Annotation of /FigKernelPackages/FIG.pm

Revision 1.454 - (view) (download) (as text)

1 :	olson	1.404	#
2 :			# Copyright (c) 2003-2006 University of Chicago and Fellowship
3 :			# for Interpretations of Genomes. All Rights Reserved.
4 :			#
5 :			# This file is part of the SEED Toolkit.
6 :			#
7 :			# The SEED Toolkit is free software. You can redistribute
8 :			# it and/or modify it under the terms of the SEED Toolkit
9 :			# Public License.
10 :			#
11 :			# You should have received a copy of the SEED Toolkit Public License
12 :			# along with this program; if not write to the University of Chicago
13 :			# at info@ci.uchicago.edu or the Fellowship for Interpretation of
14 :			# Genomes at veronika@thefig.info or download a copy from
15 :			# http://www.theseed.org/LICENSE.TXT.
16 :			#
17 :
18 :	efrank	1.1	package FIG;
19 :
20 :	olson	1.111	use strict;
21 :
22 :	overbeek	1.453	use FIG_Config;
23 :
24 :			#
25 :			# See if we need to use fcntl-based file locking. If so, import
26 :			# the package and override the global definition of flock.
27 :			# This is in place at least initially for the GPFS-based install on
28 :			# the NMPDR cluster.
29 :			#
30 :
31 :			use FileLocking;
32 :
33 :	overbeek	1.135	use Fcntl qw/:flock/; # import LOCK_* constants
34 :
35 :	olson	1.116	use POSIX;
36 :	olson	1.158	use IPC::Open2;
37 :	olson	1.329	use MIME::Base64;
38 :	olson	1.330	use File::Basename;
39 :	olson	1.359	use FileHandle;
40 :	parrello	1.394	use File::Copy;
41 :	olson	1.417	use SOAP::Lite;
42 :	parrello	1.420	use File::Path;
43 :	olson	1.116
44 :	efrank	1.1	use DBrtns;
45 :			use Sim;
46 :	olson	1.361	use Annotation;
47 :	efrank	1.1	use Blast;
48 :	overbeek	1.322	use FullLocation;
49 :	overbeek	1.36	use tree_utilities;
50 :	olson	1.93	use Subsystem;
51 :	olson	1.162	use SeedDas;
52 :	olson	1.183	use Construct;
53 :	parrello	1.200	use FIGRules;
54 :	parrello	1.210	use Tracer;
55 :	olson	1.297	use GenomeIDMap;
56 :	olson	1.260
57 :	olson	1.356	our $haveDateParse;
58 :			eval {
59 :			require Date::Parse;
60 :			import Date::Parse;
61 :			$haveDateParse = 1;
62 :			};
63 :
64 :	olson	1.245	eval { require FigGFF; };
65 :	parrello	1.390	if ($@ and T(1)) {
66 :	olson	1.260	warn $@;
67 :			}
68 :	olson	1.79
69 :			#
70 :			# Conditionally evaluate this in case its prerequisites are not available.
71 :			#
72 :
73 :	olson	1.356	our $ClearinghouseOK;
74 :			eval {
75 :	olson	1.79	require Clearinghouse;
76 :	olson	1.356	$ClearinghouseOK = 1;
77 :	olson	1.79	};
78 :	efrank	1.1
79 :	olson	1.10	use IO::Socket;
80 :
81 :	efrank	1.1	use FileHandle;
82 :
83 :			use Carp;
84 :			use Data::Dumper;
85 :	overbeek	1.25	use Time::Local;
86 :	olson	1.93	use File::Spec;
87 :	olson	1.123	use File::Copy;
88 :	olson	1.112	#
89 :			# Try to load the RPC stuff; it might fail on older versions of the software.
90 :			#
91 :			eval {
92 :			require FIGrpc;
93 :			};
94 :
95 :			my $xmlrpc_available = 1;
96 :	parrello	1.287	if ($@ ne "") {
97 :	olson	1.112	$xmlrpc_available = 0;
98 :			}
99 :
100 :	efrank	1.1
101 :	olson	1.111	use FIGAttributes;
102 :			use base 'FIGAttributes';
103 :
104 :			use vars qw(%_FunctionAttributes);
105 :
106 :			use Data::Dumper;
107 :
108 :	olson	1.124	#
109 :			# Force all new files to be all-writable.
110 :			#
111 :
112 :			umask 0;
113 :
114 :	parrello	1.210	=head1 FIG Genome Annotation System
115 :
116 :			=head2 Introduction
117 :
118 :			This is the main object for access to the SEED data store. The data store
119 :			itself is a combination of flat files and a database. The flat files can
120 :			be moved easily between systems and the database rebuilt as needed.
121 :
122 :			A reduced set of this object's functions are available via the B<SFXlate>
123 :			object. The SFXlate object uses a single database to represent all its
124 :			genomic information. It provides a much smaller capability for updating
125 :			the data, and eliminates all similarities except for bidirectional best
126 :			hits.
127 :
128 :			The key to making the FIG system work is proper configuration of the
129 :			C<FIG_Config.pm> file. This file contains names and URLs for the key
130 :			directories as well as the type and login information for the database.
131 :
132 :	parrello	1.287	FIG was designed to operate as a series of peer instances. Each instance is
133 :			updated independently by its owner, and the instances can be synchronized
134 :			using a process called a I<peer-to-peer update>. The terms
135 :			I<SEED instance> and I<peer> are used more-or-less interchangeably.
136 :
137 :			The POD documentation for this module is still in progress, and is provided
138 :			on an AS IS basis without warranty. If you have a correction and you're
139 :			not a developer, EMAIL the details to B<bruce@gigabarb.com> and I'll fold
140 :			it in.
141 :
142 :			B<NOTE>: The usage example for each method specifies whether it is static
143 :
144 :			FIG::something
145 :
146 :			or dynamic
147 :
148 :			$fig->something
149 :
150 :			If the method is static and has no parameters (C<FIG::something()>) it can
151 :	parrello	1.298	also be invoked dynamically. This is a general artifact of the
152 :	parrello	1.287	way PERL implements object-oriented programming.
153 :
154 :	parrello	1.355	=head2 Tracing
155 :
156 :			The FIG object supports tracing using the B<Tracer> module. If tracing is
157 :			inactive when the FIG object is constructed, it will call B<TSetup> using
158 :			parameters specified either in the environment variables or in the
159 :			C<FIG_Config> module. Most command-line tools should call B<TSetup> before
160 :			constructing a FIG object so that the tracing configuration can be specified
161 :			as command-line options. If the prior call to B<TSetup> has not occurred,
162 :			then the environment variables C<Trace> and C<TraceType> will be examined.
163 :			If those do not exist, the global variables I<$FIG_Config::trace_levels> and
164 :			I<$FIG_Config::trace_type> will be used.
165 :
166 :			C<Trace> and I<$FIG_Config::trace_type> specify the tracing level and categories.
167 :			Only tracing calls for the specified categories with a level less than or equal
168 :			to the trace level will be displayed. The higher the trace level or the more
169 :			the categories, the more messages will be displayed. For example, the
170 :			following Unix command will set up for tracing at level 3 for the categories
171 :			C<SQL> and C<Sprout>.
172 :
173 :	parrello	1.390	export Trace="3 SQL Sprout"
174 :	parrello	1.355
175 :			In most cases, the category names is the same as the name of the Perl package
176 :			from which the trace call was made. An asterisk (C<*>) can be used to turn on
177 :			tracing for all categories.
178 :
179 :	parrello	1.390	export Trace="2 *"
180 :	parrello	1.355
181 :			turns on tracing at level 2 for everything.
182 :
183 :			C<TraceType> and C<$FIG_Config::trace_type> determine where the tracing is going
184 :			to show up. A full treatment of all the options can be found in the documentation
185 :			for the B<Tracer> module. The most common options, however, are C<WARN>, which
186 :			converts all trace messages to warnings, and C<TEXT>, which writes them to the
187 :			standard output. The default is C<WARN>, the theory being that this is the best
188 :	parrello	1.390	option during web page construction. If you are operating from a command line
189 :			rather than a web page, you will probably want to do
190 :
191 :			export TraceType="TEXT"
192 :
193 :			to get tracing in the standard output. An alternative is
194 :
195 :			export TraceType="+>~fig/FIG/Tmp/trace.log"
196 :
197 :			which writes tracing to the standard output and copies it into the C<trace.log>
198 :			file in the C<~fig/FIG/Tmp> directory.
199 :	parrello	1.355
200 :	parrello	1.287	=head2 Hiding/Caching in a FIG object
201 :
202 :			We save the DB handle, cache taxonomies, and put a few other odds and ends in the
203 :			FIG object. We expect users to invoke these services using the object $fig constructed
204 :			using:
205 :
206 :			use FIG;
207 :			my $fig = new FIG;
208 :
209 :			$fig is then used as the basic mechanism for accessing FIG services. It is, of course,
210 :			just a hash that is used to retain/cache data. The most commonly accessed item is the
211 :			DB filehandle, which is accessed via $self->db_handle.
212 :
213 :			We cache genus/species expansions, taxonomies, distances (very crudely estimated) estimated
214 :			between genomes, and a variety of other things.
215 :
216 :	parrello	1.210	=cut
217 :
218 :	parrello	1.287
219 :	parrello	1.210	#: Constructor FIG->new();
220 :
221 :			=head2 Public Methods
222 :
223 :			=head3 new
224 :
225 :			C<< my $fig = FIG->new(); >>
226 :
227 :	parrello	1.298	This is the constructor for a FIG object. It uses no parameters. If tracing
228 :			has not yet been turned on, it will be turned on here. The tracing type and
229 :			level are specified by the configuration variables C<$FIG_Config::trace_levels>
230 :	parrello	1.301	and C<$FIG_Config::trace_type>. These defaults can be overridden using the
231 :			environment variables C<Trace> and C<TraceType>, respectively.
232 :	parrello	1.210
233 :			=cut
234 :
235 :	efrank	1.1	sub new {
236 :			my($class) = @_;
237 :
238 :	olson	1.102	#
239 :			# Check to see if we have a FIG_URL environment variable set.
240 :			# If we do, don't actually create a FIG object, but rather
241 :			# create a FIGrpc and return that as the return from this constructor.
242 :			#
243 :	parrello	1.390	if ($ENV{FIG_URL} && $xmlrpc_available) {
244 :	parrello	1.210	my $figrpc = new FIGrpc($ENV{FIG_URL});
245 :			return $figrpc;
246 :	olson	1.102	}
247 :	parrello	1.292	# Here we have the normal case. Check for default tracing. We only do this if
248 :			# the proper parameters are present and nobody else has set up tracing yet.
249 :	parrello	1.355	if (Tracer::Setups() == 0 && (defined $FIG_Config::trace_levels \|\| exists $ENV{Trace})) {
250 :	parrello	1.301	# Tracing is not active and the user has specified tracing levels, so it's safe for
251 :			# us to set it up using our own rules. First, the trace type: the default is WARN.
252 :			my $trace_type;
253 :			if (exists($ENV{TraceType})) {
254 :			$trace_type = $ENV{TraceType};
255 :			} elsif (defined($FIG_Config::trace_type)) {
256 :			$trace_type = $FIG_Config::trace_type;
257 :			} else {
258 :			$trace_type = "WARN";
259 :			}
260 :			# Now the trace levels. The environment variable wins over the FIG_Config value.
261 :			my $trace_levels = (exists($ENV{Trace}) ? $ENV{Trace} : $FIG_Config::trace_levels);
262 :			TSetup($trace_levels, $trace_type);
263 :	parrello	1.287	}
264 :	parrello	1.355	Trace("Connecting to the database.") if T(2);
265 :	parrello	1.287	# Connect to the database, then return ourselves.
266 :	efrank	1.1	my $rdbH = new DBrtns;
267 :	overbeek	1.453
268 :			my $self = {
269 :	parrello	1.210	_dbf => $rdbH,
270 :	overbeek	1.453	};
271 :
272 :			#
273 :			# If we have a readonly-database defined in the config,
274 :			# create a handle for that as well.
275 :			#
276 :
277 :			if (defined($FIG_Config::readonly_dbhost))
278 :			{
279 :			my $ro = new DBrtns($FIG_Config::dbms, $FIG_Config::readonly_db, $FIG_Config::readonly_dbuser,
280 :			$FIG_Config::readonly_dbpass, $FIG_Config::readonly_dbport, $FIG_Config::readonly_dbhost,
281 :			$FIG_Config::readonly_dbsock);
282 :			$self->{_ro_dbf} = $ro;
283 :
284 :			#
285 :			# Oh ick. All of the queries made go through the one dbf that a FIG holds. We want
286 :			# to redirect the select queries through this readonly object. We'll need
287 :			# to tell the main handle about the readonly one, and let it decide.
288 :			#
289 :
290 :			$rdbH->set_readonly_handle($ro);
291 :			}
292 :
293 :			return bless $self, $class;
294 :	efrank	1.1	}
295 :
296 :	overbeek	1.454
297 :	parrello	1.287	=head3 db_handle
298 :
299 :			C<< my $dbh = $fig->db_handle; >>
300 :
301 :			Return the handle to the internal B<DBrtns> object. This allows direct access to
302 :			the database methods.
303 :
304 :			=cut
305 :
306 :			sub db_handle {
307 :			my($self) = @_;
308 :			return $self->{_dbf};
309 :			}
310 :
311 :	overbeek	1.293	sub table_exists {
312 :			my($self,$table) = @_;
313 :
314 :			my $rdbH = $self->db_handle;
315 :			return $rdbH->table_exists($table);
316 :			}
317 :	parrello	1.292
318 :	parrello	1.287	=head3 cached
319 :
320 :			C<< my $x = $fig->cached($name); >>
321 :
322 :			Return a reference to a hash containing transient data. If no hash exists with the
323 :			specified name, create an empty one under that name and return it.
324 :
325 :			The idea behind this method is to allow clients to cache data in the FIG object for
326 :			later use. (For example, a method might cache feature data so that it can be
327 :			retrieved later without using the database.) This facility should be used sparingly,
328 :			since different clients may destroy each other's data if they use the same name.
329 :
330 :			=over 4
331 :
332 :			=item name
333 :
334 :			Name assigned to the cached data.
335 :
336 :			=item RETURN
337 :
338 :			Returns a reference to a hash that is permanently associated with the specified name.
339 :			If no such hash exists, an empty one will be created for the purpose.
340 :
341 :			=back
342 :
343 :			=cut
344 :
345 :			sub cached {
346 :			my($self,$what) = @_;
347 :
348 :			my $x = $self->{$what};
349 :			if (! $x) {
350 :			$x = $self->{$what} = {};
351 :			}
352 :			return $x;
353 :			}
354 :	parrello	1.210
355 :			=head3 get_system_name
356 :
357 :			C<< my $name = $fig->get_system_name; >>
358 :
359 :			Returns C<seed>, indicating that this is object is using the SEED
360 :			database. The same method on an SFXlate object will return C<sprout>.
361 :
362 :			=cut
363 :			#: Return Type $;
364 :			sub get_system_name {
365 :	olson	1.207	return "seed";
366 :	olson	1.205	}
367 :	parrello	1.210
368 :	parrello	1.287	=head3 DESTROY
369 :
370 :			The destructor releases the database handle.
371 :
372 :			=cut
373 :	olson	1.205
374 :	parrello	1.287	sub DESTROY {
375 :	efrank	1.1	my($self) = @_;
376 :			my($rdbH);
377 :
378 :	parrello	1.210	if ($rdbH = $self->db_handle) {
379 :			$rdbH->DESTROY;
380 :	efrank	1.1	}
381 :			}
382 :
383 :	parrello	1.355	=head3 same_seqs
384 :
385 :			C<< my $sameFlag = FIG::same_seqs($s1, $s2); >>
386 :
387 :			Return TRUE if the specified protein sequences are considered equivalent and FALSE
388 :			otherwise. The sequences should be presented in I<nr-analysis> form, which is in
389 :			reverse order and upper case with the stop codon omitted.
390 :
391 :			The sequences will be considered equivalent if the shorter matches the initial
392 :			portion of the long one and is no more than 30% smaller. Since the sequences are
393 :			in nr-analysis form, the equivalent start potions means that the sequences
394 :			have the same tail. The importance of the tail is that the stop point of a PEG
395 :			is easier to find than the start point, so a same tail means that the two
396 :			sequences are equivalent except for the choice of start point.
397 :
398 :			=over 4
399 :
400 :			=item s1
401 :
402 :			First protein sequence, reversed and with the stop codon removed.
403 :
404 :			=item s2
405 :
406 :			Second protein sequence, reversed and with the stop codon removed.
407 :
408 :			=item RETURN
409 :
410 :			Returns TRUE if the two protein sequences are equivalent, else FALSE.
411 :
412 :			=back
413 :
414 :			=cut
415 :
416 :			sub same_seqs {
417 :			my ($s1,$s2) = @_;
418 :
419 :			my $ln1 = length($s1);
420 :			my $ln2 = length($s2);
421 :
422 :			return ((abs($ln1-$ln2) < (0.3 * (($ln1 < $ln2) ? $ln1 : $ln2))) &&
423 :			((($ln1 <= $ln2) && (index($s2,$s1) == 0)) \|\|
424 :			(($ln1 > $ln2) && (index($s1,$s2) == 0))));
425 :			}
426 :
427 :	parrello	1.210	=head3 delete_genomes
428 :
429 :			C<< $fig->delete_genomes(\@genomes); >>
430 :
431 :			Delete the specified genomes from the data store. This requires making
432 :			system calls to move and delete files.
433 :
434 :			=cut
435 :			#: Return Type ;
436 :	overbeek	1.429	################################# make damn sure that you have enough disk ######################
437 :			### The following code represents a serious, major update. Normally, one simply "marks" deleted
438 :			### genomes, which is quick and does not require halting the system.
439 :	overbeek	1.7	sub delete_genomes {
440 :			my($self,$genomes) = @_;
441 :			my $tmpD = "$FIG_Config::temp/tmp.deleted.$$";
442 :			my $tmp_Data = "$FIG_Config::temp/Data.$$";
443 :
444 :			my %to_del = map { $_ => 1 } @$genomes;
445 :			open(TMP,">$tmpD") \|\| die "could not open $tmpD";
446 :
447 :			my $genome;
448 :	parrello	1.287	foreach $genome ($self->genomes) {
449 :			if (! $to_del{$genome}) {
450 :			print TMP "$genome\n";
451 :			}
452 :	overbeek	1.7	}
453 :			close(TMP);
454 :
455 :			&run("extract_genomes $tmpD $FIG_Config::data $tmp_Data");
456 :	overbeek	1.429	print STDERR "Please bring the system down for a bit\n";
457 :			system "echo \"System down due to update of genomes\n\" >> $tmp_Data/Global/why_down";
458 :	parrello	1.200	&run("mv $FIG_Config::data $FIG_Config::data.deleted");
459 :	overbeek	1.47	&run("mv $tmp_Data $FIG_Config::data");
460 :			&run("fig load_all");
461 :	overbeek	1.429	print STDERR "Now, you should think about deleting $FIG_Config::data.deleted\n";
462 :			unlink("$FIG_Config::global/why_down"); ### start allowing CGIs to run
463 :			# &run("rm -rf $FIG_Config::data.deleted");
464 :			}
465 :
466 :			### Mark a genome as deleted, but do not actually clean up anything. That whole event
467 :			### requires "delete_genomes"
468 :			###
469 :			sub mark_deleted_genomes {
470 :			my($self,$genomes) = @_;
471 :			my($genome);
472 :
473 :	overbeek	1.440	my $x = join(",",@$genomes);
474 :			&log_update("mark_deleted_genomes\t$x");
475 :
476 :	overbeek	1.429	my $rdbH = $self->db_handle;
477 :
478 :			my $n = 0;
479 :			foreach $genome (@$genomes)
480 :			{
481 :			if ($self->is_genome($genome) && open(DEL,">$FIG_Config::organisms/$genome/DELETED"))
482 :			{
483 :			print DEL "deleted\n";
484 :			$rdbH->SQL("DELETE FROM genome WHERE ( genome = '$genome' )");
485 :			$n++;
486 :			}
487 :			close(DEL);
488 :			}
489 :			return $n;
490 :			}
491 :
492 :			sub unmark_deleted_genomes {
493 :			my($self,$genomes) = @_;
494 :			my($genome);
495 :
496 :	overbeek	1.440	my $x = join(",",@$genomes);
497 :			&log_update("unmark_deleted_genomes\t$x");
498 :	overbeek	1.429	my $rdbH = $self->db_handle;
499 :
500 :			my $n = 0;
501 :			foreach $genome (@$genomes)
502 :			{
503 :			if (-s "$FIG_Config::organisms/$genome/DELETED")
504 :			{
505 :			unlink("$FIG_Config::organisms/$genome/DELETED");
506 :			&run("compute_genome_counts $genome");
507 :			$n++;
508 :			}
509 :			}
510 :			return $n;
511 :	overbeek	1.7	}
512 :	parrello	1.200
513 :	parrello	1.210	=head3 add_genome
514 :
515 :	overbeek	1.335	C<< my $ok = $fig->add_genome($genomeF, $force, $skipnr); >>
516 :	parrello	1.210
517 :			Add a new genome to the data store. A genome's data is kept in a directory
518 :	parrello	1.287	by itself, underneath the main organism directory. This method essentially
519 :			moves genome data from an external directory to the main directory and
520 :			performs some indexing tasks to integrate it.
521 :	parrello	1.210
522 :			=over 4
523 :
524 :			=item genomeF
525 :
526 :	parrello	1.287	Name of the directory containing the genome files. This should be a
527 :			fully-qualified directory name. The last segment of the directory
528 :			name should be the genome ID.
529 :	parrello	1.210
530 :	overbeek	1.331	=item force
531 :
532 :			This will ignore errors thrown by verify_genome_directory. This is bad, and you should
533 :			never do it, but I am in the situation where I need to move a genome from one machine
534 :			to another, and although I trust the genome I can't.
535 :
536 :	overbeek	1.335	=item skipnr
537 :
538 :			We don't always want to add the pooteins into the nr database. For example wih a metagnome that has been called by blastx. This will just skip appending the proteins into the NR file.
539 :
540 :	parrello	1.210	=item RETURN
541 :
542 :			Returns TRUE if successful, else FALSE.
