes. For example, visit fig\|70601.1.peg.1.
3623 :			# This is true for any genome that has a feature that crosses the origin.
3624 :			# The root of the problem lies in boundaries_of. I am working on a fix that
3625 :			# replaces boundaries_of with a more sophisticated function. When it is
3626 :			# all done, genes_in_retion should behave as desired. -- GJO, Aug. 22, 2004
3627 :			#=============================================================================
3628 :	parrello	1.200	#
3629 :	golsen	1.141	# =pod
3630 :	parrello	1.200	#
3631 :	parrello	1.287	# =head3 genes_in_region
3632 :	parrello	1.200	#
3633 :	golsen	1.141	# usage: ( $features_in_region, $min_coord, $max_coord )
3634 :			# = $fig->genes_in_region( $genome, $contig, $beg, $end )
3635 :	parrello	1.200	#
3636 :	golsen	1.141	# It is often important to be able to find the genes that occur in a specific
3637 :			# region on a chromosome. This routine is designed to provide this information.
3638 :			# It returns all genes that overlap the region ( $genome, $contig, $beg, $end ).
3639 :			# $min_coord is set to the minimum coordinate of the returned genes (which may
3640 :			# preceed the given region), and $max_coord the maximum coordinate. Because
3641 :			# the database is indexed by the leftmost and rightmost coordinates of each
3642 :			# feature, the function makes no assumption about the length of the feature, but
3643 :			# it can (and probably will) miss features spanning multiple contigs.
3644 :	parrello	1.200	#
3645 :	golsen	1.141	# =cut
3646 :	parrello	1.200	#
3647 :			#
3648 :	golsen	1.141	# sub genes_in_region {
3649 :			# my ( $self, $genome, $contig, $beg, $end ) = @_;
3650 :			# my ( $x, $db_response, $feature_id, $b1, $e1, @tmp, @bounds );
3651 :			# my ( $min_coord, $max_coord );
3652 :	parrello	1.200	#
3653 :	golsen	1.141	# my @features = ();
3654 :			# my $rdbH = $self->db_handle;
3655 :	parrello	1.200	#
3656 :	golsen	1.141	# if ( ( $db_response = $rdbH->SQL( "SELECT id
3657 :			# FROM features
3658 :			# WHERE ( contig = '$contig' )
3659 :			# AND ( genome = '$genome' )
3660 :	parrello	1.200	# AND ( minloc <= $end )
3661 :	golsen	1.141	# AND ( maxloc >= $beg );"
3662 :			# )
3663 :			# )
3664 :			# && ( @$db_response > 0 )
3665 :			# )
3666 :			# {
3667 :			# # The sort is unnecessary, but provides a consistent ordering
3668 :	parrello	1.200	#
3669 :	golsen	1.141	# @tmp = sort { ( $a->[1] cmp $b->[1] ) # contig
3670 :			# \|\| ( ($a->[2] + $a->[3] ) <=> ( $b->[2] + $b->[3] ) ) # midpoint
3671 :			# }
3672 :			# map { $feature_id = $_->[0];
3673 :			# ( ( ! $self->is_deleted_fid( $feature_id ) ) # not deleted
3674 :			# && ( $x = $self->feature_location( $feature_id ) ) # and has location
3675 :			# && ( ( @bounds = boundaries_of( $x ) ) == 3 ) # and has bounds
3676 :	parrello	1.200	# ) ? [ $feature_id, @bounds ] : ()
3677 :	golsen	1.141	# } @$db_response;
3678 :	parrello	1.200	#
3679 :	golsen	1.141	# ( $min_coord, $max_coord ) = ( 10000000000, 0 );
3680 :	parrello	1.200	#
3681 :	golsen	1.141	# foreach $x ( @tmp )
3682 :			# {
3683 :			# ( $feature_id, undef, $b1, $e1 ) = @$x;
3684 :			# push @features, $feature_id;
3685 :			# my ( $min, $max ) = ( $b1 <= $e1 ) ? ( $b1, $e1 ) : ( $e1, $b1 );
3686 :			# ( $min_coord <= $min ) \|\| ( $min_coord = $min );