543 :
544 :			=back
545 :
546 :			=cut
547 :			#: Return Type $;
548 :	efrank	1.1	sub add_genome {
549 :	overbeek	1.335	my($self,$genomeF, $force, $skipnr) = @_;
550 :	efrank	1.1
551 :	overbeek	1.440	&log_update("add_genome $genomeF $force $skipnr",$genomeF);
552 :
553 :	efrank	1.1	my $rc = 0;
554 :	olson	1.93
555 :			my(undef, $path, $genome) = File::Spec->splitpath($genomeF);
556 :
557 :	parrello	1.287	if ($genome !~ /^\d+\.\d+$/) {
558 :			warn "Invalid genome filename $genomeF\n";
559 :			return $rc;
560 :	olson	1.93	}
561 :
562 :	parrello	1.287	if (-d $FIG_Config::organisms/$genome) {
563 :			warn "Organism already exists for $genome\n";
564 :			return $rc;
565 :	olson	1.93	}
566 :	parrello	1.200
567 :	olson	1.93
568 :			#
569 :			# We're okay, it doesn't exist.
570 :			#
571 :
572 :			my @errors = `$FIG_Config::bin/verify_genome_directory $genomeF`;
573 :
574 :	parrello	1.287	if (@errors) {
575 :			warn "Errors found while verifying genome directory $genomeF:\n";
576 :			print join("", @errors);
577 :	overbeek	1.331	if (!$force) {return $rc}
578 :	parrello	1.365	else {warn "Skipped these errors and continued. You should not do this"}
579 :	olson	1.93	}
580 :	parrello	1.200
581 :	olson	1.93	&run("cp -r $genomeF $FIG_Config::organisms");
582 :			&run("chmod -R 777 $FIG_Config::organisms/$genome");
583 :	parrello	1.379
584 :	overbeek	1.353	if (-s "$FIG_Config::organisms/$genome/COMPLETE")
585 :			{
586 :	parrello	1.365	print STDERR "$genome was marked as \"complete\"\n";
587 :	overbeek	1.353	}
588 :			else
589 :			{
590 :	parrello	1.365	&run("assess_completeness $genome");
591 :			if (-s "$FIG_Config::organisms/$genome/PROBABLY_COMPLETE")
592 :			{
593 :			print STDERR "Assessed $genome to be probably complete\n";
594 :			&run("cp -p $FIG_Config::organisms/$genome/PROBABLY_COMPLETE $FIG_Config::organisms/$genome/COMPLETE");
595 :			}
596 :			else
597 :			{
598 :			print STDERR "Assessed $genome to not be probably complete\n";
599 :			}
600 :	overbeek	1.353	}
601 :	parrello	1.379
602 :	olson	1.93	&run("index_contigs $genome");
603 :			&run("compute_genome_counts $genome");
604 :			&run("load_features $genome");
605 :	parrello	1.379
606 :	olson	1.93	$rc = 1;
607 :	parrello	1.287	if (-s "$FIG_Config::organisms/$genome/Features/peg/fasta") {
608 :			&run("index_translations $genome");
609 :			my @tmp = `cut -f1 $FIG_Config::organisms/$genome/Features/peg/tbl`;
610 :			chomp @tmp;
611 :	overbeek	1.335	&run("cat $FIG_Config::organisms/$genome/Features/peg/fasta >> $FIG_Config::data/Global/nr") if (!$skipnr);
612 :	overbeek	1.370	# &run("formatdb -i $FIG_Config::data/Global/nr -p T") if (!$skipnr);
613 :	parrello	1.287	&enqueue_similarities(\@tmp);
614 :	olson	1.93	}
615 :			if ((-s "$FIG_Config::organisms/$genome/assigned_functions") \|\|
616 :	parrello	1.287	(-d "$FIG_Config::organisms/$genome/UserModels")) {
617 :			&run("add_assertions_of_function $genome");
618 :	efrank	1.1	}
619 :	parrello	1.200
620 :	efrank	1.1	return $rc;
621 :			}
622 :
623 :	overbeek	1.440	sub log_update {
624 :			my($msg,@data) = @_;
625 :
626 :			my $time_made = time;
627 :			&verify_dir("$FIG_Config::data/Logs/Tars");
628 :			my($i,$file_or_dir,@tars);
629 :			for ($i=0; ($i < @data); $i++)
630 :			{
631 :			$file_or_dir = $data[$i];
632 :			my($dir,$file);
633 :			if ($file_or_dir =~ /^(.*)\/([^\/]+)$/)
634 :			{
635 :			($dir,$file) = ($1,$2);
636 :			}
637 :			else
638 :			{
639 :			($dir,$file) = (".",$file_or_dir);
640 :			}
641 :			my $tar = "$FIG_Config::data/Logs/Tars/$time_made.$i.tgz";
642 :			&run("cd $dir; tar czf $tar $file");
643 :			push(@tars,$tar);
644 :			}
645 :			open(LOG,">>$FIG_Config::data/Logs/update.log")
646 :			\|\| die "could not open $FIG_Config::data/Logs/update.log";
647 :			print LOG "$time_made\t$msg\t",join(",",@tars),"\n";
648 :			close(LOG);
649 :			}
650 :
651 :
652 :	parrello	1.287	=head3 parse_genome_args
653 :
654 :			C<< my ($mode, @genomes) = FIG::parse_genome_args(@args); >>
655 :
656 :			Extract a list of genome IDs from an argument list. If the argument list is empty,
657 :			return all the genomes in the data store.
658 :
659 :			This is a function that is performed by many of the FIG command-line utilities. The
660 :			user has the option of specifying a list of specific genome IDs or specifying none
661 :			in order to get all of them. If your command requires additional arguments in the
662 :			command line, you can still use this method if you shift them out of the argument list
663 :			before calling. The $mode return value will be C<all> if the user asked for all of
664 :			the genomes or C<some> if he specified a list of IDs. This is useful to know if,
665 :			for example, we are loading a table. If we're loading everything, we can delete the
666 :			entire table; if we're only loading some genomes, we must delete them individually.
667 :
668 :			This method uses the genome directory rather than the database because it may be used
669 :			before the database is ready.
670 :
671 :			=over 4
672 :
673 :			=item args1, args2, ... argsN
674 :
675 :			List of genome IDs. If all genome IDs are to be processed, then this list should be
676 :			empty.
677 :
678 :			=item RETURN
679 :
680 :			Returns a list. The first element of the list is C<all> if the user is asking for all
681 :			the genome IDs and C<some> otherwise. The remaining elements of the list are the
682 :			desired genome IDs.
683 :
684 :			=back
685 :
686 :			=cut
687 :
688 :			sub parse_genome_args {
689 :			# Get the parameters.
690 :			my @args = @_;
691 :			# Check the mode.
692 :			my $mode = (@args > 0 ? 'some' : 'all');
693 :			# Build the return list.
694 :			my @retVal = ($mode);
695 :			# Process according to the mode.
696 :			if ($mode eq 'all') {
697 :			# We want all the genomes, so we get them from the organism directory.
698 :			my $orgdir = "$FIG_Config::organisms";
699 :			opendir( GENOMES, $orgdir ) \|\| Confess("Could not open directory $orgdir");
700 :			push @retVal, grep { $_ =~ /^\d/ } readdir( GENOMES );
701 :			closedir( GENOMES );
702 :			} else {
703 :			# We want only the genomes specified by the user.
704 :			push @retVal, @args;
705 :			}
706 :			# Return the result.
707 :			return @retVal;
708 :			}
709 :
710 :			=head3 reload_table
711 :
712 :			C<< $fig->reload_table($mode, $table, $flds, $xflds, $fileName, $keyList, $keyName); >>
713 :
714 :			Reload a database table from a sequential file. If I<$mode> is C<all>, the table
715 :			will be dropped and re-created. If I<$mode> is C<some>, the data for the individual
716 :			items in I<$keyList> will be deleted before the table is loaded. Thus, the load
717 :			process is optimized for the type of reload.
718 :
719 :			=over 4
720 :
721 :			=item mode
722 :
723 :			C<all> if we are reloading the entire table, C<some> if we are only reloading
724 :			specific entries.
725 :
726 :			=item table
727 :
728 :			Name of the table to reload.
729 :
730 :			=item flds
731 :
732 :			String defining the table columns, in SQL format. In general, this is a
733 :			comma-delimited set of field specifiers, each specifier consisting of the
734 :			field name followed by the field type and any optional qualifiers (such as
735 :			C<NOT NULL> or C<DEFAULT>); however, it can be anything that would appear
736 :			between the parentheses in a C<CREATE TABLE> statement. The order in which
737 :			the fields are specified is important, since it is presumed that is the
738 :			order in which they are appearing in the load file.
739 :
740 :			=item xflds
741 :
742 :			Reference to a hash that describes the indexes. The hash is keyed by index name.
743 :			The value is the index's field list. This is a comma-delimited list of field names
744 :			in order from most significant to least significant. If a field is to be indexed
745 :			in descending order, its name should be followed by the qualifier C<DESC>. For
746 :			example, the following I<$xflds> value will create two indexes, one for name followed
747 :			by creation date in reverse chronological order, and one for ID.
748 :
749 :			{ name_index => "name, createDate DESC", id_index => "id" }
750 :
751 :			=item fileName
752 :
753 :			Fully-qualified name of the file containing the data to load. Each line of the
754 :			file must correspond to a record, and the fields must be arranged in order and
755 :	parrello	1.298	tab-delimited. If the file name is omitted, the table is dropped and re-created
756 :			but not loaded.
757 :	parrello	1.287
758 :			=item keyList
759 :
760 :			Reference to a list of the IDs for the objects being reloaded. This parameter is
761 :			only used if I<$mode> is C<some>.
762 :
763 :			=item keyName (optional)
764 :
765 :			Name of the key field containing the IDs in the keylist. If omitted, C<genome> is
766 :			assumed.
767 :
768 :			=back
769 :
770 :			=cut
771 :
772 :			sub reload_table {
773 :	parrello	1.298	# Get the parameters.
774 :			my ($self, $mode, $table, $flds, $xflds, $fileName, $keyList, $keyName) = @_;
775 :	parrello	1.287	if (!defined $keyName) {
776 :			$keyName = 'genome';
777 :			}
778 :			# Get the database handler.
779 :			my $dbf = $self->{_dbf};
780 :	parrello	1.298	# Call the DBKernel method.
781 :			$dbf->reload_table($mode, $table, $flds, $xflds, $fileName, $keyList, $keyName);
782 :	parrello	1.287	}
783 :
784 :	parrello	1.210	=head3 enqueue_similarities
785 :	olson	1.93
786 :	parrello	1.287	C<< FIG::enqueue_similarities(\@fids); >>
787 :
788 :			Queue the passed Feature IDs for similarity computation. The actual
789 :			computation is performed by L</create_sim_askfor_pool>. The queue is a
790 :			persistent text file in the global data directory, and this method
791 :			essentially writes new IDs on the end of it.
792 :
793 :			=over 4
794 :
795 :			=item fids
796 :
797 :			Reference to a list of feature IDs.
798 :	olson	1.93
799 :	parrello	1.287	=back
800 :	olson	1.93
801 :			=cut
802 :	parrello	1.210	#: Return Type ;
803 :	olson	1.93	sub enqueue_similarities {
804 :	olson	1.334	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
805 :	efrank	1.1	my($fids) = @_;
806 :			my $fid;
807 :
808 :	olson	1.93	my $sim_q = "$FIG_Config::global/queued_similarities";
809 :
810 :			open(TMP,">>$sim_q")
811 :	parrello	1.287	\|\| die "could not open $sim_q";
812 :	olson	1.93
813 :			#
814 :			# We need to lock here so that if a computation is creating a snapshot of the
815 :			# queue, we block until it's done.
816 :			#
817 :
818 :			flock(TMP, LOCK_EX) or die "Cannot lock $sim_q\n";
819 :	overbeek	1.442	seek(TMP, 0, 2);
820 :	olson	1.93
821 :	parrello	1.287	foreach $fid (@$fids) {
822 :			print TMP "$fid\n";
823 :	efrank	1.1	}
824 :			close(TMP);
825 :	olson	1.10	}
826 :
827 :	olson	1.281	=head3 export_similarity_request
828 :
829 :			Creates a similarity computation request from the queued similarities and
830 :	parrello	1.287	the current NR.
831 :	olson	1.281
832 :			We keep track of the exported requests in case one gets lost.
833 :
834 :			=cut
835 :
836 :	parrello	1.287	sub export_similarity_request {
837 :	overbeek	1.439	my($self, $user_req_dir) = @_;
838 :
839 :			my $nr_file = "$user_req_dir/nr";
840 :			my $fasta_file = "$user_req_dir/fasta";
841 :			my $peg_syn_file = "$user_req_dir/peg.synonyms";
842 :	olson	1.281
843 :			my $req_dir = "$FIG_Config::fig/var/sim_requests";
844 :			&verify_dir("$FIG_Config::fig/var");
845 :			&verify_dir($req_dir);
846 :
847 :			$req_dir = "$req_dir/" . time;
848 :			&verify_dir($req_dir);
849 :
850 :			#
851 :			# Open all of our output files before zeroing out the sim queue, in case
852 :			# there is a problem.
853 :			#
854 :
855 :			open(my $user_fasta_fh, ">$fasta_file") or confess "Cannot open $fasta_file for writing: $!";
856 :			open(my $fasta_fh, ">$req_dir/fasta.in");
857 :
858 :			open(my $user_nr_fh, ">$nr_file") or confess "Cannot open $nr_file for writing: $!";
859 :			open(my $nr_fh, ">$req_dir/nr") or confess "Cannot open $req_dir/nr for writing: $!";
860 :
861 :	overbeek	1.439	open(my $user_peg_syn_fh, ">$peg_syn_file") or confess "Cannot open $peg_syn_file for writing: $!";
862 :			open(my $peg_syn_fh, ">$req_dir/peg.synonyms") or confess "Cannot open $req_dir/peg.synonyms for writing: $!";
863 :
864 :	olson	1.281	open(my $nr_read_fh, "<$FIG_Config::data/Global/nr") or die "Cannot open $FIG_Config::data/Global/nr for reading: $!";
865 :	overbeek	1.439	open(my $peg_syn_read_fh, "<$FIG_Config::data/Global/peg.synonyms") or die "Cannot open $FIG_Config::data/Global/peg.synonyms for reading: $!";
866 :	parrello	1.287
867 :	olson	1.281	my $sim_q = "$FIG_Config::global/queued_similarities";
868 :
869 :			#
870 :			# We need to lock here so that if a computation is creating a snapshot of the
871 :			# queue, we block until it's done.
872 :			#
873 :
874 :			open(my $sim_q_lock, ">>$sim_q") or confess "could not open $sim_q";
875 :			flock($sim_q_lock, LOCK_EX) or confess "Cannot lock $sim_q\n";
876 :
877 :			#
878 :			# Everything open & locked, start copying.
879 :			#
880 :	parrello	1.287
881 :	olson	1.281	copy("$sim_q", "$req_dir/q") or confess "Copy $sim_q $req_dir/q failed: $!";
882 :	overbeek	1.439	copy("$sim_q", "$user_req_dir/q") or confess "Copy $sim_q $user_req_dir/q failed: $!";
883 :	parrello	1.287
884 :	overbeek	1.442	#
885 :			# Copy the contents of the sim queue to the "expected import" queue;
886 :			# this is a list of pegs for which we expect sims to be computed and installed
887 :			# at some point.
888 :			#
889 :			# We also lock on the pending queue file.
890 :			#
891 :
892 :			if (not(open(SQ, "<$sim_q")))
893 :			{
894 :			warn "Cannot open $sim_q for reading: $!\n";
895 :			}
896 :			else
897 :			{
898 :			if (open(AW, ">>$FIG_Config::global/pending_similarities"))
899 :			{
900 :			flock(AW, LOCK_EX);
901 :			seek(AW, 0, 2);
902 :
903 :			while (<SQ>)
904 :			{
905 :			print AW @_;
906 :			}
907 :			close(AW);
908 :			}
909 :			else
910 :			{
911 :			warn "Could not open $FIG_Config::global/pending_similarities: $!\n";
912 :			}
913 :			close(SQ);
914 :			}
915 :
916 :	olson	1.281	my($buf);
917 :	parrello	1.287	while (1) {
918 :			my $n = read($nr_read_fh, $buf, 4096);
919 :			defined($n) or confess "Error reading nr: $!";
920 :			last unless $n;
921 :			syswrite($user_nr_fh, $buf) or confess "Error writing $nr_file: $!";
922 :			syswrite($nr_fh, $buf) or confess "Error writing $req_dir/nr: $!";
923 :	olson	1.281	}
924 :
925 :			close($nr_read_fh);
926 :			close($nr_fh);
927 :			close($user_nr_fh);
928 :
929 :	overbeek	1.439	while (1) {
930 :			my $n = read($peg_syn_read_fh, $buf, 4096);
931 :			defined($n) or confess "Error reading peg.synonyms: $!";
932 :			last unless $n;
933 :			syswrite($user_peg_syn_fh, $buf) or confess "Error writing $peg_syn_file: $!";
934 :			syswrite($peg_syn_fh, $buf) or confess "Error writing $req_dir/peg.synonyms: $!";
935 :			}
936 :
937 :			close($peg_syn_read_fh);
938 :			close($peg_syn_fh);
939 :			close($user_peg_syn_fh);
940 :
941 :	olson	1.281	#
942 :			# We can zero out the queue and unlock now.
943 :			#
944 :
945 :			open(F, ">$sim_q") or die "Cannot open $sim_q to truncate it: $!\n";
946 :			close(F);
947 :	parrello	1.287
948 :	olson	1.281	close($sim_q_lock);
949 :
950 :			#
951 :			# Generate the fasta input from the queued ids.
952 :			#
953 :
954 :			open(my $q_fh, "<$req_dir/q");
955 :	parrello	1.287	while (my $id = <$q_fh>) {
956 :			chomp $id;
957 :	olson	1.281
958 :	parrello	1.287	my $seq = $self->get_translation($id);
959 :	olson	1.281
960 :	parrello	1.287	display_id_and_seq($id, \$seq, $user_fasta_fh);
961 :			display_id_and_seq($id, \$seq, $fasta_fh);
962 :	olson	1.281	}
963 :			close($q_fh);
964 :
965 :			close($user_fasta_fh);
966 :			close($fasta_fh);
967 :			}
968 :
969 :	parrello	1.210	=head3 create_sim_askfor_pool
970 :	olson	1.93
971 :	parrello	1.287	C<< $fig->create_sim_askfor_pool($chunk_size); >>
972 :	olson	1.93
973 :	parrello	1.287	Creates an askfor pool, which a snapshot of the current NR and similarity
974 :			queue. This process clears the old queue.
975 :	olson	1.123
976 :			The askfor pool needs to keep track of which sequences need to be
977 :			calculated, which have been handed out, etc. To simplify this task we
978 :	olson	1.279	chunk the sequences into fairly small numbers (20k characters) and
979 :	olson	1.123	allocate work on a per-chunk basis. We make use of the relational
980 :			database to keep track of chunk status as well as the seek locations
981 :			into the file of sequence data. The initial creation of the pool
982 :			involves indexing the sequence data with seek offsets and lengths and
983 :			populating the sim_askfor_index table with this information and with
984 :			initial status information.
985 :	olson	1.93
986 :	parrello	1.287	=over 4
987 :
988 :			=item chunk_size
989 :
990 :			Number of features to put into a processing chunk. The default is 15.
991 :
992 :			=back
993 :
994 :	parrello	1.200	=cut
995 :	parrello	1.210	#: Return Type $;
996 :	parrello	1.287	sub create_sim_askfor_pool {
997 :	olson	1.123	my($self, $chunk_size) = @_;
998 :
999 :	olson	1.279	$chunk_size = 20000 unless $chunk_size =~ /^\d+$/;
1000 :	olson	1.93
1001 :	olson	1.279	my $pool_dir = "$FIG_Config::fig/var/sim_pools";
1002 :	olson	1.93	&verify_dir($pool_dir);
1003 :
1004 :			#
1005 :			# Lock the pool directory.
1006 :			#
1007 :			open(my $lock, ">$pool_dir/lockfile");
1008 :
1009 :			flock($lock, LOCK_EX);
1010 :
1011 :			my $num = 0;
1012 :	parrello	1.287	if (open(my $toc, "<$pool_dir/TOC")) {
1013 :			while (<$toc>) {
1014 :			chomp;
1015 :			# print STDERR "Have toc entry $_\n";
1016 :			my ($idx, $time, $str) = split(/\s+/, $_, 3);
1017 :	olson	1.93
1018 :	parrello	1.287	$num = max($num, $idx);
1019 :			}
1020 :			close($toc);
1021 :	olson	1.93	}
1022 :			$num++;
1023 :			open(my $toc, ">>$pool_dir/TOC") or die "Cannot write $pool_dir/TOC: $!\n";
1024 :
1025 :			print $toc "$num ", time(), " New toc entry\n";
1026 :			close($toc);
1027 :
1028 :	olson	1.123	my $cpool_id = sprintf "%04d", $num;
1029 :			my $cpool_dir = "$pool_dir/$cpool_id";
1030 :	olson	1.93
1031 :			#
1032 :			# All set, create the directory for this pool.
1033 :			#
1034 :
1035 :			&verify_dir($cpool_dir);
1036 :
1037 :			#
1038 :			# Now we can copy the nr and sim queue here.
1039 :			# Do this stuff inside an eval so we can clean up
1040 :			# the lockfile.
1041 :			#
1042 :
1043 :			eval {
1044 :	parrello	1.287	my $sim_q = "$FIG_Config::global/queued_similarities";
1045 :	olson	1.93
1046 :	parrello	1.287	copy("$sim_q", "$cpool_dir/q");
1047 :			copy("$FIG_Config::data/Global/nr", "$cpool_dir/nr");
1048 :	olson	1.93
1049 :	parrello	1.287	open(F, ">$sim_q") or die "Cannot open $sim_q to truncate it: $!\n";
1050 :			close(F);
1051 :	olson	1.93	};
1052 :	parrello	1.200
1053 :	olson	1.93	unlink("$pool_dir/lockfile");
1054 :			close($lock);
1055 :	olson	1.123
1056 :			#
1057 :			# We've created our pool; we can now run the formatdb and
1058 :			# extract the sequences for the blast run.
1059 :			#
1060 :	parrello	1.287	my $child_pid = $self->run_in_background(
1061 :			sub {
1062 :			#
1063 :			# Need to close db or there's all sorts of trouble.
1064 :			#
1065 :
1066 :			my $cmd = "$FIG_Config::ext_bin/formatdb -i $cpool_dir/nr -p T -l $cpool_dir/formatdb.log";
1067 :			print "Will run '$cmd'\n";
1068 :			&run($cmd);
1069 :			print "finished. Logfile:\n";
1070 :			print &FIG::file_read("$cpool_dir/formatdb.log");
1071 :			unlink("$cpool_dir/formatdb.pid");
1072 :			});
1073 :	olson	1.279	warn "Running formatdb in background job $child_pid\n";
1074 :	olson	1.123	open(FPID, ">$cpool_dir/formatdb.pid");
1075 :			print FPID "$child_pid\n";
1076 :			close(FPID);
1077 :
1078 :			my $db = $self->db_handle();
1079 :	parrello	1.287	if (!$db->table_exists("sim_queue")) {
1080 :			$db->create_table(tbl => "sim_queue",
1081 :			flds => "qid varchar(32), chunk_id INTEGER, seek INTEGER, len INTEGER, " .
1082 :			"assigned BOOL, finished BOOL, output_file varchar(255), " .
1083 :	olson	1.430	"worker_pid INTEGER, start_time timestamp, " .
1084 :	parrello	1.287	"assignment_expires INTEGER, worker_info varchar(255)"
1085 :			);
1086 :	olson	1.123	}
1087 :
1088 :			#
1089 :			# Write the fasta input file. Keep track of how many have been written,
1090 :			# and write seek info into the database as appropriate.
1091 :			#
1092 :
1093 :			open(my $seq_fh, ">$cpool_dir/fasta.in");
1094 :
1095 :			my($chunk_idx, $chunk_begin, $seq_idx);
1096 :
1097 :	olson	1.279	my $cur_size = 0;
1098 :
1099 :	olson	1.123	$chunk_idx = 0;
1100 :			$chunk_begin = 0;
1101 :			$seq_idx = 0;
1102 :
1103 :	olson	1.279	my $tmpfile = "$FIG_Config::temp/simseek.$$";
1104 :			open(my $tmpfh, ">$tmpfile") or confess "Cannot open tmpfile $tmpfile: $!";
1105 :
1106 :	olson	1.123	open(my $q_fh, "<$cpool_dir/q");
1107 :	parrello	1.287	while (my $id = <$q_fh>) {
1108 :			chomp $id;
1109 :	olson	1.123
1110 :	parrello	1.287	my $seq = $self->get_translation($id);
1111 :	olson	1.123
1112 :	parrello	1.287	#
1113 :			# check if we're at the beginning of a chunk
1114 :			#
1115 :
1116 :			print $seq_fh ">$id\n$seq\n";
1117 :
1118 :			#
1119 :			# Check if we're at the end of a chunk
1120 :			#
1121 :
1122 :			$cur_size += length($seq);
1123 :			if ($cur_size >= $chunk_size) {
1124 :			my $chunk_end = tell($seq_fh);
1125 :			my $chunk_len = $chunk_end - $chunk_begin;
1126 :
1127 :	olson	1.430	print $tmpfh join("\t", $cpool_id, $chunk_idx, $chunk_begin, $chunk_len, 'FALSE', 'FALSE',
1128 :			'\N', '\N', '\N', '\N', '\N'), "\n";
1129 :	parrello	1.287	$chunk_idx++;
1130 :			$chunk_begin = $chunk_end;
1131 :			$cur_size = 0;
1132 :			}
1133 :			$seq_idx++;
1134 :	olson	1.123	}
1135 :
1136 :	parrello	1.287	if ($cur_size > 0) {
1137 :			my $chunk_end = tell($seq_fh);
1138 :			my $chunk_len = $chunk_end - $chunk_begin;
1139 :	olson	1.123
1140 :	olson	1.430	print $tmpfh join("\t", $cpool_id, $chunk_idx, $chunk_begin, $chunk_len, 'FALSE', 'FALSE',
1141 :			'\N', '\N', '\N', '\N', '\N'), "\n";
1142 :	olson	1.123	}
1143 :
1144 :			close($q_fh);
1145 :			close($seq_fh);
1146 :	olson	1.279	close($tmpfh);
1147 :	olson	1.123
1148 :	olson	1.279	warn "Write seqs from $tmpfile\n";
1149 :	olson	1.123
1150 :	olson	1.279	$self->db_handle->load_table(tbl => 'sim_queue',
1151 :	parrello	1.298	file => $tmpfile);
1152 :	parrello	1.200
1153 :	olson	1.430	# unlink($tmpfile);
1154 :	parrello	1.287
1155 :	olson	1.279	# for my $seek (@seeks)
1156 :			# {
1157 :	parrello	1.298	# my($cpool_id, $chunk_idx, $chunk_begin, $chunk_len) = @$seek;
1158 :	olson	1.279
1159 :	parrello	1.298	# $db->SQL("insert into sim_queue (qid, chunk_id, seek, len, assigned, finished) " .
1160 :			# "values('$cpool_id', $chunk_idx, $chunk_begin, $chunk_len, FALSE, FALSE)");
1161 :	olson	1.279	# }
1162 :	parrello	1.200
1163 :	olson	1.123	return $cpool_id;
1164 :			}
1165 :
1166 :	parrello	1.210	#=head3 get_sim_queue
1167 :			#
1168 :			#usage: get_sim_queue($pool_id, $all_sims)
1169 :			#
1170 :			#Returns the sims in the given pool. If $all_sims is true, return the entire queue. Otherwise,
1171 :			#just return the sims awaiting processing.
1172 :			#
1173 :			#=cut
1174 :	olson	1.123
1175 :	parrello	1.287	sub get_sim_queue {
1176 :	olson	1.123	my($self, $pool_id, $all_sims) = @_;
1177 :	olson	1.279	}
1178 :
1179 :	parrello	1.287	=head3 get_sim_work
1180 :	olson	1.279
1181 :	parrello	1.287	C<< my ($nrPath, $fasta) = $fig->get_sim_work(); >>
1182 :	olson	1.279
1183 :			Get the next piece of sim computation work to be performed. Returned are
1184 :			the path to the NR and a string containing the fasta data.
1185 :
1186 :			=cut
1187 :
1188 :	parrello	1.287	sub get_sim_work {
1189 :
1190 :			my ($self) = @_;
1191 :	olson	1.279
1192 :			#
1193 :			# For now, just don't care about order of data that we get back.
1194 :			#
1195 :
1196 :			my $db = $self->db_handle();
1197 :			my $lock = FIG::SimLock->new;
1198 :
1199 :			my $work = $db->SQL(qq(SELECT qid, chunk_id, seek, len
1200 :	parrello	1.298	FROM sim_queue
1201 :	olson	1.430	WHERE not finished AND not assigned
1202 :	parrello	1.298	LIMIT 1));
1203 :	olson	1.279	print "Got work ", Dumper($work), "\n";
1204 :
1205 :	parrello	1.287	if (not $work or @$work == 0) {
1206 :			return undef;
1207 :	olson	1.279	}
1208 :
1209 :			my($cpool_id, $chunk_id, $seek, $len) = @{$work->[0]};
1210 :	parrello	1.287
1211 :	olson	1.279	my $pool_dir = "$FIG_Config::fig/var/sim_pools";
1212 :			my $cpool_dir = "$pool_dir/$cpool_id";
1213 :
1214 :			my $nr = "$cpool_dir/nr";
1215 :			open(my $fh, "<$cpool_dir/fasta.in");
1216 :			seek($fh, $seek, 0);
1217 :			my $fasta;
1218 :			read($fh, $fasta, $len);
1219 :
1220 :	olson	1.430	$db->SQL(qq(UPDATE sim_queue
1221 :			SET assigned = true
1222 :			WHERE qid = ? AND chunk_id = ?), undef,
1223 :			$cpool_id, $chunk_id);
1224 :
1225 :	olson	1.279	return($cpool_id, $chunk_id, $nr, $fasta, "$cpool_dir/out.$chunk_id");
1226 :			}
1227 :
1228 :	olson	1.430	sub sim_work_working
1229 :			{
1230 :			my($self, $pool, $chunk, $host, $pid) = @_;
1231 :
1232 :			my $db = $self->db_handle();
1233 :			my $lock = FIG::SimLock->new;
1234 :
1235 :			my $res = $db->SQL(qq(UPDATE sim_queue
1236 :			SET worker_pid = ?, start_time = NOW(), worker_info = ?
1237 :			WHERE qid = ? AND chunk_id = ?),
1238 :			undef,
1239 :			$pid, $host, $pool, $chunk);
1240 :			}
1241 :
1242 :	olson	1.279	=head3 sim_work_done
1243 :
1244 :	parrello	1.287	C<< $fig->sim_work_done($pool_id, $chunk_id, $out_file); >>
1245 :
1246 :	olson	1.279	Declare that the work in pool_id/chunk_id has been completed, and output written
1247 :			to the pool directory (get_sim_work gave it the path).
1248 :
1249 :	parrello	1.287	=over 4
1250 :
1251 :			=item pool_id
1252 :
1253 :			The ID number of the pool containing the work that just completed.
1254 :
1255 :			=item chunk_id
1256 :
1257 :			The ID number of the chunk completed.
1258 :
1259 :			=item out_file
1260 :
1261 :			The file into which the work was placed.
1262 :
1263 :			=back
1264 :
1265 :	olson	1.279	=cut
1266 :
1267 :	parrello	1.287	sub sim_work_done {
1268 :			my ($self, $pool_id, $chunk_id, $out_file) = @_;
1269 :	olson	1.279
1270 :	parrello	1.287	if (! -f $out_file) {
1271 :			Confess("sim_work_done: output file $out_file does not exist");
1272 :	olson	1.279	}
1273 :
1274 :			my $db = $self->db_handle();
1275 :			my $lock = FIG::SimLock->new;
1276 :
1277 :			my $dbh = $db->{_dbh};
1278 :
1279 :			my $rows = $dbh->do(qq(UPDATE sim_queue
1280 :	parrello	1.298	SET finished = TRUE, output_file = ?
1281 :			WHERE qid = ? and chunk_id = ?), undef, $out_file, $pool_id, $chunk_id);
1282 :	parrello	1.287	if ($rows != 1) {
1283 :			if ($dbh->errstr) {
1284 :			Confess("Update not able to set finished=TRUE: ", $dbh->errstr);
1285 :			} else {
1286 :			Confess("Update not able to set finished=TRUE");
1287 :			}
1288 :	olson	1.279	}
1289 :			#
1290 :			# Determine if this was the last piece of work for this pool. If so, we can
1291 :	parrello	1.287	# schedule the postprocessing work.
1292 :	olson	1.279	#
1293 :			# Note we're still holding the lock.
1294 :			#
1295 :
1296 :			my $out = $db->SQL(qq(SELECT chunk_id
1297 :	parrello	1.298	FROM sim_queue
1298 :			WHERE qid = ? AND not finished), undef, $pool_id);
1299 :	parrello	1.287	if (@$out == 0) {
1300 :			#
1301 :			# Pool is done.
1302 :			#
1303 :			$self->schedule_sim_pool_postprocessing($pool_id);
1304 :	olson	1.279	}
1305 :	olson	1.123	}
1306 :
1307 :	olson	1.279	=head3 schedule_sim_pool_postprocessing
1308 :
1309 :	parrello	1.287	C<< $fig->schedule_sim_pool_postprocessing($pool_id); >>
1310 :
1311 :			Schedule a job to do the similarity postprocessing for the specified pool.
1312 :
1313 :			=over 4
1314 :
1315 :			=item pool_id
1316 :
1317 :			ID of the pool whose similarity postprocessing needs to be scheduled.
1318 :	olson	1.279
1319 :	parrello	1.287	=back
1320 :	olson	1.279
1321 :			=cut
1322 :
1323 :	parrello	1.287	sub schedule_sim_pool_postprocessing {
1324 :
1325 :	olson	1.279	my($self, $pool_id) = @_;
1326 :
1327 :			my $pool_dir = "$FIG_Config::fig/var/sim_pools";
1328 :			my $cpool_dir = "$pool_dir/$pool_id";
1329 :
1330 :			my $js = JobScheduler->new();
1331 :			my $job = $js->job_create();
1332 :
1333 :			my $spath = $job->get_script_path();
1334 :			open(my $sfh, ">$spath");
1335 :			print $sfh <<END;
1336 :			#!/bin/sh
1337 :			. $FIG_Config::fig_disk/config/fig-user-env.sh
1338 :			$FIG_Config::bin/postprocess_computed_sims $pool_id
1339 :			END
1340 :
1341 :			close($sfh);
1342 :			chmod(0775, $spath);
1343 :
1344 :			#
1345 :			# Write the job ID to the subsystem queue dir.
1346 :			#
1347 :
1348 :			open(J, ">$cpool_dir/postprocess_jobid");
1349 :			print J $job->get_id(), "\n";
1350 :			close(J);
1351 :
1352 :			$job->enqueue();
1353 :			}
1354 :
1355 :			=head3 postprocess_computed_sims
1356 :
1357 :	parrello	1.287	C<< $fig->postprocess_computed_sims($pool_id); >>
1358 :
1359 :			Set up to reduce, reformat, and split the similarities in a given pool. We build
1360 :			a pipe to this pipeline:
1361 :	olson	1.279
1362 :			reduce_sims peg.synonyms 300 \| reformat_sims nr \| split_sims dest prefix
1363 :
1364 :	parrello	1.287	Then we put the new sims in the pool directory, and then copy to NewSims.
1365 :
1366 :			=over 4
1367 :
1368 :			=item pool_id
1369 :
1370 :			ID of the pool whose similarities are to be post-processed.
1371 :
1372 :			=back
1373 :	olson	1.279
1374 :			=cut
1375 :
1376 :	parrello	1.287	sub postprocess_computed_sims {
1377 :	olson	1.279	my($self, $pool_id) = @_;
1378 :
1379 :			#
1380 :			# We don't lock here because the job is already done, and we
1381 :			# shouldn't (ha, ha) ever postprocess twice.
1382 :			#
1383 :
1384 :			my $pool_dir = "$FIG_Config::fig/var/sim_pools";
1385 :			my $cpool_dir = "$pool_dir/$pool_id";
1386 :
1387 :			my $sim_dir = "$cpool_dir/NewSims";
1388 :			&verify_dir($sim_dir);
1389 :
1390 :			#
1391 :			# Open the processing pipeline.
1392 :			#
1393 :
1394 :			my $reduce = "$FIG_Config::bin/reduce_sims $FIG_Config::global/peg.synonyms 300";
1395 :			my $reformat = "$FIG_Config::bin/reformat_sims $cpool_dir/nr";
1396 :			my $split = "$FIG_Config::bin/split_sims $sim_dir sims.$pool_id";
1397 :			open(my $process, "\| $reduce \| $reformat \| $split");
1398 :
1399 :			#
1400 :			# Iterate over all the sims files, taken from the database.
1401 :			#
1402 :
1403 :			my $dbh = $self->db_handle()->{_dbh};
1404 :			my $files = $dbh->selectcol_arrayref(qq(SELECT output_file
1405 :	parrello	1.298	FROM sim_queue
1406 :			WHERE qid = ? and output_file IS NOT NULL
1407 :			ORDER BY chunk_id), undef, $pool_id);
1408 :	parrello	1.287	for my $file (@$files) {
1409 :			my $buf;
1410 :			open(my $fh, "<$file") or confess "Cannot sim input file $file: $!";
1411 :			while (read($fh, $buf, 4096)) {
1412 :			print $process $buf;
1413 :			}
1414 :			close($fh);
1415 :	olson	1.279	}
1416 :			my $res = close($process);
1417 :	parrello	1.287	if (!$res) {
1418 :			if ($!) {
1419 :			confess "Error closing process pipeline: $!";
1420 :			} else {
1421 :			confess "Process pipeline exited with status $?";
1422 :			}
1423 :	olson	1.279	}
1424 :
1425 :			#
1426 :			# If we got here, it worked. Copy the new sims files over to NewSims.
1427 :			#
1428 :
1429 :			opendir(my $simdh, $sim_dir) or confess "Cannot open $sim_dir: $!";
1430 :			my @new_sims = grep { $_ !~ /^\./ } readdir($simdh);
1431 :			closedir($simdh);
1432 :
1433 :			&verify_dir("$FIG_Config::data/NewSims");
1434 :
1435 :	parrello	1.287	for my $sim_file (@new_sims) {
1436 :			my $target = "$FIG_Config::data/NewSims/$sim_file";
1437 :			if (-s $target) {
1438 :			Confess("$target already exists");
1439 :			}
1440 :			print "copying sim file $sim_file\n";
1441 :			&FIG::run("cp $sim_dir/$sim_file $target");
1442 :			&FIG::run("$FIG_Config::bin/index_sims $target");
1443 :	olson	1.279	}
1444 :			}
1445 :
1446 :	parrello	1.210	=head3 get_active_sim_pools
1447 :	olson	1.123
1448 :	parrello	1.287	C<< @pools = $fig->get_active_sim_pools(); >>
1449 :	olson	1.123
1450 :	parrello	1.287	Return a list of the pool IDs for the sim processing queues that have
1451 :			entries awaiting computation.
1452 :	olson	1.123
1453 :			=cut
1454 :	parrello	1.210	#: Return Type @;
1455 :	parrello	1.287	sub get_active_sim_pools {
1456 :	olson	1.123	my($self) = @_;
1457 :
1458 :			my $dbh = $self->db_handle();
1459 :
1460 :			my $res = $dbh->SQL("select distinct qid from sim_queue where not finished");
1461 :			return undef unless $res;
1462 :
1463 :			return map { $_->[0] } @$res;
1464 :			}
1465 :
1466 :	parrello	1.376	=head3 compute_clusters
1467 :
1468 :			C<< my @clusterList = $fig->compute_clusters(\@pegList, $subsystem, $distance); >>
1469 :
1470 :			Partition a list of PEGs into sections that are clustered close together on
1471 :			the genome. The basic algorithm used builds a graph connecting PEGs to
1472 :			other PEGs close by them on the genome. Each connected subsection of the graph
1473 :			is then separated into a cluster. Singleton clusters are thrown away, and
1474 :			the remaining ones are sorted by length. All PEGs in the incoming list
1475 :			should belong to the same genome, but this is not a requirement. PEGs on
1476 :			different genomes will simply find themselves in different clusters.
1477 :
1478 :			=over 4
1479 :
1480 :			=item pegList
1481 :
1482 :			Reference to a list of PEG IDs.
1483 :
1484 :			=item subsystem
1485 :
1486 :			Subsystem object for the relevant subsystem. This parameter is not used, but is
1487 :			required for compatability with Sprout.
1488 :
1489 :			=item distance (optional)
1490 :
1491 :			The maximum distance between PEGs that makes them considered close. If omitted,
1492 :			the distance is 5000 bases.
1493 :
1494 :			=item RETURN
1495 :
1496 :			Returns a list of lists. Each sub-list is a cluster of PEGs.
1497 :
1498 :			=back
1499 :
1500 :			=cut
1501 :
1502 :			sub compute_clusters {
1503 :			# Get the parameters.
1504 :			my ($self, $pegList, $subsystem, $distance) = @_;
1505 :			if (! defined $distance) {
1506 :			$distance = 5000;
1507 :			}
1508 :	overbeek	1.434
1509 :			my($peg,%by_contig);
1510 :			foreach $peg (@$pegList)
1511 :			{
1512 :			my $loc;
1513 :			if ($loc = $self->feature_location($peg))
1514 :			{
1515 :			my ($contig,$beg,$end) = &FIG::boundaries_of($loc);
1516 :			my $genome = &FIG::genome_of($peg);
1517 :			push(@{$by_contig{"$genome\t$contig"}},[($beg+$end)/2,$peg]);
1518 :			}
1519 :			}
1520 :
1521 :	parrello	1.376	my @clusters = ();
1522 :	overbeek	1.434	foreach my $tuple (keys(%by_contig))
1523 :			{
1524 :			my $x = $by_contig{$tuple};
1525 :			my @pegs = sort { $a->[0] <=> $b->[0] } @$x;
1526 :			while ($x = shift @pegs)
1527 :			{
1528 :			my $clust = [$x->[1]];
1529 :			while ((@pegs > 0) && (abs($pegs[0]->[0] - $x->[0]) <= $distance))
1530 :			{
1531 :			$x = shift @pegs;
1532 :			push(@$clust,$x->[1]);
1533 :			}
1534 :
1535 :			if (@$clust > 1)
1536 :			{
1537 :			push(@clusters,$clust);
1538 :			}
1539 :			}
1540 :	parrello	1.376	}
1541 :	overbeek	1.434	return sort { @$b <=> @$a } @clusters;
1542 :	parrello	1.376	}
1543 :
1544 :	parrello	1.210	=head3 get_sim_pool_info
1545 :	olson	1.123
1546 :	parrello	1.287	C<< my ($total_entries, $n_finished, $n_assigned, $n_unassigned) = $fig->get_sim_pool_info($pool_id); >>
1547 :
1548 :			Return information about the given sim pool.
1549 :
1550 :			=over 4
1551 :
1552 :			=item pool_id
1553 :
1554 :			Pool ID of the similarity processing queue whose information is desired.
1555 :
1556 :			=item RETURN
1557 :
1558 :			Returns a four-element list. The first is the number of features in the
1559 :			queue; the second is the number of features that have been processed; the
1560 :			third is the number of features that have been assigned to a
1561 :			processor, and the fourth is the number of features left over.
1562 :	olson	1.123
1563 :	parrello	1.287	=back
1564 :	olson	1.123
1565 :			=cut
1566 :	parrello	1.210	#: Return Type @;
1567 :	parrello	1.287	sub get_sim_pool_info {
1568 :
1569 :	olson	1.123	my($self, $pool_id) = @_;
1570 :			my($dbh, $res, $total_entries, $n_finished, $n_assigned, $n_unassigned);
1571 :
1572 :			$dbh = $self->db_handle();
1573 :
1574 :			$res = $dbh->SQL("select count(chunk_id) from sim_queue where qid = '$pool_id'");
1575 :	parrello	1.200	$total_entries = $res->[0]->[0];
1576 :	olson	1.123
1577 :			$res = $dbh->SQL("select count(chunk_id) from sim_queue where qid = '$pool_id' and finished");
1578 :			$n_finished = $res->[0]->[0];
1579 :
1580 :			$res = $dbh->SQL("select count(chunk_id) from sim_queue where qid = '$pool_id' and assigned and not finished");
1581 :			$n_assigned = $res->[0]->[0];
1582 :
1583 :			$res = $dbh->SQL("select count(chunk_id) from sim_queue where qid = '$pool_id' and not finished and not assigned");
1584 :			$n_unassigned = $res->[0]->[0];
1585 :
1586 :			return ($total_entries, $n_finished, $n_assigned, $n_unassigned);
1587 :	olson	1.93	}
1588 :
1589 :	parrello	1.210	#=head3 get_sim_chunk
1590 :			#
1591 :			#usage: get_sim_chunk($n_seqs, $worker_id)
1592 :			#
1593 :			#Returns a chunk of $n_seqs of work.