3687 :			# ( $max_coord >= $max ) \|\| ( $max_coord = $max );
3688 :			# }
3689 :			# }
3690 :	parrello	1.200	#
3691 :	golsen	1.141	# return ( @features ) ? ( [ @features ], $min_coord, $max_coord )
3692 :			# : ( [], undef, undef );
3693 :			# }
3694 :
3695 :			# These will be part of the fix to genes_in_region. -- GJO
3696 :
3697 :	parrello	1.287	=head3 regions_spanned
3698 :
3699 :			C<< my ( [ $contig, $beg, $end ], ... ) = $fig->regions_spanned( $loc ); >>
3700 :	golsen	1.141
3701 :	parrello	1.287	or
3702 :	golsen	1.141
3703 :	parrello	1.287	C<< my ( [ $contig, $beg, $end ], ... ) = FIG::regions_spanned( $loc ); >>
3704 :	golsen	1.141
3705 :			The location of a feature in a scalar context is
3706 :
3707 :	parrello	1.287	contig_b1_e1, contig_b2_e2, ... [one contig_b_e for each segment]
3708 :
3709 :			This routine takes as input a scalar location in the above form
3710 :			and reduces it to one or more regions spanned by the gene. This
3711 :			involves combining regions in the location string that are on the
3712 :			same contig and going in the same direction. Unlike L</boundaries_of>,
3713 :			which returns one region in which the entire gene can be found,
3714 :			B<regions_spanned> handles wrapping through the orgin, features
3715 :			split over contigs and exons that are not ordered nicely along
3716 :			the chromosome (ugly but true).
3717 :	golsen	1.141
3718 :	parrello	1.287	=over 4
3719 :
3720 :			=item loc
3721 :
3722 :			The location string for a feature.
3723 :
3724 :			=item RETURN
3725 :
3726 :			Returns a list of list references. Each inner list contains a contig ID, a starting
3727 :			position, and an ending position. The starting position may be numerically greater
3728 :			than the ending position (which indicates a backward-traveling gene). It is
3729 :			guaranteed that the entire feature is covered by the regions in the list.
3730 :
3731 :			=back
3732 :	golsen	1.141
3733 :			=cut
3734 :
3735 :			sub regions_spanned {
3736 :			shift if UNIVERSAL::isa( $_[0], __PACKAGE__ );
3737 :			my( $location ) = ( @_ == 1 ) ? $_[0] : $_[1];
3738 :			defined( $location ) \|\| return undef;
3739 :
3740 :			my @regions = ();
3741 :
3742 :			my ( $cur_contig, $cur_beg, $cur_end, $cur_dir );
3743 :			my ( $contig, $beg, $end, $dir );
3744 :			my @segs = split( /\s,\s/, $location ); # should not have space, but ...
3745 :			@segs \|\| return undef;
3746 :
3747 :			# Process the first segment
3748 :
3749 :			my $seg = shift @segs;
3750 :			( ( $cur_contig, $cur_beg, $cur_end ) = ( $seg =~ /^(\S+)_(\d+)_\d+$/ ) )
3751 :			\|\| return undef;
3752 :			$cur_dir = ( $cur_end >= $cur_beg ) ? 1 : -1;
3753 :
3754 :			foreach $seg ( @segs ) {
3755 :	parrello	1.298	( ( $contig, $beg, $end ) = ( $seg =~ /^(\S+)_(\d+)_\d+$/ ) ) \|\| next;
3756 :			$dir = ( $end >= $beg ) ? 1 : -1;
3757 :	golsen	1.141
3758 :	parrello	1.298	# Is this a continuation? Update end
3759 :	golsen	1.141
3760 :	parrello	1.298	if ( ( $contig eq $cur_contig )
3761 :			&& ( $dir == $cur_dir )
3762 :			&& ( ( ( $dir > 0 ) && ( $end > $cur_end ) )
3763 :			\|\| ( ( $dir < 0 ) && ( $end < $cur_end ) ) )
3764 :			)
3765 :			{
3766 :			$cur_end = $end;
3767 :			}
3768 :	golsen	1.141
3769 :	parrello	1.298	# Not a continuation. Report previous and update current.