1594 :			#
1595 :			#From Ross, about how sims are processed:
1596 :			#
1597 :			#Here is how I process them:
1598 :			#
1599 :			#
1600 :			# bash$ cd /Volumes/seed/olson/Sims/June22.out
1601 :			# bash$ for i in really*
1602 :			# > do
1603 :			# > cat < $i >> /Volumes/laptop/new.sims
1604 :			# > done
1605 :			#
1606 :			#
1607 :			#Then, I need to "reformat" them by adding to columns to each one
1608 :			# and split the result into files of about 3M each This I do using
1609 :			#
1610 :			#reduce_sims /Volumes/laptop/NR/NewNR/peg.synonyms.june21 300 < /Volumes/laptop/new.sims \|
1611 :			# reformat_sims /Volumes/laptop/NR/NewNR/checked.nr.june21 > /Volumes/laptop/reformated.sims
1612 :			#rm /Volumes/laptop/new.sims
1613 :			#split_sims /Volumes/laptop/NewSims sims.june24 reformated.sims
1614 :			#rm reformatted.sims
1615 :			#
1616 :			#=cut
1617 :	olson	1.93
1618 :	parrello	1.287	sub get_sim_chunk {
1619 :	parrello	1.210	my($self, $n_seqs, $worker_id) = @_;
1620 :			}
1621 :	olson	1.123
1622 :	parrello	1.210	=head3 get_local_hostname
1623 :	parrello	1.200
1624 :	parrello	1.287	C<< my $result = FIG::get_local_hostname(); >>
1625 :
1626 :			Return the local host name for the current processor. The name may be
1627 :			stored in a configuration file, or we may have to get it from the
1628 :			operating system.
1629 :	olson	1.123
1630 :	olson	1.93	=cut
1631 :	parrello	1.213	#: Return Type $;
1632 :	olson	1.10	sub get_local_hostname {
1633 :	olson	1.52
1634 :			#
1635 :			# See if there is a FIGdisk/config/hostname file. If there
1636 :			# is, force the hostname to be that.
1637 :			#
1638 :
1639 :			my $hostfile = "$FIG_Config::fig_disk/config/hostname";
1640 :	parrello	1.287	if (-f $hostfile) {
1641 :			my $fh;
1642 :			if (open($fh, $hostfile)) {
1643 :			my $hostname = <$fh>;
1644 :			chomp($hostname);
1645 :			return $hostname;
1646 :			}
1647 :	olson	1.52	}
1648 :	parrello	1.200
1649 :	olson	1.10	#
1650 :			# First check to see if we our hostname is correct.
1651 :			#
1652 :			# Map it to an IP address, and try to bind to that ip.
1653 :			#
1654 :
1655 :	overbeek	1.435	local $/ = "\n";
1656 :
1657 :	olson	1.10	my $tcp = getprotobyname('tcp');
1658 :	parrello	1.200
1659 :	olson	1.10	my $hostname = `hostname`;
1660 :	overbeek	1.435	chomp $hostname;
1661 :	olson	1.10
1662 :			my @hostent = gethostbyname($hostname);
1663 :
1664 :	parrello	1.287	if (@hostent > 0) {
1665 :			my $sock;
1666 :			my $ip = $hostent[4];
1667 :
1668 :			socket($sock, PF_INET, SOCK_STREAM, $tcp);
1669 :			if (bind($sock, sockaddr_in(0, $ip))) {
1670 :			#
1671 :			# It worked. Reverse-map back to a hopefully fqdn.
1672 :			#
1673 :
1674 :			my @rev = gethostbyaddr($ip, AF_INET);
1675 :			if (@rev > 0) {
1676 :			my $host = $rev[0];
1677 :			#
1678 :			# Check to see if we have a FQDN.
1679 :			#
1680 :
1681 :			if ($host =~ /\./) {
1682 :			#
1683 :			# Good.
1684 :			#
1685 :			return $host;
1686 :			} else {
1687 :			#
1688 :			# We didn't get a fqdn; bail and return the IP address.
1689 :			#
1690 :			return get_hostname_by_adapter()
1691 :			}
1692 :			} else {
1693 :			return inet_ntoa($ip);
1694 :			}
1695 :			} else {
1696 :			#
1697 :			# Our hostname must be wrong; we can't bind to the IP
1698 :			# address it maps to.
1699 :			# Return the name associated with the adapter.
1700 :			#
1701 :			return get_hostname_by_adapter()
1702 :			}
1703 :			} else {
1704 :			#
1705 :			# Our hostname isn't known to DNS. This isn't good.
1706 :			# Return the name associated with the adapter.
1707 :			#
1708 :			return get_hostname_by_adapter()
1709 :			}
1710 :			}
1711 :
1712 :			=head3 get_hostname_by_adapter
1713 :	parrello	1.200
1714 :	parrello	1.287	C<< my $name = FIG::get_hostname_by_adapter(); >>
1715 :	olson	1.10
1716 :	parrello	1.287	Return the local host name for the current network environment.
1717 :	parrello	1.213
1718 :			=cut
1719 :			#: Return Type $;
1720 :	olson	1.10	sub get_hostname_by_adapter {
1721 :			#
1722 :			# Attempt to determine our local hostname based on the
1723 :			# network environment.
1724 :			#
1725 :			# This implementation reads the routing table for the default route.
1726 :			# We then look at the interface config for the interface that holds the default.
1727 :			#
1728 :			#
1729 :			# Linux routing table:
1730 :			# [olson@yips 0.0.0]$ netstat -rn
1731 :			# Kernel IP routing table
1732 :			# Destination Gateway Genmask Flags MSS Window irtt Iface
1733 :			# 140.221.34.32 0.0.0.0 255.255.255.224 U 0 0 0 eth0
1734 :			# 169.254.0.0 0.0.0.0 255.255.0.0 U 0 0 0 eth0
1735 :			# 127.0.0.0 0.0.0.0 255.0.0.0 U 0 0 0 lo
1736 :			# 0.0.0.0 140.221.34.61 0.0.0.0 UG 0 0 0 eth0
1737 :	parrello	1.200	#
1738 :	olson	1.10	# Mac routing table:
1739 :	parrello	1.200	#
1740 :	olson	1.10	# bash-2.05a$ netstat -rn
1741 :			# Routing tables
1742 :	parrello	1.200	#
1743 :	olson	1.10	# Internet:
1744 :			# Destination Gateway Flags Refs Use Netif Expire
1745 :			# default 140.221.11.253 UGSc 12 120 en0
1746 :			# 127.0.0.1 127.0.0.1 UH 16 8415486 lo0
1747 :			# 140.221.8/22 link#4 UCS 12 0 en0
1748 :			# 140.221.8.78 0:6:5b:f:51:c4 UHLW 0 183 en0 408
1749 :			# 140.221.8.191 0:3:93:84:ab:e8 UHLW 0 92 en0 622
1750 :			# 140.221.8.198 0:e0:98:8e:36:e2 UHLW 0 5 en0 691
1751 :			# 140.221.9.6 0:6:5b:f:51:d6 UHLW 1 63 en0 1197
1752 :			# 140.221.10.135 0:d0:59:34:26:34 UHLW 2 2134 en0 1199
1753 :			# 140.221.10.152 0:30:1b:b0:ec:dd UHLW 1 137 en0 1122
1754 :			# 140.221.10.153 127.0.0.1 UHS 0 0 lo0
1755 :			# 140.221.11.37 0:9:6b:53:4e:4b UHLW 1 624 en0 1136
1756 :			# 140.221.11.103 0:30:48:22:59:e6 UHLW 3 973 en0 1016
1757 :			# 140.221.11.224 0:a:95:6f:7:10 UHLW 1 1 en0 605
1758 :			# 140.221.11.237 0:1:30:b8:80:c0 UHLW 0 0 en0 1158
1759 :			# 140.221.11.250 0:1:30:3:1:0 UHLW 0 0 en0 1141
1760 :			# 140.221.11.253 0:d0:3:e:70:a UHLW 13 0 en0 1199
1761 :			# 169.254 link#4 UCS 0 0 en0
1762 :	parrello	1.200	#
1763 :	olson	1.10	# Internet6:
1764 :			# Destination Gateway Flags Netif Expire
1765 :			# UH lo0
1766 :			# fe80::%lo0/64 Uc lo0
1767 :			# link#1 UHL lo0
1768 :			# fe80::%en0/64 link#4 UC en0
1769 :			# 0:a:95:a8:26:68 UHL lo0
1770 :			# ff01::/32 U lo0
1771 :			# ff02::%lo0/32 UC lo0
1772 :			# ff02::%en0/32 link#4 UC en0
1773 :
1774 :			my($fh);
1775 :
1776 :	parrello	1.287	if (!open($fh, "netstat -rn \|")) {
1777 :			warn "Cannot run netstat to determine local IP address\n";
1778 :			return "localhost";
1779 :	olson	1.10	}
1780 :
1781 :			my $interface_name;
1782 :	parrello	1.200
1783 :	parrello	1.287	while (<$fh>) {
1784 :			my @cols = split();
1785 :	olson	1.10
1786 :	parrello	1.287	if ($cols[0] eq "default" \|\| $cols[0] eq "0.0.0.0") {
1787 :			$interface_name = $cols[$#cols];
1788 :			}
1789 :	olson	1.10	}
1790 :			close($fh);
1791 :	parrello	1.200
1792 :	olson	1.11	# print "Default route on $interface_name\n";
1793 :	olson	1.10
1794 :			#
1795 :			# Find ifconfig.
1796 :			#
1797 :
1798 :			my $ifconfig;
1799 :
1800 :	parrello	1.287	for my $dir ((split(":", $ENV{PATH}), "/sbin", "/usr/sbin")) {
1801 :			if (-x "$dir/ifconfig") {
1802 :			$ifconfig = "$dir/ifconfig";
1803 :			last;
1804 :			}
1805 :	olson	1.10	}
1806 :
1807 :	parrello	1.287	if ($ifconfig eq "") {
1808 :			warn "Ifconfig not found\n";
1809 :			return "localhost";
1810 :	olson	1.10	}
1811 :	olson	1.11	# print "Foudn $ifconfig\n";
1812 :	olson	1.10
1813 :	parrello	1.287	if (!open($fh, "$ifconfig $interface_name \|")) {
1814 :			warn "Could not run $ifconfig: $!\n";
1815 :			return "localhost";
1816 :	olson	1.10	}
1817 :
1818 :			my $ip;
1819 :	parrello	1.287	while (<$fh>) {
1820 :			#
1821 :			# Mac:
1822 :			# inet 140.221.10.153 netmask 0xfffffc00 broadcast 140.221.11.255
1823 :			# Linux:
1824 :			# inet addr:140.221.34.37 Bcast:140.221.34.63 Mask:255.255.255.224
1825 :			#
1826 :
1827 :			chomp;
1828 :			s/^\s*//;
1829 :
1830 :			# print "Have '$_'\n";
1831 :			if (/inet\s+addr:(\d+\.\d+\.\d+\.\d+)\s+/) {
1832 :			#
1833 :			# Linux hit.
1834 :			#
1835 :			$ip = $1;
1836 :			# print "Got linux $ip\n";
1837 :			last;
1838 :			} elsif (/inet\s+(\d+\.\d+\.\d+\.\d+)\s+/) {
1839 :			#
1840 :			# Mac hit.
1841 :			#
1842 :			$ip = $1;
1843 :			# print "Got mac $ip\n";
1844 :			last;
1845 :			}
1846 :	olson	1.10	}
1847 :			close($fh);
1848 :
1849 :	parrello	1.287	if ($ip eq "") {
1850 :			warn "Didn't find an IP\n";
1851 :			return "localhost";
1852 :	olson	1.10	}
1853 :
1854 :			return $ip;
1855 :	efrank	1.1	}
1856 :
1857 :	parrello	1.213	=head3 get_seed_id
1858 :
1859 :	parrello	1.287	C<< my $id = FIG::get_seed_id(); >>
1860 :
1861 :			Return the Universally Unique ID for this SEED instance. If one
1862 :			does not exist, it will be created.
1863 :	parrello	1.213
1864 :			=cut
1865 :			#: Return type $;
1866 :	olson	1.38	sub get_seed_id {
1867 :			#
1868 :			# Retrieve the seed identifer from FIGdisk/config/seed_id.
1869 :			#
1870 :			# If it's not there, create one, and make it readonly.
1871 :			#
1872 :			my $id;
1873 :			my $id_file = "$FIG_Config::fig_disk/config/seed_id";
1874 :	parrello	1.287	if (! -f $id_file) {
1875 :			my $newid = `uuidgen`;
1876 :			if (!$newid) {
1877 :			die "Cannot run uuidgen: $!";
1878 :			}
1879 :	olson	1.38
1880 :	parrello	1.287	chomp($newid);
1881 :			my $fh = new FileHandle(">$id_file");
1882 :			if (!$fh) {
1883 :			die "error creating $id_file: $!";
1884 :			}
1885 :			print $fh "$newid\n";
1886 :			$fh->close();
1887 :			chmod(0444, $id_file);
1888 :	olson	1.38	}
1889 :			my $fh = new FileHandle("<$id_file");
1890 :			$id = <$fh>;
1891 :			chomp($id);
1892 :			return $id;
1893 :			}
1894 :
1895 :	parrello	1.287	=head3 get_release_info
1896 :	olson	1.155
1897 :	parrello	1.287	C<< my ($name, $id, $inst, $email, $parent_id, $description) = FIG::get_release_info(); >>
1898 :	olson	1.155
1899 :	parrello	1.287	Return the current data release information..
1900 :	olson	1.195
1901 :			The release info comes from the file FIG/Data/RELEASE. It is formatted as:
1902 :
1903 :	parrello	1.287	<release-name>
1904 :			<unique id>
1905 :			<institution>
1906 :			<contact email>
1907 :			<unique id of data release this release derived from>
1908 :			<description>
1909 :	olson	1.195
1910 :			For instance:
1911 :
1912 :	parrello	1.287	-----
1913 :			SEED Data Release, 09/15/2004.
1914 :			4148208C-1DF2-11D9-8417-000A95D52EF6
1915 :			ANL/FIG
1916 :			olson@mcs.anl.gov
1917 :
1918 :			Test release.
1919 :			-----
1920 :	olson	1.195
1921 :			If no RELEASE file exists, this routine will create one with a new unique ID. This
1922 :			lets a peer optimize the data transfer by being able to cache ID translations
1923 :			from this instance.
1924 :	olson	1.155
1925 :			=cut
1926 :	parrello	1.213	#: Return Type @;
1927 :	parrello	1.287	sub get_release_info {
1928 :	olson	1.196	my($fig, $no_create) = @_;
1929 :	olson	1.195
1930 :			my $rel_file = "$FIG_Config::data/RELEASE";
1931 :
1932 :	parrello	1.287	if (! -f $rel_file and !$no_create) {
1933 :	parrello	1.298	#
1934 :			# Create a new one.
1935 :			#
1936 :	olson	1.195
1937 :	parrello	1.287	my $newid = `uuidgen`;
1938 :			if (!$newid) {
1939 :			die "Cannot run uuidgen: $!";
1940 :			}
1941 :	olson	1.195
1942 :	parrello	1.287	chomp($newid);
1943 :	olson	1.195
1944 :	parrello	1.287	my $relinfo = "Automatically generated release info " . localtime();
1945 :			my $inst = "Unknown";
1946 :			my $contact = "Unknown";
1947 :			my $parent = "";
1948 :			my( $a, $b, $e, $v, $env ) = $fig->genome_counts;
1949 :			my $description = "Automatically generated release info\n";
1950 :			$description .= "Contains $a archaeal, $b bacterial, $e eukaryal, $v viral and $env environmental genomes.\n";
1951 :
1952 :			my $fh = new FileHandle(">$rel_file");
1953 :			if (!$fh) {
1954 :			warn "error creating $rel_file: $!";
1955 :			return undef;
1956 :			}
1957 :			print $fh "$relinfo\n";
1958 :			print $fh "$newid\n";
1959 :			print $fh "$inst\n";
1960 :			print $fh "$contact\n";
1961 :			print $fh "$parent\n";
1962 :			print $fh $description;
1963 :			$fh->close();
1964 :			chmod(0444, $rel_file);
1965 :	olson	1.195	}
1966 :
1967 :	parrello	1.287	if (open(my $fh, $rel_file)) {
1968 :			my(@lines) = <$fh>;
1969 :			close($fh);
1970 :	parrello	1.200
1971 :	parrello	1.287	chomp(@lines);
1972 :	parrello	1.200
1973 :	parrello	1.287	my($info, $id, $inst, $contact, $parent, @desc) = @lines;
1974 :	olson	1.195
1975 :	parrello	1.287	return ($info, $id, $inst, $contact, $parent, join("\n", @desc));
1976 :	olson	1.195	}
1977 :	olson	1.155
1978 :			return undef;
1979 :			}
1980 :
1981 :	parrello	1.406	=head3 Title
1982 :
1983 :			C<< my $title = $fig->Title(); >>
1984 :
1985 :			Return the title of this database. For SEED, this will return SEED, for Sprout
1986 :			it will return NMPDR, and so forth.
1987 :
1988 :			=cut
1989 :
1990 :			sub Title {
1991 :			return "SEED";
1992 :			}
1993 :
1994 :	parrello	1.376	=head3 FIG
1995 :
1996 :			C<< my $realFig = $fig->FIG(); >>
1997 :
1998 :			Return this object. This method is provided for compatability with SFXlate.
1999 :
2000 :			=cut
2001 :
2002 :			sub FIG {
2003 :			my ($self) = @_;
2004 :			return $self;
2005 :			}
2006 :
2007 :	parrello	1.287	=head3 get_peer_last_update
2008 :	olson	1.155
2009 :	parrello	1.287	C<< my $date = $fig->get_peer_last_update($peer_id); >>
2010 :	parrello	1.213
2011 :	olson	1.155	Return the timestamp from the last successful peer-to-peer update with
2012 :	parrello	1.287	the given peer. If the specified peer has made updates, comparing this
2013 :			timestamp to the timestamp of the updates can tell you whether or not
2014 :			the updates have been integrated into your SEED data store.
2015 :	olson	1.155
2016 :			We store this information in FIG/Data/Global/Peers/<peer-id>.
2017 :
2018 :	parrello	1.287	=over 4
2019 :
2020 :			=item peer_id
2021 :
2022 :			Universally Unique ID for the desired peer.
2023 :
2024 :			=item RETURN
2025 :
2026 :			Returns the date/time stamp for the last peer-to-peer updated performed
2027 :			with the identified SEED instance.
2028 :
2029 :			=back
2030 :
2031 :	olson	1.155	=cut
2032 :	parrello	1.213	#: Return Type $;
2033 :	parrello	1.287	sub get_peer_last_update {
2034 :	olson	1.155	my($self, $peer_id) = @_;
2035 :
2036 :			my $dir = "$FIG_Config::data/Global/Peers";
2037 :			&verify_dir($dir);
2038 :			$dir .= "/$peer_id";
2039 :			&verify_dir($dir);
2040 :
2041 :			my $update_file = "$dir/last_update";
2042 :	parrello	1.287	if (-f $update_file) {
2043 :			my $time = file_head($update_file, 1);
2044 :			chomp $time;
2045 :			return $time;
2046 :			} else {
2047 :			return undef;
2048 :	olson	1.155	}
2049 :			}
2050 :
2051 :	parrello	1.287	=head3 set_peer_last_update
2052 :	parrello	1.213
2053 :	parrello	1.287	C<< $fig->set_peer_last_update($peer_id, $time); >>
2054 :	parrello	1.213
2055 :	parrello	1.287	Manually set the update timestamp for a specified peer. This informs
2056 :			the SEED that you have all of the assignments and updates from a
2057 :			particular SEED instance as of a certain date.
2058 :	parrello	1.213
2059 :			=cut
2060 :			#: Return Type ;
2061 :
2062 :	parrello	1.287	sub set_peer_last_update {
2063 :	olson	1.155	my($self, $peer_id, $time) = @_;
2064 :
2065 :			my $dir = "$FIG_Config::data/Global/Peers";
2066 :			&verify_dir($dir);
2067 :			$dir .= "/$peer_id";
2068 :			&verify_dir($dir);
2069 :
2070 :			my $update_file = "$dir/last_update";
2071 :			open(F, ">$update_file");
2072 :			print F "$time\n";
2073 :			close(F);
2074 :			}
2075 :
2076 :	redwards	1.302	=head3 clean_spaces
2077 :
2078 :	parrello	1.320	Remove any extra spaces from input fields. This will (currently) remove ^\s, \s$, and concatenate multiple spaces into one.
2079 :	redwards	1.302
2080 :			my $input=$fig->clean_spaces($cgi->param('input'));
2081 :
2082 :			=cut
2083 :
2084 :			sub clean_spaces
2085 :			{
2086 :			my ($self, $s)=@_;
2087 :			# note at the moment I do not use \s because that recognizes \t and \n too. This should only remove multiple spaces.
2088 :	parrello	1.320	$s =~ s/^ +//;
2089 :	redwards	1.302	$s =~ s/ +$//;
2090 :			$s =~ s/ +/ /g;
2091 :			return $s;
2092 :			}
2093 :
2094 :
2095 :
2096 :	parrello	1.213	=head3 cgi_url
2097 :
2098 :	parrello	1.287	C<< my $url = FIG::$fig->cgi_url(); >>
2099 :
2100 :			Return the URL for the CGI script directory.
2101 :	parrello	1.213
2102 :			=cut
2103 :			#: Return Type $;
2104 :	efrank	1.1	sub cgi_url {
2105 :	overbeek	1.377	# return &plug_url($FIG_Config::cgi_url);
2106 :
2107 :			#
2108 :			# In order to globally make relative references work properly, return ".".
2109 :			# This might break some stuff in p2p, but this will get us most of the way there.
2110 :			# The things that break we can repair by inspecting the value of $ENV{SCRIPT_NAME}
2111 :			#
2112 :			return ".";
2113 :	efrank	1.1	}
2114 :	parrello	1.200
2115 :	overbeek	1.382	=head3 top_link
2116 :
2117 :			C<< my $url = FIG::top_link(); >>
2118 :
2119 :			Return the relative URL for the top of the CGI script directory.
2120 :
2121 :			We determine this based on the SCRIPT_NAME environment variable, falling
2122 :			back to FIG_Config::cgi_base if necessary.
2123 :
2124 :			=cut
2125 :
2126 :			sub top_link
2127 :			{
2128 :
2129 :			#
2130 :			# Determine if this is a toplevel cgi or one in one of the subdirs (currently
2131 :			# just /p2p).
2132 :			#
2133 :
2134 :			my @parts = split(/\//, $ENV{SCRIPT_NAME});
2135 :			my $top;
2136 :			if ($parts[-2] eq 'FIG')
2137 :			{
2138 :			$top = '.';
2139 :			# warn "toplevel @parts\n";
2140 :			}
2141 :			elsif ($parts[-3] eq 'FIG')
2142 :			{
2143 :			$top = '..';
2144 :			# warn "subdir @parts\n";
2145 :			}
2146 :			else
2147 :			{
2148 :			$top = $FIG_Config::cgi_base;
2149 :			# warn "other @parts\n";
2150 :			}
2151 :
2152 :			return $top;
2153 :			}
2154 :
2155 :	parrello	1.213	=head3 temp_url
2156 :
2157 :	parrello	1.287	C<< my $url = FIG::temp_url(); >>
2158 :
2159 :			Return the URL of the temporary file directory.
2160 :	parrello	1.213
2161 :			=cut
2162 :			#: Return Type $;
2163 :	efrank	1.1	sub temp_url {
2164 :	overbeek	1.377	# return &plug_url($FIG_Config::temp_url);
2165 :
2166 :			#
2167 :			# Similarly, make this relative.
2168 :			#
2169 :			return "../FIG-Tmp";
2170 :	efrank	1.1	}
2171 :	parrello	1.200
2172 :	parrello	1.213	=head3 plug_url
2173 :
2174 :	parrello	1.287	C<< my $url2 = $fig->plug_url($url); >>
2175 :
2176 :			or
2177 :
2178 :			C<< my $url2 = $fig->plug_url($url); >>
2179 :
2180 :			Change the domain portion of a URL to point to the current domain. This essentially
2181 :			relocates URLs into the current environment.
2182 :
2183 :			=over 4
2184 :
2185 :			=item url
2186 :
2187 :			URL to relocate.
2188 :
2189 :			=item RETURN
2190 :
2191 :			Returns a new URL with the base portion converted to the current operating host.
2192 :			If the URL does not begin with C<http://>, the URL will be returned unmodified.
2193 :
2194 :			=back
2195 :	parrello	1.213
2196 :			=cut
2197 :			#: Return Type $;
2198 :	efrank	1.1	sub plug_url {
2199 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
2200 :	efrank	1.1	my($url) = @_;
2201 :
2202 :	golsen	1.44	my $name;
2203 :
2204 :			# Revised by GJO
2205 :			# First try to get url from the current http request
2206 :
2207 :			if ( defined( $ENV{ 'HTTP_HOST' } ) # This is where $cgi->url gets its value
2208 :			&& ( $name = $ENV{ 'HTTP_HOST' } )
2209 :			&& ( $url =~ s~^http://[^/]*~http://$name~ ) # ~ is delimiter
2210 :			) {}
2211 :
2212 :			# Otherwise resort to alternative sources
2213 :
2214 :			elsif ( ( $name = &get_local_hostname )
2215 :			&& ( $url =~ s~^http://[^/]*~http://$name~ ) # ~ is delimiter
2216 :			) {}
2217 :
2218 :	efrank	1.1	return $url;
2219 :			}
2220 :
2221 :	parrello	1.213	=head3 file_read
2222 :
2223 :	parrello	1.287	C<< my $text = $fig->file_read($fileName); >>
2224 :
2225 :			or
2226 :
2227 :			C<< my @lines = $fig->file_read($fileName); >>
2228 :
2229 :			or
2230 :
2231 :			C<< my $text = FIG::file_read($fileName); >>
2232 :
2233 :			or
2234 :
2235 :			C<< my @lines = FIG::file_read($fileName); >>
2236 :
2237 :			Read an entire file into memory. In a scalar context, the file is returned
2238 :			as a single text string with line delimiters included. In a list context, the
2239 :			file is returned as a list of lines, each line terminated by a line
2240 :			delimiter. (For a method that automatically strips the line delimiters,
2241 :			use C<Tracer::GetFile>.)
2242 :
2243 :			=over 4
2244 :
2245 :			=item fileName
2246 :
2247 :			Fully-qualified name of the file to read.
2248 :
2249 :			=item RETURN
2250 :
2251 :			In a list context, returns a list of the file lines. In a scalar context, returns
2252 :			a string containing all the lines of the file with delimiters included.
2253 :	parrello	1.213
2254 :	parrello	1.287	=back
2255 :	parrello	1.213
2256 :			=cut
2257 :			#: Return Type $;
2258 :			#: Return Type @;
2259 :	parrello	1.287	sub file_read {
2260 :
2261 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
2262 :	parrello	1.287	my($fileName) = @_;
2263 :			return file_head($fileName, '*');
2264 :	olson	1.90
2265 :			}
2266 :
2267 :
2268 :	parrello	1.213	=head3 file_head
2269 :
2270 :	parrello	1.287	C<< my $text = $fig->file_head($fileName, $count); >>
2271 :
2272 :			or
2273 :
2274 :			C<< my @lines = $fig->file_head($fileName, $count); >>
2275 :	parrello	1.213
2276 :	parrello	1.287	or
2277 :	parrello	1.213
2278 :	parrello	1.287	C<< my $text = FIG::file_head($fileName, $count); >>
2279 :	olson	1.90
2280 :	parrello	1.287	or
2281 :	olson	1.90
2282 :	parrello	1.287	C<< my @lines = FIG::file_head($fileName, $count); >>
2283 :	olson	1.90
2284 :	parrello	1.287	Read a portion of a file into memory. In a scalar context, the file portion is
2285 :			returned as a single text string with line delimiters included. In a list
2286 :			context, the file portion is returned as a list of lines, each line terminated
2287 :			by a line delimiter.
2288 :	olson	1.155
2289 :	parrello	1.287	=over 4
2290 :	olson	1.90
2291 :	parrello	1.287	=item fileName
2292 :	olson	1.90
2293 :	parrello	1.287	Fully-qualified name of the file to read.
2294 :	efrank	1.1
2295 :	parrello	1.287	=item count (optional)
2296 :	efrank	1.1
2297 :	parrello	1.287	Number of lines to read from the file. If omitted, C<1> is assumed. If the
2298 :			non-numeric string C<*> is specified, the entire file will be read.
2299 :	efrank	1.1
2300 :	parrello	1.287	=item RETURN
2301 :	efrank	1.1
2302 :	parrello	1.287	In a list context, returns a list of the desired file lines. In a scalar context, returns
2303 :			a string containing the desired lines of the file with delimiters included.
2304 :	efrank	1.1
2305 :	parrello	1.287	=back
2306 :	efrank	1.1
2307 :			=cut
2308 :	parrello	1.287	#: Return Type $;
2309 :			#: Return Type @;
2310 :			sub file_head {
2311 :	efrank	1.1
2312 :	parrello	1.287	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
2313 :			my($file, $count) = @_;
2314 :	efrank	1.1
2315 :	parrello	1.287	my ($n, $allFlag);
2316 :			if ($count eq '*') {
2317 :	olson	1.304	Trace("Full file read for \"$file\".") if T(3);
2318 :	parrello	1.287	$allFlag = 1;
2319 :			$n = 0;
2320 :			} else {
2321 :			$allFlag = 0;
2322 :			$n = (!$count ? 1 : $count);
2323 :	olson	1.304	Trace("Reading $n record(s) from \"$file\".") if T(3);
2324 :	parrello	1.287	}
2325 :	efrank	1.1
2326 :	parrello	1.287	if (open(my $fh, "<$file")) {
2327 :	parrello	1.298	my(@ret, $i);
2328 :	parrello	1.287	$i = 0;
2329 :			while (<$fh>) {
2330 :			push(@ret, $_);
2331 :			$i++;
2332 :			last if !$allFlag && $i >= $n;
2333 :			}
2334 :			close($fh);
2335 :			if (wantarray) {
2336 :			return @ret;
2337 :			} else {
2338 :			return join("", @ret);
2339 :			}
2340 :	efrank	1.1	}
2341 :			}
2342 :
2343 :			################ Basic Routines [ existed since WIT ] ##########################
2344 :
2345 :	parrello	1.287	=head3 min
2346 :
2347 :			C<< my $min = FIG::min(@x); >>
2348 :
2349 :			or
2350 :
2351 :			C<< my $min = $fig->min(@x); >>
2352 :
2353 :			Return the minimum numeric value from a list.
2354 :
2355 :			=over 4
2356 :
2357 :			=item x1, x2, ... xN
2358 :	efrank	1.1
2359 :	parrello	1.287	List of numbers to process.
2360 :	efrank	1.1
2361 :	parrello	1.287	=item RETURN
2362 :	efrank	1.1
2363 :	parrello	1.287	Returns the numeric value of the list entry possessing the lowest value. Returns
2364 :			C<undef> if the list is empty.
2365 :	efrank	1.1
2366 :	parrello	1.287	=back
2367 :	efrank	1.1
2368 :			=cut
2369 :	parrello	1.213	#: Return Type $;
2370 :	efrank	1.1	sub min {
2371 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
2372 :	efrank	1.1	my(@x) = @_;
2373 :			my($min,$i);
2374 :
2375 :			(@x > 0) \|\| return undef;
2376 :			$min = $x[0];
2377 :	parrello	1.287	for ($i=1; ($i < @x); $i++) {
2378 :			$min = ($min > $x[$i]) ? $x[$i] : $min;
2379 :	efrank	1.1	}
2380 :			return $min;
2381 :			}
2382 :
2383 :	parrello	1.287	=head3 max
2384 :
2385 :			C<< my $max = FIG::max(@x); >>
2386 :
2387 :			or
2388 :
2389 :			C<< my $max = $fig->max(@x); >>
2390 :	efrank	1.1
2391 :	parrello	1.287	Return the maximum numeric value from a list.
2392 :	efrank	1.1
2393 :	parrello	1.287	=over 4
2394 :
2395 :			=item x1, x2, ... xN
2396 :
2397 :			List of numbers to process.
2398 :
2399 :			=item RETURN
2400 :
2401 :			Returns the numeric value of t/he list entry possessing the highest value. Returns
2402 :			C<undef> if the list is empty.
2403 :	efrank	1.1
2404 :	parrello	1.287	=back
2405 :	efrank	1.1
2406 :			=cut
2407 :	parrello	1.213	#: Return Type $;
2408 :	efrank	1.1	sub max {
2409 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
2410 :	efrank	1.1	my(@x) = @_;
2411 :			my($max,$i);
2412 :
2413 :			(@x > 0) \|\| return undef;
2414 :			$max = $x[0];
2415 :	parrello	1.287	for ($i=1; ($i < @x); $i++) {
2416 :			$max = ($max < $x[$i]) ? $x[$i] : $max;
2417 :	efrank	1.1	}
2418 :			return $max;
2419 :			}
2420 :
2421 :	parrello	1.287	=head3 between
2422 :	efrank	1.1
2423 :	parrello	1.287	C<< my $flag = FIG::between($x, $y, $z); >>
2424 :	efrank	1.1
2425 :	parrello	1.287	or
2426 :
2427 :			C<< my $flag = $fig->between($x, $y, $z); >>
2428 :
2429 :			Determine whether or not $y is between $x and $z.
2430 :
2431 :			=over 4
2432 :
2433 :			=item x
2434 :
2435 :			First edge number.
2436 :
2437 :			=item y
2438 :	efrank	1.1
2439 :	parrello	1.287	Number to examine.
2440 :
2441 :			=item z
2442 :
2443 :			Second edge number.
2444 :
2445 :			=item RETURN
2446 :
2447 :			Return TRUE if the number I<$y> is between the numbers I<$x> and I<$z>. The check
2448 :			is inclusive (that is, if I<$y> is equal to I<$x> or I<$z> the function returns
2449 :			TRUE), and the order of I<$x> and I<$z> does not matter. If I<$x> is lower than
2450 :			I<$z>, then the return is TRUE if I<$x> <= I<$y> <= I<$z>. If I<$z> is lower,
2451 :			then the return is TRUE if I<$x> >= I$<$y> >= I<$z>.
2452 :
2453 :			=back
2454 :	efrank	1.1
2455 :			=cut
2456 :	parrello	1.213	#: Return Type $;
2457 :	efrank	1.1	sub between {
2458 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
2459 :	efrank	1.1	my($x,$y,$z) = @_;
2460 :
2461 :	parrello	1.287	if ($x < $z) {
2462 :			return (($x <= $y) && ($y <= $z));
2463 :			} else {
2464 :			return (($x >= $y) && ($y >= $z));
2465 :	efrank	1.1	}
2466 :			}
2467 :
2468 :	parrello	1.287	=head3 standard_genetic_code
2469 :	efrank	1.1
2470 :	parrello	1.287	C<< my $code = FIG::standard_genetic_code(); >>
2471 :	efrank	1.1
2472 :	parrello	1.287	Return a hash containing the standard translation of nucleotide triples to proteins.
2473 :			Methods such as L</translate> can take a translation scheme as a parameter. This method
2474 :			returns the default translation scheme. The scheme is implemented as a reference to a
2475 :			hash that contains nucleotide triplets as keys and has protein letters as values.
2476 :	efrank	1.1
2477 :			=cut
2478 :	parrello	1.213	#: Return Type $;
2479 :	efrank	1.1	sub standard_genetic_code {
2480 :	parrello	1.200
2481 :	efrank	1.1	my $code = {};
2482 :
2483 :			$code->{"AAA"} = "K";
2484 :			$code->{"AAC"} = "N";
2485 :			$code->{"AAG"} = "K";
2486 :			$code->{"AAT"} = "N";
2487 :			$code->{"ACA"} = "T";
2488 :			$code->{"ACC"} = "T";
2489 :			$code->{"ACG"} = "T";
2490 :			$code->{"ACT"} = "T";
2491 :			$code->{"AGA"} = "R";
2492 :			$code->{"AGC"} = "S";
2493 :			$code->{"AGG"} = "R";
2494 :			$code->{"AGT"} = "S";
2495 :			$code->{"ATA"} = "I";
2496 :			$code->{"ATC"} = "I";
2497 :			$code->{"ATG"} = "M";
2498 :			$code->{"ATT"} = "I";
2499 :			$code->{"CAA"} = "Q";
2500 :			$code->{"CAC"} = "H";
2501 :			$code->{"CAG"} = "Q";
2502 :			$code->{"CAT"} = "H";
2503 :			$code->{"CCA"} = "P";
2504 :			$code->{"CCC"} = "P";
2505 :			$code->{"CCG"} = "P";
2506 :			$code->{"CCT"} = "P";
2507 :			$code->{"CGA"} = "R";
2508 :			$code->{"CGC"} = "R";
2509 :			$code->{"CGG"} = "R";
2510 :			$code->{"CGT"} = "R";
2511 :			$code->{"CTA"} = "L";
2512 :			$code->{"CTC"} = "L";
2513 :			$code->{"CTG"} = "L";
2514 :			$code->{"CTT"} = "L";
2515 :			$code->{"GAA"} = "E";
2516 :			$code->{"GAC"} = "D";
2517 :			$code->{"GAG"} = "E";
2518 :			$code->{"GAT"} = "D";
2519 :			$code->{"GCA"} = "A";
2520 :			$code->{"GCC"} = "A";
2521 :			$code->{"GCG"} = "A";
2522 :			$code->{"GCT"} = "A";
2523 :			$code->{"GGA"} = "G";
2524 :			$code->{"GGC"} = "G";
2525 :			$code->{"GGG"} = "G";
2526 :			$code->{"GGT"} = "G";
2527 :			$code->{"GTA"} = "V";
2528 :			$code->{"GTC"} = "V";
2529 :			$code->{"GTG"} = "V";
2530 :			$code->{"GTT"} = "V";
2531 :			$code->{"TAA"} = "*";
2532 :			$code->{"TAC"} = "Y";
2533 :			$code->{"TAG"} = "*";
2534 :			$code->{"TAT"} = "Y";
2535 :			$code->{"TCA"} = "S";
2536 :			$code->{"TCC"} = "S";
2537 :			$code->{"TCG"} = "S";
2538 :			$code->{"TCT"} = "S";
2539 :			$code->{"TGA"} = "*";
2540 :			$code->{"TGC"} = "C";
2541 :			$code->{"TGG"} = "W";
2542 :			$code->{"TGT"} = "C";
2543 :			$code->{"TTA"} = "L";
2544 :			$code->{"TTC"} = "F";
2545 :			$code->{"TTG"} = "L";
2546 :			$code->{"TTT"} = "F";
2547 :	parrello	1.200
2548 :	efrank	1.1	return $code;
2549 :			}
2550 :
2551 :	parrello	1.287	=head3 translate
2552 :
2553 :			C<< my $aa_seq = &FIG::translate($dna_seq, $code, $fix_start); >>
2554 :
2555 :			Translate a DNA sequence to a protein sequence using the specified genetic code.
2556 :			If I<$fix_start> is TRUE, will translate an initial C<TTG> or C<GTG> code to
2557 :			C<M>. (In the standard genetic code, these two combinations normally translate
2558 :			to C<V> and C<L>, respectively.)
2559 :
2560 :			=over 4
2561 :	efrank	1.1
2562 :	parrello	1.287	=item dna_seq
2563 :	efrank	1.1
2564 :	parrello	1.287	DNA sequence to translate. Note that the DNA sequence can only contain
2565 :			known nucleotides.
2566 :	efrank	1.1
2567 :	parrello	1.287	=item code
2568 :	efrank	1.1
2569 :	parrello	1.287	Reference to a hash specifying the translation code. The hash is keyed by
2570 :			nucleotide triples, and the value for each key is the corresponding protein
2571 :			letter. If this parameter is omitted, the L</standard_genetic_code> will be
2572 :			used.
2573 :	efrank	1.1
2574 :	parrello	1.287	=item fix_start
2575 :
2576 :			TRUE if the first triple is to get special treatment, else FALSE. If TRUE,
2577 :			then a value of C<TTG> or C<GTG> in the first position will be translated to
2578 :			C<M> instead of the value specified in the translation code.
2579 :
2580 :			=item RETURN
2581 :
2582 :			Returns a string resulting from translating each nucleotide triple into a
2583 :			protein letter.
2584 :
2585 :			=back
2586 :
2587 :			=cut
2588 :			#: Return Type $;
2589 :			sub translate {
2590 :			shift if UNIVERSAL::isa($_[0],__PACKAGE__);
2591 :
2592 :			my( $dna,$code,$start ) = @_;
2593 :			my( $i,$j,$ln );
2594 :			my( $x,$y );
2595 :			my( $prot );
2596 :
2597 :			if (! defined($code)) {
2598 :			$code = &FIG::standard_genetic_code;
2599 :	efrank	1.1	}
2600 :			$ln = length($dna);
2601 :			$prot = "X" x ($ln/3);
2602 :			$dna =~ tr/a-z/A-Z/;
2603 :
2604 :	parrello	1.287	for ($i=0,$j=0; ($i < ($ln-2)); $i += 3,$j++) {
2605 :			$x = substr($dna,$i,3);
2606 :			if ($y = $code->{$x}) {
2607 :			substr($prot,$j,1) = $y;
2608 :	efrank	1.1	}
2609 :			}
2610 :	parrello	1.200
2611 :	parrello	1.287	if (($start) && ($ln >= 3) && (substr($dna,0,3) =~ /^[GT]TG$/)) {
2612 :			substr($prot,0,1) = 'M';
2613 :	efrank	1.1	}
2614 :			return $prot;
2615 :			}
2616 :
2617 :	parrello	1.287	=head3 reverse_comp
2618 :
2619 :			C<< my $dnaR = FIG::reverse_comp($dna); >>
2620 :
2621 :			or
2622 :
2623 :			C<< my $dnaR = $fig->reverse_comp($dna); >>
2624 :
2625 :			Return the reverse complement os the specified DNA sequence.
2626 :	efrank	1.1
2627 :	parrello	1.287	NOTE: for extremely long DNA strings, use L</rev_comp>, which allows you to
2628 :			pass the strings around in the form of pointers.
2629 :	efrank	1.1
2630 :	parrello	1.287	=over 4
2631 :
2632 :			=item dna
2633 :	efrank	1.1
2634 :	parrello	1.287	DNA sequence whose reverse complement is desired.
2635 :
2636 :			=item RETURN
2637 :
2638 :			Returns the reverse complement of the incoming DNA sequence.
2639 :
2640 :			=back
2641 :	efrank	1.1
2642 :			=cut
2643 :	parrello	1.213	#: Return Type $;
2644 :	efrank	1.1	sub reverse_comp {
2645 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
2646 :	efrank	1.1	my($seq) = @_;
2647 :
2648 :			return ${&rev_comp(\$seq)};
2649 :			}
2650 :
2651 :	parrello	1.287	=head3 rev_comp
2652 :
2653 :			C<< my $dnaRP = FIG::rev_comp(\$dna); >>
2654 :
2655 :			or
2656 :
2657 :			C<< my $dnaRP = $fig->rev_comp(\$dna); >>
2658 :
2659 :			Return the reverse complement of the specified DNA sequence. The DNA sequence
2660 :			is passed in as a string reference rather than a raw string for performance
2661 :			reasons. If this is unnecessary, use L</reverse_comp>, which processes strings
2662 :			instead of references to strings.
2663 :
2664 :			=over 4
2665 :
2666 :			=item dna
2667 :
2668 :			Reference to the DNA sequence whose reverse complement is desired.
2669 :
2670 :			=item RETURN
2671 :
2672 :			Returns a reference to the reverse complement of the incoming DNA sequence.