3770 :	golsen	1.141
3771 :	parrello	1.298	else
3772 :			{
3773 :			push @regions, [ $cur_contig, $cur_beg, $cur_end ];
3774 :			( $cur_contig, $cur_beg, $cur_end, $cur_dir )
3775 :			= ( $contig, $beg, $end, $dir );
3776 :			}
3777 :	golsen	1.141	}
3778 :
3779 :			# There should alwasy be a valid, unreported region.
3780 :
3781 :			push @regions, [ $cur_contig, $cur_beg, $cur_end ];
3782 :
3783 :			return wantarray ? @regions : \@regions;
3784 :			}
3785 :
3786 :	parrello	1.287	=head3 filter_regions
3787 :
3788 :			C<< my @regions = FIG::filter_regions( $contig, $min, $max, @regions ); >>
3789 :
3790 :			or
3791 :
3792 :			C<< my \@regions = FIG::filter_regions( $contig, $min, $max, @regions ); >>
3793 :
3794 :			or
3795 :
3796 :			C<< my @regions = FIG::filter_regions( $contig, $min, $max, \@regions ); >>
3797 :
3798 :			or
3799 :
3800 :			C<< my \@regions = FIG::filter_regions( $contig, $min, $max, \@regions ); >>
3801 :
3802 :			Filter a list of regions to those that overlap a specified section of a
3803 :			particular contig. Region definitions correspond to those produced
3804 :			by L</regions_spanned>. That is, C<[>I<contig>C<,>I<beg>C<,>I<end>C<]>.
3805 :			In the function call, either I<$contig> or I<$min> and I<$max> can be
3806 :			undefined (permitting anything). So, for example,
3807 :
3808 :			my @regions = FIG::filter_regions(undef, 1, 5000, $regionList);
3809 :
3810 :			would return all regions in C<$regionList> that overlap the first
3811 :			5000 base pairs in any contig. Conversely,
3812 :
3813 :			my @regions = FIG::filter_regions('NC_003904', undef, undef, $regionList);
3814 :	golsen	1.141
3815 :	parrello	1.287	would return all regions on the contig C<NC_003904>.
3816 :	golsen	1.141
3817 :	parrello	1.287	=over 4
3818 :
3819 :			=item contig
3820 :
3821 :			ID of the contig whose regions are to be passed by the filter, or C<undef>
3822 :			if the contig doesn't matter.
3823 :
3824 :			=item min
3825 :
3826 :			Leftmost position of the region used for filtering. Only regions which contain
3827 :			at least one base pair at or beyond this position will be passed. A value
3828 :			of C<undef> is equivalent to zero.
3829 :
3830 :			=item max
3831 :
3832 :			Rightmost position of the region used for filtering. Only regions which contain
3833 :			at least one base pair on or before this position will be passed. A value
3834 :			of C<undef> is equivalent to the length of the contig.
3835 :
3836 :			=item regionList
3837 :	golsen	1.141
3838 :	parrello	1.287	A list of regions, or a reference to a list of regions. Each region is a
3839 :			reference to a three-element list, the first element of which is a contig
3840 :			ID, the second element of which is the start position, and the third
3841 :			element of which is the ending position. (The ending position can be
3842 :			before the starting position if the region is backward-traveling.)
3843 :
3844 :			=item RETURN
3845 :
3846 :			In a scalar context, returns a reference to a list of the filtered regions.
3847 :			In a list context, returns the list itself.
3848 :
3849 :			=back
3850 :	golsen	1.141
3851 :			=cut
3852 :
3853 :			sub filter_regions {
3854 :			my ( $contig, $min, $max, @regions ) = @_;
3855 :
3856 :			@regions \|\| return ();
3857 :			( ref( $regions[0] ) eq "ARRAY" ) \|\| return undef;
3858 :
3859 :			# Is it a region list, or a reference to a region list?
3860 :
3861 :			if ( ref( $regions[0]->[0] ) eq "ARRAY" ) { @regions = @{ $regions[0] } }
3862 :
3863 :			if ( ! defined( $contig ) )
3864 :			{
3865 :			( defined( $min ) && defined( $max ) ) \|\| return undef;
3866 :			}
3867 :			else # with a defined contig name, allow undefined range
3868 :			{
3869 :			defined( $min ) \|\| ( $min = 1 );
3870 :			defined( $max ) \|\| ( $max = 1000000000 );
3871 :			}
3872 :			( $min <= $max ) \|\| return ();
3873 :
3874 :			my ( $c, $b, $e );
3875 :			my @filtered = grep { ( @$_ >= 3 ) # Allow extra fields?