2673 :
2674 :			=back
2675 :	parrello	1.213
2676 :			=cut
2677 :			#: Return Type $;
2678 :	efrank	1.1	sub rev_comp {
2679 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
2680 :	efrank	1.1	my( $seqP ) = @_;
2681 :			my( $rev );
2682 :
2683 :			$rev = reverse( $$seqP );
2684 :	overbeek	1.317	$rev =~ tr/A-Z/a-z/;
2685 :			$rev =~ tr/acgtumrwsykbdhv/tgcaakywsrmvhdb/;
2686 :	efrank	1.1	return \$rev;
2687 :			}
2688 :
2689 :	overbeek	1.454	sub verify_external_tool {
2690 :			my(@progs) = @_;
2691 :
2692 :			my $prog;
2693 :			foreach $prog (@progs)
2694 :			{
2695 :			my @tmp = `which $prog`;
2696 :			if ($tmp[0] =~ /^no $prog/)
2697 :			{
2698 :			print STDERR $tmp[0];
2699 :			exit(1);
2700 :			}
2701 :			}
2702 :			}
2703 :
2704 :	parrello	1.287	=head3 verify_dir
2705 :
2706 :			C<< FIG::verify_dir($dir); >>
2707 :	efrank	1.1
2708 :	parrello	1.287	or
2709 :	efrank	1.1
2710 :	parrello	1.287	C<< $fig->verify_dir($dir); >>
2711 :	efrank	1.1
2712 :	parrello	1.287	Insure that the specified directory exists. If it must be created, the permissions will
2713 :			be set to C<0777>.
2714 :	efrank	1.1
2715 :			=cut
2716 :
2717 :			sub verify_dir {
2718 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
2719 :	efrank	1.1	my($dir) = @_;
2720 :
2721 :	olson	1.416	if (!defined($dir))
2722 :			{
2723 :			Confess("FIG::verify_dir: missing \$dir argument\n");
2724 :			}
2725 :			if ($dir eq "")
2726 :			{
2727 :			confess("FIG::verify_dir: refusing to create a directory named ''\n");
2728 :			}
2729 :
2730 :	parrello	1.287	if (-d $dir) {
2731 :			return
2732 :			}
2733 :	olson	1.416	if ($dir =~ /^(.*)\/[^\/]+$/ and $1 ne '') {
2734 :	parrello	1.287	&verify_dir($1);
2735 :	efrank	1.1	}
2736 :	parrello	1.287	mkdir($dir,0777) \|\| Confess("Could not make directory $dir: $!");
2737 :	efrank	1.1	}
2738 :
2739 :	parrello	1.287	=head3 run
2740 :	efrank	1.1
2741 :	parrello	1.287	C<< FIG::run($cmd); >>
2742 :	overbeek	1.283
2743 :	parrello	1.287	or
2744 :
2745 :			C<< $fig->run($cmd); >>
2746 :	overbeek	1.283
2747 :	parrello	1.287	Run a command. If the command fails, the error will be traced.
2748 :	overbeek	1.283
2749 :			=cut
2750 :
2751 :	parrello	1.287	sub run {
2752 :			shift if UNIVERSAL::isa($_[0],__PACKAGE__);
2753 :			my($cmd) = @_;
2754 :
2755 :	overbeek	1.363	if ($ENV{FIG_VERBOSE}) {
2756 :	parrello	1.287	my @tmp = `date`;
2757 :			chomp @tmp;
2758 :			print STDERR "$tmp[0]: running $cmd\n";
2759 :			}
2760 :			Trace("Running command: $cmd") if T(3);
2761 :			(system($cmd) == 0) \|\| Confess("FAILED: $cmd");
2762 :			}
2763 :
2764 :	olson	1.388	=head3 run_gathering_output
2765 :
2766 :			C<< FIG::run_gathering_output($cmd, @args); >>
2767 :
2768 :			or
2769 :
2770 :			C<< $fig->run_gathering_output($cmd, @args); >>
2771 :
2772 :			Run a command, gathering the output. This is similar to the backtick
2773 :			operator, but it does not invoke the shell. Note that the argument list
2774 :			must be explicitly passed one command line argument per argument to
2775 :			run_gathering_output.
2776 :
2777 :			If the command fails, the error will be traced.
2778 :
2779 :			=cut
2780 :
2781 :			sub run_gathering_output {
2782 :			shift if UNIVERSAL::isa($_[0],__PACKAGE__);
2783 :			my($cmd, @args) = @_;
2784 :
2785 :			#
2786 :			# Run the command in a safe fork-with-pipe/exec.
2787 :			#
2788 :
2789 :			my $pid = open(PROC_READ, "-\|");
2790 :
2791 :			if ($pid == 0)
2792 :			{
2793 :			exec { $cmd } $cmd, @args;
2794 :			die "could not execute $cmd @args: $!\n";
2795 :			}
2796 :
2797 :			if (wantarray)
2798 :			{
2799 :			my @out;
2800 :			while (<PROC_READ>)
2801 :			{
2802 :			push(@out, $_);
2803 :			}
2804 :			if (!close(PROC_READ))
2805 :			{
2806 :			Confess("FAILED: $cmd @args with error return $?");
2807 :			}
2808 :			return @out;
2809 :			}
2810 :			else
2811 :			{
2812 :			my $out = '';
2813 :
2814 :			while (<PROC_READ>)
2815 :			{
2816 :			$out .= $_;
2817 :			}
2818 :			if (!close(PROC_READ))
2819 :			{
2820 :			Confess("FAILED: $cmd @args with error return $?");
2821 :			}
2822 :			return $out;
2823 :			}
2824 :			}
2825 :
2826 :	parrello	1.287	=head3 augment_path
2827 :
2828 :			C<< FIG::augment_path($dirName); >>
2829 :	overbeek	1.283
2830 :	parrello	1.287	Add a directory to the system path.
2831 :	overbeek	1.283
2832 :	parrello	1.287	This method adds a new directory to the front of the system path. It looks in the
2833 :			configuration file to determine whether this is Windows or Unix, and uses the
2834 :			appropriate separator.
2835 :	efrank	1.1
2836 :	parrello	1.287	=over 4
2837 :	efrank	1.1
2838 :	parrello	1.287	=item dirName
2839 :
2840 :			Name of the directory to add to the path.
2841 :
2842 :			=back
2843 :	efrank	1.1
2844 :			=cut
2845 :
2846 :	parrello	1.287	sub augment_path {
2847 :			my ($dirName) = @_;
2848 :			if ($FIG_Config::win_mode) {
2849 :			$ENV{PATH} = "$dirName;$ENV{PATH}";
2850 :			} else {
2851 :			$ENV{PATH} = "$dirName:$ENV{PATH}";
2852 :	overbeek	1.278	}
2853 :	efrank	1.1	}
2854 :
2855 :	parrello	1.287	=head3 read_fasta_record
2856 :	gdpusch	1.45
2857 :	parrello	1.287	C<< my ($seq_id, $seq_pointer, $comment) = FIG::read_fasta_record(\*FILEHANDLE); >>
2858 :	gdpusch	1.45
2859 :	parrello	1.287	or
2860 :	gdpusch	1.45
2861 :	parrello	1.287	C<< my ($seq_id, $seq_pointer, $comment) = $fig->read_fasta_record(\*FILEHANDLE); >>
2862 :	gdpusch	1.45
2863 :	parrello	1.287	Read and parse the next logical record of a FASTA file. A FASTA logical record
2864 :			consists of multiple lines of text. The first line begins with a C<< > >> symbol
2865 :			and contains the sequence ID followed by an optional comment. (NOTE: comments
2866 :			are currently deprecated, because not all tools handle them properly.) The
2867 :			remaining lines contain the sequence data.
2868 :
2869 :			This method uses a trick to smooth its operation: the line terminator character
2870 :			is temporarily changed to C<< \n> >> so that a single read operation brings in
2871 :			the entire logical record.
2872 :	gdpusch	1.45
2873 :	parrello	1.287	=over 4
2874 :	gdpusch	1.45
2875 :	parrello	1.287	=item FILEHANDLE
2876 :	gdpusch	1.45
2877 :	parrello	1.287	Open handle of the FASTA file. If not specified, C<STDIN> is assumed.
2878 :
2879 :			=item RETURN
2880 :
2881 :			If we are at the end of the file, returns C<undef>. Otherwise, returns a
2882 :			three-element list. The first element is the sequence ID, the second is
2883 :			a pointer to the sequence data (that is, a string reference as opposed to
2884 :			as string), and the third is the comment.
2885 :
2886 :			=back
2887 :	gdpusch	1.45
2888 :			=cut
2889 :	parrello	1.213	#: Return Type @;
2890 :	parrello	1.287	sub read_fasta_record {
2891 :
2892 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
2893 :	gdpusch	1.45	my ($file_handle) = @_;
2894 :	parrello	1.287	my ($old_end_of_record, $fasta_record, @lines, $head, $sequence, $seq_id, $comment, @parsed_fasta_record);
2895 :	parrello	1.200
2896 :	gdpusch	1.45	if (not defined($file_handle)) { $file_handle = \*STDIN; }
2897 :	parrello	1.200
2898 :	gdpusch	1.45	$old_end_of_record = $/;
2899 :			$/ = "\n>";
2900 :	parrello	1.200
2901 :	parrello	1.287	if (defined($fasta_record = <$file_handle>)) {
2902 :			chomp $fasta_record;
2903 :			@lines = split( /\n/, $fasta_record );
2904 :			$head = shift @lines;
2905 :			$head =~ s/^>?//;
2906 :			$head =~ m/^(\S+)/;
2907 :			$seq_id = $1;
2908 :			if ($head =~ m/^\S+\s+(.*)$/) { $comment = $1; } else { $comment = ""; }
2909 :			$sequence = join( "", @lines );
2910 :			@parsed_fasta_record = ( $seq_id, \$sequence, $comment );
2911 :			} else {
2912 :			@parsed_fasta_record = ();
2913 :	gdpusch	1.45	}
2914 :	parrello	1.200
2915 :	gdpusch	1.45	$/ = $old_end_of_record;
2916 :	parrello	1.200
2917 :	gdpusch	1.45	return @parsed_fasta_record;
2918 :			}
2919 :
2920 :	parrello	1.287	=head3 display_id_and_seq
2921 :
2922 :			C<< FIG::display_id_and_seq($id_and_comment, $seqP, $fh); >>
2923 :
2924 :			or
2925 :
2926 :	parrello	1.355	C<< $fig->display_id_and_seq($id_and_comment, \$seqP, $fh); >>
2927 :	parrello	1.287
2928 :			Display a fasta ID and sequence to the specified open file. This method is designed
2929 :			to work well with L</read_fasta_sequence> and L</rev_comp>, because it takes as
2930 :			input a string pointer rather than a string. If the file handle is omitted it
2931 :			defaults to STDOUT.
2932 :
2933 :			The output is formatted into a FASTA record. The first line of the output is
2934 :			preceded by a C<< > >> symbol, and the sequence is split into 60-character
2935 :			chunks displayed one per line. Thus, this method can be used to produce
2936 :			FASTA files from data gathered by the rest of the system.
2937 :
2938 :			=over 4
2939 :
2940 :			=item id_and_comment
2941 :
2942 :			The sequence ID and (optionally) the comment from the sequence's FASTA record.
2943 :			The ID
2944 :	gdpusch	1.45
2945 :	parrello	1.287	=item seqP
2946 :	efrank	1.1
2947 :	parrello	1.287	Reference to a string containing the sequence. The sequence is automatically
2948 :			formatted into 60-character chunks displayed one per line.
2949 :	efrank	1.1
2950 :	parrello	1.287	=item fh
2951 :	efrank	1.1
2952 :	parrello	1.287	Open file handle to which the ID and sequence should be output. If omitted,
2953 :	parrello	1.355	C<\*STDOUT> is assumed.
2954 :	parrello	1.287
2955 :			=back
2956 :	efrank	1.1
2957 :			=cut
2958 :
2959 :	parrello	1.287	sub display_id_and_seq {
2960 :	mkubal	1.53
2961 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
2962 :	parrello	1.287
2963 :	overbeek	1.326	my( $id, $seqP, $fh ) = @_;
2964 :	parrello	1.200
2965 :	efrank	1.1	if (! defined($fh) ) { $fh = \*STDOUT; }
2966 :	parrello	1.200
2967 :	efrank	1.1	print $fh ">$id\n";
2968 :	overbeek	1.326	&display_seq($seqP, $fh);
2969 :	efrank	1.1	}
2970 :
2971 :	parrello	1.355	=head3 display_seq
2972 :	parrello	1.287
2973 :	parrello	1.355	C<< FIG::display_seq(\$seqP, $fh); >>
2974 :	parrello	1.287
2975 :			or
2976 :
2977 :	parrello	1.355	C<< $fig->display_seq(\$seqP, $fh); >>
2978 :	parrello	1.287
2979 :			Display a fasta sequence to the specified open file. This method is designed
2980 :			to work well with L</read_fasta_sequence> and L</rev_comp>, because it takes as
2981 :			input a string pointer rather than a string. If the file handle is omitted it
2982 :			defaults to STDOUT.
2983 :
2984 :			The sequence is split into 60-character chunks displayed one per line for
2985 :			readability.
2986 :
2987 :			=over 4
2988 :
2989 :			=item seqP
2990 :
2991 :			Reference to a string containing the sequence.
2992 :
2993 :			=item fh
2994 :
2995 :			Open file handle to which the sequence should be output. If omitted,
2996 :			C<STDOUT> is assumed.
2997 :
2998 :			=back
2999 :
3000 :			=cut
3001 :
3002 :	efrank	1.1	sub display_seq {
3003 :	parrello	1.287
3004 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
3005 :	parrello	1.287
3006 :	overbeek	1.326	my ( $seqP, $fh ) = @_;
3007 :	efrank	1.1	my ( $i, $n, $ln );
3008 :	parrello	1.200
3009 :	efrank	1.1	if (! defined($fh) ) { $fh = \*STDOUT; }
3010 :
3011 :	overbeek	1.326	$n = length($$seqP);
3012 :	efrank	1.1	# confess "zero-length sequence ???" if ( (! defined($n)) \|\| ($n == 0) );
3013 :	parrello	1.287	for ($i=0; ($i < $n); $i += 60) {
3014 :			if (($i + 60) <= $n) {
3015 :	overbeek	1.326	$ln = substr($$seqP,$i,60);
3016 :	parrello	1.287	} else {
3017 :	overbeek	1.326	$ln = substr($$seqP,$i,($n-$i));
3018 :	parrello	1.287	}
3019 :			print $fh "$ln\n";
3020 :	efrank	1.1	}
3021 :			}
3022 :
3023 :			########## I commented the pods on the following routines out, since they should not
3024 :			########## be part of the SOAP/WSTL interface
3025 :			#=pod
3026 :			#
3027 :	parrello	1.287	#=head3 file2N
3028 :	efrank	1.1	#
3029 :			#usage: $n = $fig->file2N($file)
3030 :			#
3031 :			#In some of the databases I need to store filenames, which can waste a lot of
3032 :			#space. Hence, I maintain a database for converting filenames to/from integers.
3033 :			#
3034 :			#=cut
3035 :			#
3036 :	parrello	1.328	sub file2N :Scalar {
3037 :	efrank	1.1	my($self,$file) = @_;
3038 :			my($relational_db_response);
3039 :
3040 :			my $rdbH = $self->db_handle;
3041 :
3042 :	olson	1.403	#
3043 :			# Strip the figdisk path from the file. N2file replaces it if the path
3044 :			# in the database is relative.
3045 :			#
3046 :			$file =~ s,^$FIG_Config::fig_disk/,,;
3047 :
3048 :	efrank	1.1	if (($relational_db_response = $rdbH->SQL("SELECT fileno FROM file_table WHERE ( file = \'$file\')")) &&
3049 :	parrello	1.298	(@$relational_db_response == 1)) {
3050 :	parrello	1.287	return $relational_db_response->[0]->[0];
3051 :			} elsif (($relational_db_response = $rdbH->SQL("SELECT MAX(fileno) FROM file_table ")) && (@$relational_db_response == 1) && ($relational_db_response->[0]->[0])) {
3052 :			my $fileno = $relational_db_response->[0]->[0] + 1;
3053 :			if ($rdbH->SQL("INSERT INTO file_table ( file, fileno ) VALUES ( \'$file\', $fileno )")) {
3054 :			return $fileno;
3055 :			}
3056 :			} elsif ($rdbH->SQL("INSERT INTO file_table ( file, fileno ) VALUES ( \'$file\', 1 )")) {
3057 :			return 1;
3058 :	efrank	1.1	}
3059 :			return undef;
3060 :			}
3061 :
3062 :			#=pod
3063 :			#
3064 :	parrello	1.287	#=head3 N2file
3065 :	efrank	1.1	#
3066 :			#usage: $filename = $fig->N2file($n)
3067 :			#
3068 :			#In some of the databases I need to store filenames, which can waste a lot of
3069 :			#space. Hence, I maintain a database for converting filenames to/from integers.
3070 :			#
3071 :			#=cut
3072 :			#
3073 :	overbeek	1.364	sub N2file :Scalar
3074 :			{
3075 :	efrank	1.1	my($self,$fileno) = @_;
3076 :	overbeek	1.364
3077 :			#
3078 :			# Cache outputs. This results in a huge savings of time when files are
3079 :			# accessed multiple times (as in when a bunch of sims are requested).
3080 :			#
3081 :
3082 :			my $fcache = $self->cached("_n2file");
3083 :	parrello	1.379
3084 :	overbeek	1.364	my $fname;
3085 :			if (defined($fname = $fcache->{$fileno}))
3086 :			{
3087 :	parrello	1.365	return $fname;
3088 :	overbeek	1.364	}
3089 :	efrank	1.1
3090 :			my $rdbH = $self->db_handle;
3091 :	parrello	1.379
3092 :	overbeek	1.364	my $relational_db_response = $rdbH->SQL("SELECT file FROM file_table WHERE ( fileno = $fileno )");
3093 :	efrank	1.1
3094 :	overbeek	1.364	if ($relational_db_response and @$relational_db_response == 1)
3095 :			{
3096 :	parrello	1.365	$fname = $relational_db_response->[0]->[0];
3097 :	olson	1.403
3098 :	parrello	1.420	#
3099 :			# If $fname is relative, prepend the base of the fig_disk.
3100 :			# (Updated to use PERL's system-independent filename utilities.
3101 :			#
3102 :
3103 :			$fname = File::Spec->rel2abs($fname, $FIG_Config::fig_disk);
3104 :
3105 :	parrello	1.365	$fcache->{$fileno} = $fname;
3106 :			return $fname;
3107 :	efrank	1.1	}
3108 :			return undef;
3109 :			}
3110 :
3111 :
3112 :			#=pod
3113 :			#
3114 :	parrello	1.287	#=head3 openF
3115 :	efrank	1.1	#
3116 :			#usage: $fig->openF($filename)
3117 :			#
3118 :			#Parts of the system rely on accessing numerous different files. The most obvious case is
3119 :			#the situation with similarities. It is important that the system be able to run in cases in
3120 :			#which an arbitrary number of files cannot be open simultaneously. This routine (with closeF) is
3121 :			#a hack to handle this. I should probably just pitch them and insist that the OS handle several
3122 :			#hundred open filehandles.
3123 :			#
3124 :			#=cut
3125 :			#
3126 :			sub openF {
3127 :			my($self,$file) = @_;
3128 :			my($fxs,$x,@fxs,$fh);
3129 :
3130 :			$fxs = $self->cached('_openF');
3131 :	parrello	1.287	if ($x = $fxs->{$file}) {
3132 :			$x->[1] = time();
3133 :			return $x->[0];
3134 :	efrank	1.1	}
3135 :	parrello	1.200
3136 :	efrank	1.1	@fxs = keys(%$fxs);
3137 :	parrello	1.287	if (defined($fh = new FileHandle "<$file")) {
3138 :			if (@fxs >= 50) {
3139 :			@fxs = sort { $fxs->{$a}->[1] <=> $fxs->{$b}->[1] } @fxs;
3140 :			$x = $fxs->{$fxs[0]};
3141 :			undef $x->[0];
3142 :			delete $fxs->{$fxs[0]};
3143 :			}
3144 :			$fxs->{$file} = [$fh,time()];
3145 :			return $fh;
3146 :	efrank	1.1	}
3147 :			return undef;
3148 :			}
3149 :
3150 :			#=pod
3151 :			#
3152 :	parrello	1.287	#=head3 closeF
3153 :	efrank	1.1	#
3154 :			#usage: $fig->closeF($filename)
3155 :			#
3156 :			#Parts of the system rely on accessing numerous different files. The most obvious case is
3157 :			#the situation with similarities. It is important that the system be able to run in cases in
3158 :			#which an arbitrary number of files cannot be open simultaneously. This routine (with openF) is
3159 :			#a hack to handle this. I should probably just pitch them and insist that the OS handle several
3160 :			#hundred open filehandles.
3161 :			#
3162 :			#=cut
3163 :			#
3164 :			sub closeF {
3165 :			my($self,$file) = @_;
3166 :			my($fxs,$x);
3167 :
3168 :	parrello	1.287	if (($fxs = $self->{_openF}) && ($x = $fxs->{$file})) {
3169 :			undef $x->[0];
3170 :			delete $fxs->{$file};
3171 :	efrank	1.1	}
3172 :			}
3173 :
3174 :	parrello	1.287	=head3 ec_name
3175 :
3176 :			C<< my $enzymatic_function = $fig->ec_name($ec); >>
3177 :	efrank	1.1
3178 :	parrello	1.287	Returns the enzymatic name corresponding to the specified enzyme code.
3179 :	efrank	1.1
3180 :	parrello	1.287	=over 4
3181 :
3182 :			=item ec
3183 :	efrank	1.1
3184 :	parrello	1.287	Code number for the enzyme whose name is desired. The code number is actually
3185 :			a string of digits and periods (e.g. C<1.2.50.6>).
3186 :
3187 :			=item RETURN
3188 :
3189 :			Returns the name of the enzyme specified by the indicated code, or a null string
3190 :			if the code is not found in the database.
3191 :
3192 :			=back
3193 :	efrank	1.1
3194 :			=cut
3195 :
3196 :			sub ec_name {
3197 :			my($self,$ec) = @_;
3198 :
3199 :			($ec =~ /^\d+\.\d+\.\d+\.\d+$/) \|\| return "";
3200 :			my $rdbH = $self->db_handle;
3201 :			my $relational_db_response = $rdbH->SQL("SELECT name FROM ec_names WHERE ( ec = \'$ec\' )");
3202 :
3203 :			return (@$relational_db_response == 1) ? $relational_db_response->[0]->[0] : "";
3204 :			return "";
3205 :			}
3206 :
3207 :	parrello	1.287	=head3 all_roles
3208 :	efrank	1.1
3209 :	parrello	1.287	C<< my @roles = $fig->all_roles; >>
3210 :	efrank	1.1
3211 :	parrello	1.287	Return a list of the known roles. Currently, this is a list of the enzyme codes and names.
3212 :	efrank	1.1
3213 :	parrello	1.287	The return value is a list of list references. Each element of the big list contains an
3214 :			enzyme code (EC) followed by the enzymatic name.
3215 :	efrank	1.1
3216 :			=cut
3217 :
3218 :			sub all_roles {
3219 :			my($self) = @_;
3220 :
3221 :			my $rdbH = $self->db_handle;
3222 :			my $relational_db_response = $rdbH->SQL("SELECT ec,name FROM ec_names");
3223 :
3224 :			return @$relational_db_response;
3225 :			}
3226 :
3227 :	parrello	1.287	=head3 expand_ec
3228 :	efrank	1.1
3229 :	parrello	1.287	C<< my $expanded_ec = $fig->expand_ec($ec); >>
3230 :	efrank	1.1
3231 :			Expands "1.1.1.1" to "1.1.1.1 - alcohol dehydrogenase" or something like that.
3232 :
3233 :			=cut
3234 :
3235 :			sub expand_ec {
3236 :			my($self,$ec) = @_;
3237 :			my($name);
3238 :
3239 :			return ($name = $self->ec_name($ec)) ? "$ec - $name" : $ec;
3240 :			}
3241 :
3242 :	parrello	1.287	=head3 clean_tmp
3243 :	efrank	1.1
3244 :	parrello	1.287	C<< FIG::clean_tmp(); >>
3245 :	efrank	1.1
3246 :	parrello	1.287	Delete temporary files more than two days old.
3247 :	efrank	1.1
3248 :			We store temporary files in $FIG_Config::temp. There are specific classes of files
3249 :			that are created and should be saved for at least a few days. This routine can be
3250 :			invoked to clean out those that are over two days old.
3251 :
3252 :			=cut
3253 :
3254 :			sub clean_tmp {
3255 :
3256 :			my($file);
3257 :	parrello	1.287	if (opendir(TMP,"$FIG_Config::temp")) {
3258 :			# change the pattern to pick up other files that need to be cleaned up
3259 :			my @temp = grep { $_ =~ /^(Geno\|tmp)/ } readdir(TMP);
3260 :			foreach $file (@temp) {
3261 :			if (-M "$FIG_Config::temp/$file" > 2) {
3262 :			unlink("$FIG_Config::temp/$file");
3263 :			}
3264 :			}
3265 :	efrank	1.1	}
3266 :			}
3267 :
3268 :			################ Routines to process genomes and genome IDs ##########################
3269 :
3270 :
3271 :	parrello	1.287	=head3 genomes
3272 :	efrank	1.1
3273 :	parrello	1.287	C<< my @genome_ids = $fig->genomes($complete, $restrictions, $domain); >>
3274 :	efrank	1.1
3275 :	parrello	1.287	Return a list of genome IDs. If called with no parameters, all genome IDs
3276 :			in the database will be returned.
3277 :	efrank	1.1
3278 :			Genomes are assigned ids of the form X.Y where X is the taxonomic id maintained by
3279 :			NCBI for the species (not the specific strain), and Y is a sequence digit assigned to
3280 :			this particular genome (as one of a set with the same genus/species). Genomes also
3281 :			have versions, but that is a separate issue.
3282 :
3283 :	parrello	1.287	=over 4
3284 :
3285 :			=item complete
3286 :
3287 :			TRUE if only complete genomes should be returned, else FALSE.
3288 :
3289 :			=item restrictions
3290 :
3291 :			TRUE if only restriction genomes should be returned, else FALSE.
3292 :
3293 :			=item domain
3294 :
3295 :			Name of the domain from which the genomes should be returned. Possible values are
3296 :			C<Bacteria>, C<Virus>, C<Eukaryota>, C<unknown>, C<Archaea>, and
3297 :			C<Environmental Sample>. If no domain is specified, all domains will be
3298 :			eligible.
3299 :
3300 :			=item RETURN
3301 :
3302 :			Returns a list of all the genome IDs with the specified characteristics.
3303 :
3304 :			=back
3305 :
3306 :	efrank	1.1	=cut
3307 :	parrello	1.320	#: Return Type @;
3308 :	parrello	1.328	sub genomes :Remote :List {
3309 :	golsen	1.150	my( $self, $complete, $restrictions, $domain ) = @_;
3310 :	overbeek	1.13
3311 :			my $rdbH = $self->db_handle;
3312 :
3313 :			my @where = ();
3314 :	parrello	1.287	if ($complete) {
3315 :			push(@where, "( complete = \'1\' )")
3316 :	overbeek	1.13	}
3317 :
3318 :	parrello	1.287	if ($restrictions) {
3319 :			push(@where, "( restrictions = \'1\' )")
3320 :	overbeek	1.13	}
3321 :	golsen	1.150
3322 :	parrello	1.287	if ($domain) {
3323 :			push( @where, "( maindomain = '$domain' )" )
3324 :	golsen	1.150	}
3325 :
3326 :	overbeek	1.13	my $relational_db_response;
3327 :	parrello	1.287	if (@where > 0) {
3328 :			my $where = join(" AND ",@where);
3329 :			$relational_db_response = $rdbH->SQL("SELECT genome FROM genome where $where");
3330 :			} else {
3331 :			$relational_db_response = $rdbH->SQL("SELECT genome FROM genome");
3332 :	overbeek	1.13	}
3333 :			my @genomes = sort { $a <=> $b } map { $_->[0] } @$relational_db_response;
3334 :	efrank	1.1	return @genomes;
3335 :			}
3336 :
3337 :	parrello	1.287	=head3 is_complete
3338 :
3339 :			C<< my $flag = $fig->is_complete($genome); >>
3340 :
3341 :			Return TRUE if the genome with the specified ID is complete, else FALSE.
3342 :
3343 :			=over 4
3344 :
3345 :			=item genome
3346 :
3347 :			ID of the relevant genome.
3348 :
3349 :			=item RETURN
3350 :
3351 :			Returns TRUE if there is a complete genome in the database with the specified ID,
3352 :			else FALSE.
3353 :
3354 :			=back
3355 :
3356 :			=cut
3357 :
3358 :	overbeek	1.180	sub is_complete {
3359 :			my($self,$genome) = @_;
3360 :
3361 :			my $rdbH = $self->db_handle;
3362 :			my $relational_db_response = $rdbH->SQL("SELECT genome FROM genome where (genome = '$genome') AND (complete = '1')");
3363 :			return (@$relational_db_response == 1)
3364 :	parrello	1.287	}
3365 :
3366 :	overbeek	1.421	sub is_genome {
3367 :			my($self,$genome) = @_;
3368 :			my($x,$y);
3369 :
3370 :			if (! ($x = $self->{_is_genome}))
3371 :			{
3372 :			$x = $self->{_is_genome} = {};
3373 :			}
3374 :
3375 :			if (defined($y = $x->{$genome})) { return $y }
3376 :			my $rdbH = $self->db_handle;
3377 :			my $relational_db_response = $rdbH->SQL("SELECT genome FROM genome where (genome = '$genome')");
3378 :			$y = (@$relational_db_response == 1);
3379 :			$x->{$genome} = $y;
3380 :			return $y;
3381 :			}
3382 :
3383 :	parrello	1.287	=head3 genome_counts
3384 :
3385 :			C<< my ($arch, $bact, $euk, $vir, $env, $unk) = $fig->genome_counts($complete); >>
3386 :
3387 :			Count the number of genomes in each domain. If I<$complete> is TRUE, only complete
3388 :			genomes will be included in the counts.
3389 :
3390 :			=over 4
3391 :
3392 :			=item complete
3393 :
3394 :			TRUE if only complete genomes are to be counted, FALSE if all genomes are to be
3395 :			counted
3396 :
3397 :			=item RETURN
3398 :
3399 :			A six-element list containing the number of genomes in each of six categories--
3400 :			Archaea, Bacteria, Eukaryota, Viral, Environmental, and Unknown, respectively.
3401 :
3402 :			=back
3403 :
3404 :			=cut
3405 :	golsen	1.150
3406 :	efrank	1.2	sub genome_counts {
3407 :	overbeek	1.13	my($self,$complete) = @_;
3408 :			my($x,$relational_db_response);
3409 :	efrank	1.2
3410 :	overbeek	1.13	my $rdbH = $self->db_handle;
3411 :
3412 :	parrello	1.287	if ($complete) {
3413 :			$relational_db_response = $rdbH->SQL("SELECT genome, maindomain FROM genome where complete = '1'");
3414 :			} else {
3415 :			$relational_db_response = $rdbH->SQL("SELECT genome,maindomain FROM genome");
3416 :	overbeek	1.13	}
3417 :
3418 :	gdpusch	1.107	my ($arch, $bact, $euk, $vir, $env, $unk) = (0, 0, 0, 0, 0, 0);
3419 :	parrello	1.287	if (@$relational_db_response > 0) {
3420 :			foreach $x (@$relational_db_response) {
3421 :			if ($x->[1] =~ /^archaea/i) { ++$arch }
3422 :			elsif ($x->[1] =~ /^bacter/i) { ++$bact }
3423 :			elsif ($x->[1] =~ /^eukar/i) { ++$euk }
3424 :			elsif ($x->[1] =~ /^vir/i) { ++$vir }
3425 :			elsif ($x->[1] =~ /^env/i) { ++$env }
3426 :			else { ++$unk }
3427 :	parrello	1.298	}
3428 :	efrank	1.2	}
3429 :	parrello	1.200
3430 :	gdpusch	1.107	return ($arch, $bact, $euk, $vir, $env, $unk);
3431 :			}
3432 :
3433 :
3434 :	parrello	1.287	=head3 genome_domain
3435 :
3436 :			C<< my $domain = $fig->genome_domain($genome_id); >>
3437 :
3438 :			Find the domain of a genome.
3439 :	gdpusch	1.107
3440 :	parrello	1.287	=over 4
3441 :
3442 :			=item genome_id
3443 :	gdpusch	1.107
3444 :	parrello	1.287	ID of the genome whose domain is desired.
3445 :	gdpusch	1.107
3446 :	parrello	1.287	=item RETURN
3447 :
3448 :			Returns the name of the genome's domain (archaea, bacteria, etc.), or C<undef> if
3449 :			the genome is not in the database.
3450 :	gdpusch	1.107
3451 :	parrello	1.292	=back
3452 :
3453 :	gdpusch	1.107	=cut
3454 :
3455 :			sub genome_domain {
3456 :			my($self,$genome) = @_;
3457 :			my $relational_db_response;
3458 :			my $rdbH = $self->db_handle;
3459 :	parrello	1.200
3460 :	parrello	1.287	if ($genome) {
3461 :			if (($relational_db_response = $rdbH->SQL("SELECT genome,maindomain FROM genome WHERE ( genome = \'$genome\' )"))
3462 :			&& (@$relational_db_response == 1)) {
3463 :			# die Dumper($relational_db_response);
3464 :			return $relational_db_response->[0]->[1];
3465 :			}
3466 :	gdpusch	1.107	}
3467 :			return undef;
3468 :	efrank	1.2	}
3469 :
3470 :	gdpusch	1.92
3471 :	parrello	1.287	=head3 genome_pegs
3472 :	gdpusch	1.92
3473 :	parrello	1.287	C<< my $num_pegs = $fig->genome_pegs($genome_id); >>
3474 :	gdpusch	1.92
3475 :	parrello	1.287	Return the number of protein-encoding genes (PEGs) for a specified
3476 :			genome.
3477 :	gdpusch	1.92
3478 :	parrello	1.287	=over 4
3479 :
3480 :			=item genome_id
3481 :
3482 :			ID of the genome whose PEG count is desired.
3483 :
3484 :			=item RETURN
3485 :
3486 :			Returns the number of PEGs for the specified genome, or C<undef> if the genome
3487 :			is not indexed in the database.
3488 :
3489 :			=back
3490 :	gdpusch	1.92
3491 :			=cut
3492 :
3493 :			sub genome_pegs {
3494 :			my($self,$genome) = @_;
3495 :			my $relational_db_response;
3496 :			my $rdbH = $self->db_handle;
3497 :	parrello	1.200
3498 :	parrello	1.287	if ($genome) {
3499 :			if (($relational_db_response = $rdbH->SQL("SELECT pegs FROM genome WHERE ( genome = \'$genome\' )"))
3500 :			&& (@$relational_db_response == 1)) {
3501 :			return $relational_db_response->[0]->[0];
3502 :			}
3503 :	gdpusch	1.92	}
3504 :			return undef;
3505 :			}
3506 :
3507 :
3508 :	parrello	1.287	=head3 genome_rnas
3509 :
3510 :			C<< my $num_rnas = $fig->genome_rnas($genome_id); >>
3511 :
3512 :			Return the number of RNA-encoding genes for a genome.
3513 :			"$genome_id" is indexed in the "genome" database, and 'undef' otherwise.
3514 :	efrank	1.1
3515 :	parrello	1.287	=over 4
3516 :
3517 :			=item genome_id
3518 :
3519 :			ID of the genome whose RNA count is desired.
3520 :
3521 :			=item RETURN
3522 :	gdpusch	1.92
3523 :	parrello	1.287	Returns the number of RNAs for the specified genome, or C<undef> if the genome
3524 :			is not indexed in the database.
3525 :	gdpusch	1.92
3526 :	parrello	1.287	=back
3527 :	gdpusch	1.92
3528 :			=cut
3529 :
3530 :			sub genome_rnas {
3531 :			my($self,$genome) = @_;
3532 :			my $relational_db_response;
3533 :			my $rdbH = $self->db_handle;
3534 :	parrello	1.200
3535 :	parrello	1.287	if ($genome) {
3536 :			if (($relational_db_response = $rdbH->SQL("SELECT rnas FROM genome WHERE ( genome = \'$genome\' )"))
3537 :			&& (@$relational_db_response == 1)) {
3538 :			return $relational_db_response->[0]->[0];
3539 :			}
3540 :	gdpusch	1.92	}
3541 :			return undef;
3542 :			}
3543 :
3544 :
3545 :	parrello	1.287	=head3 genome_szdna
3546 :
3547 :			usage: $szdna = $fig->genome_szdna($genome_id);
3548 :
3549 :			Return the number of DNA base-pairs in a genome's contigs.
3550 :
3551 :			=over 4
3552 :
3553 :			=item genome_id
3554 :
3555 :			ID of the genome whose base-pair count is desired.
3556 :	gdpusch	1.92
3557 :	parrello	1.287	=item RETURN
3558 :	efrank	1.1
3559 :	parrello	1.287	Returns the number of base pairs in the specified genome's contigs, or C<undef>
3560 :			if the genome is not indexed in the database.
3561 :	gdpusch	1.91
3562 :	parrello	1.287	=back
3563 :	gdpusch	1.91
3564 :			=cut
3565 :
3566 :	gdpusch	1.92	sub genome_szdna {
3567 :	gdpusch	1.91	my($self,$genome) = @_;
3568 :			my $relational_db_response;
3569 :			my $rdbH = $self->db_handle;
3570 :	parrello	1.200
3571 :	parrello	1.287	if ($genome) {
3572 :			if (($relational_db_response =
3573 :			$rdbH->SQL("SELECT szdna FROM genome WHERE ( genome = \'$genome\' )"))
3574 :			&& (@$relational_db_response == 1)) {
3575 :
3576 :			return $relational_db_response->[0]->[0];
3577 :
3578 :			}
3579 :	gdpusch	1.91	}
3580 :			return undef;
3581 :			}
3582 :
3583 :	parrello	1.287	=head3 genome_version
3584 :	gdpusch	1.91
3585 :	parrello	1.287	C<< my $version = $fig->genome_version($genome_id); >>
3586 :	gdpusch	1.91
3587 :	parrello	1.287	Return the version number of the specified genome.
3588 :	efrank	1.1
3589 :			Versions are incremented for major updates. They are put in as major
3590 :			updates of the form 1.0, 2.0, ...
3591 :
3592 :			Users may do local "editing" of the DNA for a genome, but when they do,
3593 :			they increment the digits to the right of the decimal. Two genomes remain
3594 :	parrello	1.200	comparable only if the versions match identically. Hence, minor updating should be
3595 :	efrank	1.1	committed only by the person/group responsible for updating that genome.
3596 :
3597 :			We can, of course, identify which genes are identical between any two genomes (by matching
3598 :			the DNA or amino acid sequences). However, the basic intent of the system is to
3599 :			support editing by the main group issuing periodic major updates.
3600 :
3601 :	parrello	1.287	=over 4
3602 :
3603 :			=item genome_id
3604 :
3605 :			ID of the genome whose version is desired.
3606 :
3607 :			=item RETURN
3608 :
3609 :			Returns the version number of the specified genome, or C<undef> if the genome is not in
3610 :			the data store or no version number has been assigned.
3611 :
3612 :			=back
3613 :
3614 :	efrank	1.1	=cut
3615 :
3616 :	parrello	1.328	sub genome_version :Scalar {
3617 :	efrank	1.1	my($self,$genome) = @_;
3618 :
3619 :			my(@tmp);
3620 :			if ((-s "$FIG_Config::organisms/$genome/VERSION") &&
3621 :	parrello	1.298	(@tmp = `cat $FIG_Config::organisms/$genome/VERSION`) &&
3622 :			($tmp[0] =~ /^(\S+)$/)) {
3623 :			return $1;
3624 :	efrank	1.1	}
3625 :			return undef;
3626 :			}
3627 :
3628 :	parrello	1.287	=head3 genome_md5sum
3629 :	olson	1.236
3630 :	parrello	1.287	C<< my $md5sum = $fig->genome_md5sum($genome_id); >>
3631 :	olson	1.236
3632 :	parrello	1.287	Returns the MD5 checksum of the specified genome.
3633 :	olson	1.236
3634 :			The checksum of a genome is defined as the checksum of its signature file. The signature
3635 :			file consists of tab-separated lines, one for each contig, ordered by the contig id.
3636 :	parrello	1.287	Each line contains the contig ID, the length of the contig in nucleotides, and the
3637 :	olson	1.236	MD5 checksum of the nucleotide data, with uppercase letters forced to lower case.
3638 :
3639 :	parrello	1.287	The checksum is indexed in the database. If you know a genome's checksum, you can use
3640 :			the L</genome_with_md5sum> method to find its ID in the database.
3641 :
3642 :			=over 4
3643 :
3644 :			=item genome
3645 :
3646 :			ID of the genome whose checksum is desired.
3647 :
3648 :			=item RETURN
3649 :
3650 :			Returns the specified genome's checksum, or C<undef> if the genome is not in the
3651 :			database.
3652 :
3653 :			=back
3654 :	olson	1.236
3655 :			=cut
3656 :
3657 :	parrello	1.328	sub genome_md5sum :Scalar {
3658 :	olson	1.236	my($self,$genome) = @_;
3659 :			my $relational_db_response;
3660 :			my $rdbH = $self->db_handle;
3661 :
3662 :	parrello	1.287	if ($genome) {
3663 :			if (($relational_db_response =
3664 :			$rdbH->SQL("SELECT md5sum FROM genome_md5sum WHERE ( genome = \'$genome\' )"))
3665 :			&& (@$relational_db_response == 1)) {
3666 :			return $relational_db_response->[0]->[0];
3667 :			}
3668 :	olson	1.236	}
3669 :			return undef;
3670 :			}
3671 :
3672 :	parrello	1.287	=head3 genome_with_md5sum
3673 :
3674 :			C<< my $genome = $fig->genome_with_md5sum($cksum); >>
3675 :
3676 :			Find a genome with the specified checksum.
3677 :
3678 :			The MD5 checksum is computed from the content of the genome (see L</genome_md5sum>). This method
3679 :			can be used to determine if a genome already exists for a specified content.
3680 :
3681 :			=over 4
3682 :
3683 :			=item cksum
3684 :
3685 :			Checksum to use for searching the genome table.
3686 :	olson	1.260
3687 :	parrello	1.287	=item RETURN
3688 :
3689 :			The ID of a genome with the specified checksum, or C<undef> if no such genome exists.
3690 :	olson	1.260
3691 :	parrello	1.287	=back
3692 :	olson	1.260
3693 :			=cut
3694 :
3695 :	parrello	1.328	sub genome_with_md5sum :Scalar {
3696 :	olson	1.260	my($self,$cksum) = @_;
3697 :			my $relational_db_response;
3698 :			my $rdbH = $self->db_handle;
3699 :
3700 :	parrello	1.287	if (($relational_db_response =
3701 :			$rdbH->SQL("SELECT genome FROM genome_md5sum WHERE ( md5sum = \'$cksum\' )"))
3702 :	parrello	1.298	&& (@$relational_db_response == 1)) {
3703 :			return $relational_db_response->[0]->[0];
3704 :	olson	1.260	}
3705 :
3706 :			return undef;
3707 :			}
3708 :
3709 :	parrello	1.287	=head3 contig_md5sum
3710 :
3711 :			C<< my $cksum = $fig->contig_md5sum($genome, $contig); >>
3712 :
3713 :			Return the MD5 checksum for a contig. The MD5 checksum is computed from the content
3714 :			of the contig. This method retrieves the checksum stored in the database. The checksum
3715 :			can be compared to the checksum of an external contig as a cheap way of seeing if they
3716 :			match.
3717 :
3718 :			=over 4
3719 :
3720 :			=item genome
3721 :
3722 :			ID of the genome containing the contig.
3723 :
3724 :			=item contig
3725 :
3726 :			ID of the relevant contig.
3727 :
3728 :			=item RETURN
3729 :
3730 :			Returns the checksum of the specified contig, or C<undef> if the contig is not in the
3731 :			database.
3732 :
3733 :			=back
3734 :
3735 :			=cut
3736 :
3737 :	parrello	1.328	sub contig_md5sum :Scalar {
3738 :	olson	1.237	my($self, $genome, $contig) = @_;
3739 :			my $relational_db_response;
3740 :			my $rdbH = $self->db_handle;
3741 :
3742 :	parrello	1.287	if ($genome) {
3743 :			if (($relational_db_response =
3744 :			$rdbH->SQL(qq(SELECT md5 FROM contig_md5sums WHERE (genome = ? AND contig = ?)), undef, $genome, $contig))
3745 :			&& (@$relational_db_response == 1)) {
3746 :			return $relational_db_response->[0]->[0];
3747 :			}
3748 :	olson	1.237	}
3749 :			return undef;
3750 :			}
3751 :
3752 :	parrello	1.287	=head3 genus_species
3753 :
3754 :			C<< my $gs = $fig->genus_species($genome_id); >>
3755 :
3756 :			Return the genus, species, and possibly also the strain of a specified genome.