3876 :			&& ( ( $c, $b, $e ) = @$_ )
3877 :			&& ( ( ! defined( $contig ) ) \|\| ( $c eq $contig ) )
3878 :			&& ( ( $e >= $b ) \|\| ( ( $b, $e ) = ( $e, $b ) ) )
3879 :			&& ( ( $b <= $max ) && ( $e >= $min ) )
3880 :			} @regions;
3881 :
3882 :			return wantarray ? @filtered : \@filtered;
3883 :			}
3884 :
3885 :	parrello	1.287	=head3 close_genes
3886 :
3887 :			C<< my @features = $fig->close_genes($fid, $dist); >>
3888 :
3889 :			Return all features within a certain distance of a specified other feature.
3890 :
3891 :			This method is a quick way to get genes that are near another gene. It calls
3892 :			L</boundaries_of> to get the boundaries of the incoming gene, then passes
3893 :			the region computed to L</genes_in_region>.
3894 :
3895 :			So, for example, if the specified I<$dist> is 500, the method would select
3896 :			a region that extends 500 base pairs to either side of the boundaries for
3897 :			the gene I<$fid>, and pass it to C<genes_in_region> for analysis. The
3898 :			features returned would be those that overlap the selected region. Note
3899 :			that the flaws inherent in C<genes_in_region> are also inherent in this
3900 :			method: if a feature is more than 10000 base pairs long, it may not
3901 :			be caught even though it has an overlap in the specified region.
3902 :
3903 :			=over 4
3904 :
3905 :			=item fid
3906 :
3907 :			ID of the relevant feature.
3908 :
3909 :			=item dist
3910 :
3911 :			Desired maximum distance.
3912 :
3913 :			=item RETURN
3914 :
3915 :			Returns a list of feature IDs for genes that overlap or are close to the boundaries
3916 :			for the specified incoming feature.
3917 :
3918 :			=back
3919 :
3920 :			=cut
3921 :	golsen	1.141
3922 :	efrank	1.1	sub close_genes {
3923 :			my($self,$fid,$dist) = @_;
3924 :	parrello	1.200
3925 :	mkubal	1.147	# warn "In close_genes, self=$self, fid=$fid";
3926 :	parrello	1.200
3927 :	efrank	1.1	my $loc = $self->feature_location($fid);
3928 :			if ($loc)
3929 :			{
3930 :	parrello	1.298	my($contig,$beg,$end) = &FIG::boundaries_of($loc);
3931 :			if ($contig && $beg && $end)
3932 :			{
3933 :			my $min = &min($beg,$end) - $dist;
3934 :			my $max = &max($beg,$end) + $dist;
3935 :			my $feat;
3936 :			($feat,undef,undef) = $self->genes_in_region(&FIG::genome_of($fid),$contig,$min,$max);
3937 :			return @$feat;
3938 :			}
3939 :	efrank	1.1	}
3940 :			return ();
3941 :			}
3942 :
3943 :	parrello	1.287	=head3 adjacent_genes
3944 :
3945 :			C<< my ($left_fid, $right_fid) = $fig->adjacent_genes($fid, $dist); >>
3946 :
3947 :			Return the IDs of the genes immediately to the left and right of a specified
3948 :			feature.
3949 :
3950 :			This method gets a list of the features within the specified distance of
3951 :			the incoming feature (using L</close_genes>), and then chooses the two
3952 :			closest to the feature found. If the incoming feature is on the + strand,
3953 :			these are features to the left and the right. If the incoming feature is
3954 :			on the - strand, the features will be returned in reverse order.
3955 :
3956 :			=over 4
3957 :
3958 :			=item fid
3959 :
3960 :			ID of the feature whose neighbors are desired.
3961 :
3962 :			=item dist
3963 :
3964 :			Maximum permissible distance to the neighbors.