3757 :
3758 :			This method converts a genome ID into a more recognizble species name. The species name
3759 :			is stored directly in the genome table of the database. Essentially, if the strain is
3760 :			present in the database, it will be returned by this method, and if it's not present,
3761 :			it won't.
3762 :	efrank	1.1
3763 :	parrello	1.287	=over 4
3764 :
3765 :			=item genome_id
3766 :
3767 :			ID of the genome whose name is desired.
3768 :	efrank	1.1
3769 :	parrello	1.287	=item RETURN
3770 :
3771 :			Returns the scientific species name associated with the specified ID, or C<undef> if the
3772 :			ID is not in the database.
3773 :	efrank	1.1
3774 :	parrello	1.287	=back
3775 :	efrank	1.1
3776 :			=cut
3777 :	parrello	1.320	#: Return Type $;
3778 :	parrello	1.328	sub genus_species :Scalar {
3779 :	efrank	1.1	my ($self,$genome) = @_;
3780 :	overbeek	1.13	my $ans;
3781 :	efrank	1.1
3782 :			my $genus_species = $self->cached('_genus_species');
3783 :	parrello	1.287	if (! ($ans = $genus_species->{$genome})) {
3784 :			my $rdbH = $self->db_handle;
3785 :			my $relational_db_response = $rdbH->SQL("SELECT genome,gname FROM genome");
3786 :			my $pair;
3787 :			foreach $pair (@$relational_db_response) {
3788 :			$genus_species->{$pair->[0]} = $pair->[1];
3789 :			}
3790 :			$ans = $genus_species->{$genome};
3791 :	efrank	1.1	}
3792 :			return $ans;
3793 :			}
3794 :
3795 :	parrello	1.287	=head3 org_of
3796 :
3797 :			C<< my $org = $fig->org_of($prot_id); >>
3798 :
3799 :			Return the genus/species name of the organism containing a protein. Note that in this context
3800 :			I<protein> is not a certain string of amino acids but a protein encoding region on a specific
3801 :			contig.
3802 :
3803 :			For a FIG protein ID (e.g. C<fig\|134537.1.peg.123>), the organism and strain
3804 :			information is always available. In the case of external proteins, we can usually
3805 :			determine an organism, but not anything more precise than genus/species (and
3806 :			often not that). When the organism name is not present, a null string is returned.
3807 :
3808 :			=over 4
3809 :
3810 :			=item prot_id
3811 :	efrank	1.1
3812 :	parrello	1.287	Protein or feature ID.
3813 :	efrank	1.1
3814 :	parrello	1.287	=item RETURN
3815 :
3816 :			Returns the displayable scientific name (genus, species, and strain) of the organism containing
3817 :			the identified PEG. If the name is not available, returns a null string. If the PEG is not found,
3818 :			returns C<undef>.
3819 :	efrank	1.1
3820 :	parrello	1.287	=back
3821 :	efrank	1.1
3822 :			=cut
3823 :
3824 :			sub org_of {
3825 :			my($self,$prot_id) = @_;
3826 :			my $relational_db_response;
3827 :			my $rdbH = $self->db_handle;
3828 :
3829 :	parrello	1.287	if ($prot_id =~ /^fig\\|/) {
3830 :			return $self->is_deleted_fid( $prot_id) ? undef
3831 :			: $self->genus_species( $self->genome_of( $prot_id ) ) \|\| "";
3832 :	efrank	1.1	}
3833 :
3834 :	parrello	1.287	if (($relational_db_response =
3835 :			$rdbH->SQL("SELECT org FROM external_orgs WHERE ( prot = \'$prot_id\' )")) &&
3836 :			(@$relational_db_response >= 1)) {
3837 :			$relational_db_response->[0]->[0] =~ s/^\d+://;
3838 :			return $relational_db_response->[0]->[0];
3839 :	efrank	1.1	}
3840 :			return "";
3841 :			}
3842 :
3843 :	parrello	1.287	=head3 genus_species_domain
3844 :
3845 :			C<< my ($gs, $domain) = $fig->genus_species_domain($genome_id); >>
3846 :
3847 :			Returns a genome's genus and species (and strain if that has been properly
3848 :			recorded) in a printable form, along with its domain. This method is similar
3849 :			to L</genus_species>, except it also returns the domain name (archaea,
3850 :			bacteria, etc.).
3851 :
3852 :			=over 4
3853 :
3854 :			=item genome_id
3855 :
3856 :			ID of the genome whose species and domain information is desired.
3857 :	golsen	1.130
3858 :	parrello	1.287	=item RETURN
3859 :	golsen	1.130
3860 :	parrello	1.287	Returns a two-element list. The first element is the species name and the
3861 :			second is the domain name.
3862 :	golsen	1.130
3863 :	parrello	1.287	=back
3864 :	golsen	1.130
3865 :			=cut
3866 :
3867 :			sub genus_species_domain {
3868 :			my ($self, $genome) = @_;
3869 :
3870 :			my $genus_species_domain = $self->cached('_genus_species_domain');
3871 :	parrello	1.287	if ( ! $genus_species_domain->{ $genome } ) {
3872 :			my $rdbH = $self->db_handle;
3873 :			my $relational_db_response = $rdbH->SQL("SELECT genome,gname,maindomain FROM genome");
3874 :			my $triple;
3875 :			foreach $triple ( @$relational_db_response ) {
3876 :			$genus_species_domain->{ $triple->[0] } = [ $triple->[1], $triple->[2] ];
3877 :			}
3878 :	golsen	1.130	}
3879 :			my $gsdref = $genus_species_domain->{ $genome };
3880 :			return $gsdref ? @$gsdref : ( "", "" );
3881 :			}
3882 :
3883 :	parrello	1.287	=head3 domain_color
3884 :
3885 :			C<< my $web_color = FIG::domain_color($domain); >>
3886 :
3887 :			Return the web color string associated with a specified domain. The colors are
3888 :			extremely subtle (86% luminance), so they absolutely require a black background.
3889 :			Archaea are slightly cyan, bacteria are slightly magenta, eukaryota are slightly
3890 :			yellow, viruses are slightly silver, environmental samples are slightly gray,
3891 :			and unknown or invalid domains are pure white.
3892 :
3893 :			=over 4
3894 :
3895 :			=item domain
3896 :
3897 :			Name of the domain whose color is desired.
3898 :
3899 :			=item RETURN
3900 :
3901 :			Returns a web color string for the specified domain (e.g. C<#FFDDFF> for
3902 :			bacteria).
3903 :
3904 :			=back
3905 :
3906 :			=cut
3907 :	golsen	1.130
3908 :			my %domain_color = ( AR => "#DDFFFF", BA => "#FFDDFF", EU => "#FFFFDD",
3909 :			VI => "#DDDDDD", EN => "#BBBBBB" );
3910 :
3911 :			sub domain_color {
3912 :			my ($domain) = @_;
3913 :			defined $domain \|\| return "#FFFFFF";
3914 :			return $domain_color{ uc substr($domain, 0, 2) } \|\| "#FFFFFF";
3915 :			}
3916 :
3917 :	parrello	1.287	=head3 org_and_color_of
3918 :	golsen	1.130
3919 :	parrello	1.287	C<< my ($org, $color) = $fig->org_and_domain_of($prot_id); >>
3920 :	golsen	1.130
3921 :	parrello	1.287	Return the best guess organism and domain html color string of an organism.
3922 :			In the case of external proteins, we can usually determine an organism, but not
3923 :			anything more precise than genus/species (and often not that).
3924 :
3925 :			=over 4
3926 :
3927 :			=item prot_id
3928 :
3929 :			Relevant protein or feature ID.
3930 :
3931 :			=item RETURN
3932 :	golsen	1.130
3933 :	parrello	1.287	Returns a two-element list. The first element is the displayable organism name, and the second
3934 :			is an HTML color string based on the domain (see L</domain_color>).
3935 :	golsen	1.130
3936 :	parrello	1.287	=back
3937 :	golsen	1.130
3938 :			=cut
3939 :
3940 :			sub org_and_color_of {
3941 :			my($self,$prot_id) = @_;
3942 :			my $relational_db_response;
3943 :			my $rdbH = $self->db_handle;
3944 :
3945 :	parrello	1.287	if ($prot_id =~ /^fig\\|/) {
3946 :			my( $gs, $domain ) = $self->genus_species_domain($self->genome_of($prot_id));
3947 :			return ( $gs, domain_color( $domain ) );
3948 :	golsen	1.130	}
3949 :
3950 :	parrello	1.287	if (($relational_db_response =
3951 :			$rdbH->SQL("SELECT org FROM external_orgs WHERE ( prot = \'$prot_id\' )")) &&
3952 :			(@$relational_db_response >= 1)) {
3953 :			return ($relational_db_response->[0]->[0], "#FFFFFF");
3954 :	golsen	1.130	}
3955 :			return ("", "#FFFFFF");
3956 :			}
3957 :
3958 :	redwards	1.310	=head3 partial_genus_matching
3959 :
3960 :			Return a list of genome IDs that match a partial genus.
3961 :
3962 :	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)
3963 :	redwards	1.310
3964 :			=cut
3965 :
3966 :			sub partial_genus_matching {
3967 :	redwards	1.311	my ($self, $gen, $complete)=@_;
3968 :			return grep {$self->genus_species($_) =~ /$gen/i} $self->genomes($complete);
3969 :	redwards	1.310	}
3970 :
3971 :
3972 :	parrello	1.287	=head3 abbrev
3973 :
3974 :			C<< my $abbreviated_name = FIG::abbrev($genome_name); >>
3975 :	golsen	1.130
3976 :	parrello	1.287	or
3977 :	efrank	1.1
3978 :	parrello	1.287	C<< my $abbreviated_name = $fig->abbrev($genome_name); >>
3979 :	efrank	1.1
3980 :	parrello	1.287	Abbreviate a genome name to 10 characters or less.
3981 :	efrank	1.1
3982 :			For alignments and such, it is very useful to be able to produce an abbreviation of genus/species.
3983 :			That's what this does. Note that multiple genus/species might reduce to the same abbreviation, so
3984 :			be careful (disambiguate them, if you must).
3985 :
3986 :	parrello	1.287	The abbreviation is formed from the first three letters of the species name followed by the
3987 :			first three letters of the genus name followed by the first three letters of the species name and
3988 :			then the next four nonblank characters.
3989 :
3990 :			=over 4
3991 :
3992 :			=item genome_name
3993 :
3994 :			The name to abbreviate.
3995 :
3996 :			=item RETURN
3997 :
3998 :			An abbreviated version of the specified name.
3999 :
4000 :			=back
4001 :
4002 :	efrank	1.1	=cut
4003 :
4004 :	parrello	1.328	sub abbrev :Scalar {
4005 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
4006 :	efrank	1.1	my($genome_name) = @_;
4007 :
4008 :			$genome_name =~ s/^(\S{3})\S+/$1./;
4009 :	overbeek	1.198	$genome_name =~ s/^(\S+)\s+(\S{3})\S+/$1$2./;
4010 :	overbeek	1.257	$genome_name =~ s/ //g;
4011 :	parrello	1.287	if (length($genome_name) > 10) {
4012 :	parrello	1.298	$genome_name = substr($genome_name,0,10);
4013 :	efrank	1.1	}
4014 :			return $genome_name;
4015 :			}
4016 :
4017 :			################ Routines to process Features and Feature IDs ##########################
4018 :
4019 :	parrello	1.287	=head3 ftype
4020 :
4021 :			C<< my $type = FIG::ftype($fid); >>
4022 :	efrank	1.1
4023 :	parrello	1.287	or
4024 :	efrank	1.1
4025 :	parrello	1.287	C<< my $type = $fig->ftype($fid); >>
4026 :	efrank	1.1
4027 :			Returns the type of a feature, given the feature ID. This just amounts
4028 :	parrello	1.287	to lifting it out of the feature ID, since features have IDs of the form
4029 :	efrank	1.1
4030 :	parrello	1.287	fig\|x.y.f.n
4031 :	efrank	1.1
4032 :			where
4033 :			x.y is the genome ID
4034 :	parrello	1.287	f is the type of feature
4035 :	efrank	1.1	n is an integer that is unique within the genome/type
4036 :
4037 :	parrello	1.287	=over 4
4038 :
4039 :			=item fid
4040 :
4041 :			FIG ID of the feature whose type is desired.
4042 :
4043 :			=item RETURN
4044 :
4045 :			Returns the feature type (e.g. C<peg>, C<rna>, C<pi>, or C<pp>), or C<undef> if the
4046 :			feature ID is not a FIG ID.
4047 :
4048 :			=back
4049 :
4050 :	efrank	1.1	=cut
4051 :
4052 :			sub ftype {
4053 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
4054 :	efrank	1.1	my($feature_id) = @_;
4055 :
4056 :	parrello	1.287	if ($feature_id =~ /^fig\\|\d+\.\d+\.([^\.]+)/) {
4057 :	parrello	1.365	return $1;
4058 :	efrank	1.1	}
4059 :			return undef;
4060 :			}
4061 :
4062 :	parrello	1.287	=head3 genome_of
4063 :
4064 :			C<< my $genome_id = $fig->genome_of($fid); >>
4065 :
4066 :			or
4067 :
4068 :			C<< my $genome_id = FIG::genome_of($fid); >>
4069 :
4070 :			Return the genome ID from a feature ID.
4071 :	efrank	1.1
4072 :	parrello	1.287	=over 4
4073 :
4074 :			=item fid
4075 :
4076 :			ID of the feature whose genome ID is desired.
4077 :
4078 :			=item RETURN
4079 :	efrank	1.1
4080 :	parrello	1.287	If the feature ID is a FIG ID, returns the genome ID embedded inside it; otherwise, it
4081 :			returns C<undef>.
4082 :	efrank	1.1
4083 :	parrello	1.287	=back
4084 :	efrank	1.1
4085 :			=cut
4086 :
4087 :
4088 :	parrello	1.328	sub genome_of :Scalar {
4089 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
4090 :	parrello	1.200	my $prot_id = (@_ == 1) ? $_[0] : $_[1];
4091 :	efrank	1.1
4092 :			if ($prot_id =~ /^fig\\|(\d+\.\d+)/) { return $1; }
4093 :			return undef;
4094 :			}
4095 :
4096 :	parrello	1.287	=head3 genome_and_peg_of
4097 :
4098 :			C<< my ($genome_id, $peg_number = FIG::genome_and_peg_of($fid); >>
4099 :
4100 :			C<< my ($genome_id, $peg_number = $fig->genome_and_peg_of($fid); >>
4101 :	olson	1.96
4102 :	parrello	1.287	Return the genome ID and peg number from a feature ID.
4103 :	olson	1.96
4104 :	parrello	1.287	=over 4
4105 :
4106 :			=item prot_id
4107 :
4108 :			ID of the feature whose genome and PEG number as desired.
4109 :
4110 :			=item RETURN
4111 :
4112 :			Returns the genome ID and peg number associated with a feature if the feature
4113 :			is represented by a FIG ID, else C<undef>.
4114 :
4115 :			=back
4116 :	olson	1.96
4117 :			=cut
4118 :
4119 :			sub genome_and_peg_of {
4120 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
4121 :	parrello	1.200	my $prot_id = (@_ == 1) ? $_[0] : $_[1];
4122 :	olson	1.96
4123 :	parrello	1.287	if ($prot_id =~ /^fig\\|(\d+\.\d+)\.peg\.(\d+)/) {
4124 :	parrello	1.298	return ($1, $2);
4125 :	olson	1.96	}
4126 :			return undef;
4127 :			}
4128 :
4129 :	parrello	1.287	=head3 by_fig_id
4130 :
4131 :			C<< my @sorted_by_fig_id = sort { FIG::by_fig_id($a,$b) } @fig_ids; >>
4132 :
4133 :			Compare two feature IDs.
4134 :
4135 :			This function is designed to assist in sorting features by ID. The sort is by
4136 :			genome ID followed by feature type and then feature number.
4137 :
4138 :			=over 4
4139 :
4140 :			=item a
4141 :	efrank	1.1
4142 :	parrello	1.287	First feature ID.
4143 :	efrank	1.1
4144 :	parrello	1.287	=item b
4145 :	efrank	1.1
4146 :	parrello	1.287	Second feature ID.
4147 :
4148 :			=item RETURN
4149 :
4150 :			Returns a negative number if the first parameter is smaller, zero if both parameters
4151 :			are equal, and a positive number if the first parameter is greater.
4152 :
4153 :			=back
4154 :	efrank	1.1
4155 :			=cut
4156 :
4157 :			sub by_fig_id {
4158 :			my($a,$b) = @_;
4159 :			my($g1,$g2,$t1,$t2,$n1,$n2);
4160 :			if (($a =~ /^fig\\|(\d+\.\d+).([^\.]+)\.(\d+)$/) && (($g1,$t1,$n1) = ($1,$2,$3)) &&
4161 :	parrello	1.298	($b =~ /^fig\\|(\d+\.\d+).([^\.]+)\.(\d+)$/) && (($g2,$t2,$n2) = ($1,$2,$3))) {
4162 :			($g1 <=> $g2) or ($t1 cmp $t2) or ($n1 <=> $n2);
4163 :	parrello	1.287	} else {
4164 :	parrello	1.298	$a cmp $b;
4165 :	efrank	1.1	}
4166 :			}
4167 :
4168 :	olson	1.357	=head3 by_genome_id
4169 :
4170 :			C<< my @sorted_by_genome_id = sort { FIG::by_genome_id($a,$b) } @genome_ids; >>
4171 :
4172 :			Compare two genome IDs.
4173 :
4174 :	parrello	1.379	This function is designed to assist in sorting genomes by ID.
4175 :	olson	1.357
4176 :			=over 4
4177 :
4178 :			=item a
4179 :
4180 :			First genome ID.
4181 :
4182 :			=item b
4183 :
4184 :			Second genome ID.
4185 :
4186 :			=item RETURN
4187 :
4188 :			Returns a negative number if the first parameter is smaller, zero if both parameters
4189 :			are equal, and a positive number if the first parameter is greater.
4190 :
4191 :			=back
4192 :
4193 :			=cut
4194 :
4195 :			sub by_genome_id {
4196 :			my($a,$b) = @_;
4197 :			my($g1,$g2,$s1, $s2);
4198 :			if (($a =~ /^(\d+)\.(\d+)$/) && (($g1, $s1) = ($1, $2)) &&
4199 :	parrello	1.365	($b =~ /^(\d+)\.(\d+)$/) && (($g2, $s2) = ($1, $2))) {
4200 :	olson	1.357	($g1 <=> $g2) or ($s1 <=> $s2);
4201 :			} else {
4202 :			$a cmp $b;
4203 :			}
4204 :			}
4205 :
4206 :	parrello	1.287	=head3 genes_in_region
4207 :	efrank	1.1
4208 :	parrello	1.287	C<< my ($features_in_region, $beg1, $end1) = $fig->genes_in_region($genome, $contig, $beg, $end, size_limit); >>
4209 :	efrank	1.1
4210 :	parrello	1.287	Locate features that overlap a specified region of a contig. This includes features that begin or end
4211 :			outside that region, just so long as some part of the feature can be found in the region of interest.
4212 :	efrank	1.1
4213 :			It is often important to be able to find the genes that occur in a specific region on
4214 :			a chromosome. This routine is designed to provide this information. It returns all genes
4215 :	parrello	1.287	that overlap positions from I<$beg> through I<$end> in the specified contig.
4216 :
4217 :			The I<$size_limit> parameter limits the search process. It is presumed that no features are longer than the
4218 :			specified size limit. A shorter size limit means you'll miss some features; a longer size limit significantly
4219 :			slows the search process. For prokaryotes, a value of C<10000> (the default) seems to work best.
4220 :
4221 :			=over 4
4222 :
4223 :			=item genome
4224 :
4225 :			ID of the genome containing the relevant contig.
4226 :
4227 :			=item contig
4228 :
4229 :			ID of the relevant contig.
4230 :
4231 :			=item beg
4232 :
4233 :			Position of the first base pair in the region of interest.
4234 :
4235 :			=item end
4236 :
4237 :			Position of the last base pair in the region of interest.
4238 :
4239 :			=item size_limit
4240 :
4241 :			Maximum allowable size for a feature. If omitted, C<10000> is assumed.
4242 :
4243 :			=item RETURN
4244 :	efrank	1.1
4245 :	parrello	1.287	Returns a three-element list. The first element is a reference to a list of the feature IDs found. The second
4246 :			element is the position of the leftmost base pair in any feature found. This may be well before the region of
4247 :			interest begins or it could be somewhere inside. The third element is the position of the rightmost base pair
4248 :			in any feature found. Again, this can be somewhere inside the region or it could be well to the right of it.
4249 :
4250 :			=back
4251 :	efrank	1.1
4252 :			=cut
4253 :	parrello	1.213	#: Return Type @;
4254 :	efrank	1.1	sub genes_in_region {
4255 :	parrello	1.287	my($self, $genome, $contig, $beg, $end, $pad) = @_;
4256 :			if (!defined $pad) { $pad = 10000; }
4257 :	efrank	1.1	my($x,$relational_db_response,$feature_id,$b1,$e1,@feat,@tmp,$l,$u);
4258 :
4259 :			my $rdbH = $self->db_handle;
4260 :
4261 :	parrello	1.200	my $minV = $beg - $pad;
4262 :	efrank	1.1	my $maxV = $end + $pad;
4263 :	parrello	1.287	if (($relational_db_response = $rdbH->SQL("SELECT id FROM features "
4264 :			. " WHERE ( minloc > $minV ) AND ( minloc < $maxV ) AND ( maxloc < $maxV) AND "
4265 :			. " ( genome = \'$genome\' ) AND ( contig = \'$contig\' );")) &&
4266 :			(@$relational_db_response >= 1)) {
4267 :			@tmp = sort { ($a->[1] cmp $b->[1]) or (($a->[2]+$a->[3]) <=> ($b->[2]+$b->[3])) }
4268 :			map { $feature_id = $_->[0]; $x = $self->feature_location($feature_id); $x ? [$feature_id,&boundaries_of($x)] : ()
4269 :			} @$relational_db_response;