3965 :
3966 :			=item RETURN
3967 :
3968 :			Returns a two-element list containing the IDs of the features on either side
3969 :			of the incoming feature.
3970 :
3971 :			=back
3972 :
3973 :			=cut
3974 :
3975 :	mkubal	1.147	sub adjacent_genes
3976 :			{
3977 :			my ($self, $fid, $dist) = @_;
3978 :			my (@close, $strand, $i);
3979 :	parrello	1.200
3980 :	mkubal	1.147	# warn "In adjacent_genes, self=$self, fid=$fid";
3981 :	parrello	1.200
3982 :
3983 :	mkubal	1.147	$strand = $self->strand_of($fid);
3984 :	parrello	1.200
3985 :	mkubal	1.147	$dist = $dist \|\| 2000;
3986 :			@close = $self->close_genes($fid, $dist);
3987 :			for ($i=0; $i < @close; ++$i) { last if ($close[$i] eq $fid); }
3988 :	parrello	1.200
3989 :	redwards	1.157	# RAE note that if $self->strand_of($close[$i-1]) ne $strand then left/right neighbors
3990 :			# were never set! oops!
3991 :	parrello	1.200
3992 :	redwards	1.157	# I think the concept of Left and right is confused here. In my mind, left and right
3993 :			# are independent of strand ?? E.g. take a look at PEG fig\|196600.1.peg.1806
3994 :			# this is something like
3995 :			#
3996 :			# ---> <--1805--- --1806--> <--1807-- <----
3997 :			#
3998 :			# 1805 is always the left neighbor, no?
3999 :
4000 :			my ($left_neighbor, $right_neighbor) = ($close[$i-1], $close[$i+1]);
4001 :	parrello	1.200
4002 :	parrello	1.287	# if (0) # this was if ($i > 0) I just skip this whole section!
4003 :			# {
4004 :	parrello	1.298	# if ($self->strand_of($close[$i-1]) eq $strand) { $left_neighbor = $close[$i-1]; }
4005 :	parrello	1.287	# }
4006 :
4007 :			if ($i < $#close)
4008 :	mkubal	1.147	{
4009 :	parrello	1.298	if ($self->strand_of($close[$i+1]) eq $strand) { $right_neighbor = $close[$i+1]; }
4010 :	mkubal	1.147	}
4011 :	parrello	1.200
4012 :	parrello	1.287	# ...return genes in transcription order...
4013 :			if ($strand eq '-')
4014 :	mkubal	1.147	{
4015 :	parrello	1.298	($left_neighbor, $right_neighbor) = ($right_neighbor, $left_neighbor);
4016 :	mkubal	1.147	}
4017 :	parrello	1.200
4018 :	parrello	1.287	return ($left_neighbor, $right_neighbor) ;
4019 :			}
4020 :
4021 :			=head3 feature_location
4022 :
4023 :			C<< my $loc = $fig->feature_location($fid); >>
4024 :
4025 :			or
4026 :
4027 :			C<< my @loc = $fig->feature_location($fid);; >>
4028 :
4029 :			Return the location of a feature. The location consists
4030 :			of a list of (contigID, begin, end) triples encoded
4031 :			as strings with an underscore delimiter. So, for example,
4032 :			C<NC_002755_100_199> indicates a location starting at position
4033 :			100 and extending through 199 on the contig C<NC_002755>. If
4034 :			the location goes backward, the start location will be higher
4035 :			than the end location (e.g. C<NC_002755_199_100>).
4036 :
4037 :			In a scalar context, this method returns the locations as a
4038 :			comma-delimited string
4039 :	parrello	1.200
4040 :	parrello	1.287	NC_002755_100_199,NC_002755_210_498
4041 :	mkubal	1.147
4042 :	parrello	1.287	In a list context, the locations are returned as a list
4043 :	efrank	1.1
4044 :	parrello	1.287	(NC_002755_100_199, NC_002755_210_498)
4045 :	efrank	1.1
4046 :	parrello	1.287	=over 4
4047 :	efrank	1.1
4048 :	parrello	1.287	=item fid
4049 :	efrank	1.1
4050 :	parrello	1.287	ID of the feature whose location is desired.
4051 :	efrank	1.1
4052 :	parrello	1.287	=item RETURN
4053 :	efrank	1.1
4054 :	parrello	1.287	Returns the locations of a feature, either as a comma-delimited
4055 :			string or a list.
4056 :	efrank	1.1
4057 :	parrello	1.287	=back
4058 :	efrank	1.1
4059 :			=cut
4060 :
4061 :	olson	1.111	sub feature_location :scalar :list {
4062 :	efrank	1.1	my($self,$feature_id) = @_;
4063 :			my($relational_db_response,$locations,$location);
4064 :	parrello	1.200
4065 :	mkubal	1.147	# warn "In feature_location, self=$self, fid=$feature_id";
4066 :	parrello	1.200
4067 :	overbeek	1.136	if ($self->is_deleted_fid($feature_id)) { return undef }
4068 :
4069 :	efrank	1.1	$locations = $self->cached('_location');
4070 :	parrello	1.287	if (! ($location = $locations->{$feature_id})) {
4071 :			my $rdbH = $self->db_handle;
4072 :			if (($relational_db_response = $rdbH->SQL("SELECT location FROM features WHERE ( id = \'$feature_id\' )")) &&
4073 :			(@$relational_db_response == 1)) {
4074 :			$locations->{$feature_id} = $location = $relational_db_response->[0]->[0];
4075 :			}
4076 :	efrank	1.1	}
4077 :
4078 :	parrello	1.287	if ($location) {
4079 :			return wantarray() ? split(/,/,$location) : $location;
4080 :	efrank	1.1	}
4081 :			return undef;
4082 :			}
4083 :
4084 :	parrello	1.298	=head3 contig_of
4085 :
4086 :			C<< my $contigID = $fig->contig_of($location); >>
4087 :
4088 :			Return the ID of the contig containing a location.
4089 :
4090 :			This method only works with SEED-style locations (I<contigID>C<_>I<beg>C<_>I<end>).
4091 :			For more comprehensive location parsing, use the B<Location> object.
4092 :
4093 :			=over 4
4094 :
4095 :			=item location
4096 :
4097 :			A SEED-style location (I<contigID>C<_>I<beg>C<_>I<end>), or a comma-delimited list
4098 :			of SEED-style locations. In the latter case, only the first location in the list will
4099 :			be processed.
4100 :
4101 :			=item RETURN
4102 :
4103 :			Returns the contig ID from the first location in the incoming string.
4104 :
4105 :			=back
4106 :
4107 :			=cut
4108 :	parrello	1.287
4109 :	mkubal	1.147	sub contig_of
4110 :			{
4111 :			my ($self, $locus) = @_;
4112 :	parrello	1.200
4113 :	olson	1.159	$locus =~ m/^([^,]+)_\d+_\d+/;
4114 :	parrello	1.200
4115 :	mkubal	1.147	return $1;
4116 :			}
4117 :
4118 :	parrello	1.298	=head3 beg_of
4119 :
4120 :			C<< my $beg = $fig->beg_of($location); >>
4121 :
4122 :			Return the beginning point of a location.
4123 :
4124 :			This method only works with SEED-style locations (I<contigID>C<_>I<beg>C<_>I<end>).
4125 :			For more comprehensive location parsing, use the B<Location> object.
4126 :
4127 :			=over 4
4128 :
4129 :			=item location
4130 :
4131 :			A SEED-style location (I<contigID>C<_>I<beg>C<_>I<end>), or a comma-delimited list
4132 :			of SEED-style locations. In the latter case, only the first location in the list will
4133 :			be processed.
4134 :
4135 :			=item RETURN
4136 :
4137 :			Returns the beginning point from the first location in the incoming string.
4138 :
4139 :			=back
4140 :
4141 :			=cut
4142 :
4143 :	mkubal	1.147	sub beg_of
4144 :			{
4145 :			my ($self, $locus) = @_;
4146 :	parrello	1.200
4147 :	olson	1.159	$locus =~ m/^[^,]+_(\d+)_\d+/;
4148 :	parrello	1.200
4149 :	mkubal	1.147	return $1;
4150 :			}
4151 :
4152 :	parrello	1.298	=head3 end_of
4153 :
4154 :			C<< my $end = $fig->end_of($location); >>
4155 :
4156 :			Return the ending point of a location.
4157 :
4158 :			This method only works with SEED-style locations (I<contigID>C<_>I<beg>C<_>I<end>).
4159 :			For more comprehensive location parsing, use the B<Location> object.
4160 :
4161 :			=over 4
4162 :
4163 :			=item location
4164 :
4165 :			A SEED-style location (I<contigID>C<_>I<beg>C<_>I<end>), or a comma-delimited list
4166 :			of SEED-style locations. In the latter case, only the first location in the list will
4167 :			be processed.
4168 :
4169 :			=item RETURN
4170 :
4171 :			Returns the contig ID from the first location in the incoming string.
4172 :
4173 :			=back
4174 :
4175 :			=cut
4176 :
4177 :	mkubal	1.147	sub end_of
4178 :			{
4179 :			my ($self, $locus) = @_;
4180 :	parrello	1.200
4181 :	mkubal	1.147	$locus =~ m/\S+_\d+_(\d+)$/;
4182 :	parrello	1.200
4183 :	mkubal	1.147	return $1;
4184 :			}
4185 :
4186 :	parrello	1.298	=head3 strand_of
4187 :
4188 :			C<< my $strand = $fig->contig_of($location); >>
4189 :
4190 :			Return the strand (C<+> or C<->) of a location.
4191 :
4192 :			This method only works with SEED-style locations (I<contigID>C<_>I<beg>C<_>I<end>).
4193 :			For more comprehensive location parsing, use the B<Location> object.
4194 :
4195 :			=over 4
4196 :
4197 :			=item location
4198 :
4199 :			A comma-delimited list of SEED-style location (I<contigID>C<_>I<beg>C<_>I<end>).
4200 :
4201 :			=item RETURN
4202 :
4203 :			Returns C<+> if the list describes a forward-oriented location, and C<-> if the list
4204 :			described a backward-oriented location.
4205 :
4206 :			=back
4207 :
4208 :			=cut
4209 :
4210 :	parrello	1.200	sub strand_of
4211 :	mkubal	1.147	{
4212 :			my ($self, $fid) = @_;
4213 :			my ($beg, $end);
4214 :	parrello	1.200
4215 :	mkubal	1.147	# warn "In strand_of, self=$self, fid=$fid";
4216 :	parrello	1.200
4217 :	mkubal	1.147	(undef, $beg, $end) = $self->boundaries_of($self->feature_location($fid));
4218 :	parrello	1.200
4219 :	mkubal	1.147	if ($beg < $end) { return '+'; } else { return '-'; }
4220 :			}
4221 :
4222 :	parrello	1.287	=head3 find_contig_with_checksum
4223 :	olson	1.158
4224 :	parrello	1.298	C<< my $contigID = $fig->find_contig_with_checksum($genome, $checksum); >>
4225 :
4226 :	olson	1.158	Find a contig in the given genome with the given checksum.
4227 :
4228 :	parrello	1.298	This method is useful for determining if a particular contig has already been
4229 :			recorded for the given genome. The checksum is computed from the contig contents,
4230 :			so a matching checksum indicates that the contigs may have the same content.
4231 :
4232 :			=over 4
4233 :
4234 :			=item genome
4235 :
4236 :			ID of the genome whose contigs are to be examined.
4237 :
4238 :			=item checksum
4239 :
4240 :			Checksum value for the desired contig.
4241 :
4242 :			=item RETURN
4243 :
4244 :			Returns the ID of a contig in the given genome that has the caller-specified checksum,
4245 :			or C<undef> if no such contig exists.
4246 :
4247 :			=back
4248 :
4249 :	olson	1.158	=cut
4250 :
4251 :			sub find_contig_with_checksum
4252 :			{
4253 :			my($self, $genome, $checksum) = @_;
4254 :	parrello	1.200
4255 :	olson	1.158	#
4256 :			# This implementation scans all the contig files for the organism; when
4257 :			# we have contig checksums in the database this will simplify
4258 :			# significantly.
4259 :			#
4260 :			# For some efficiency, we cache the checksums we compute along the way since
4261 :			# it's probably likely we'll poke at other contigs for this organism.
4262 :			#
4263 :