Annotation of /FigKernelPackages/FIG.pm

Revision 1.623 - (view) (download) (as text)

1 :	gdpusch	1.600	# -- perl --
2 :			########################################################################
3 :	olson	1.404	# Copyright (c) 2003-2006 University of Chicago and Fellowship
4 :			# for Interpretations of Genomes. All Rights Reserved.
5 :			#
6 :			# This file is part of the SEED Toolkit.
7 :	parrello	1.518	#
8 :	olson	1.404	# The SEED Toolkit is free software. You can redistribute
9 :			# it and/or modify it under the terms of the SEED Toolkit
10 :	parrello	1.518	# Public License.
11 :	olson	1.404	#
12 :			# You should have received a copy of the SEED Toolkit Public License
13 :			# along with this program; if not write to the University of Chicago
14 :			# at info@ci.uchicago.edu or the Fellowship for Interpretation of
15 :			# Genomes at veronika@thefig.info or download a copy from
16 :			# http://www.theseed.org/LICENSE.TXT.
17 :	gdpusch	1.600	########################################################################
18 :	olson	1.404
19 :	efrank	1.1	package FIG;
20 :
21 :	olson	1.111	use strict;
22 :
23 :	overbeek	1.453	use FIG_Config;
24 :
25 :			#
26 :			# See if we need to use fcntl-based file locking. If so, import
27 :			# the package and override the global definition of flock.
28 :			# This is in place at least initially for the GPFS-based install on
29 :			# the NMPDR cluster.
30 :			#
31 :
32 :			use FileLocking;
33 :
34 :	overbeek	1.135	use Fcntl qw/:flock/; # import LOCK_* constants
35 :
36 :	olson	1.116	use POSIX;
37 :	olson	1.158	use IPC::Open2;
38 :	olson	1.329	use MIME::Base64;
39 :	olson	1.330	use File::Basename;
40 :	olson	1.359	use FileHandle;
41 :	parrello	1.394	use File::Copy;
42 :	olson	1.417	use SOAP::Lite;
43 :	parrello	1.420	use File::Path;
44 :	overbeek	1.484	use LWP::UserAgent;
45 :	olson	1.116
46 :	efrank	1.1	use DBrtns;
47 :			use Sim;
48 :	olson	1.361	use Annotation;
49 :	efrank	1.1	use Blast;
50 :	overbeek	1.322	use FullLocation;
51 :	overbeek	1.36	use tree_utilities;
52 :	olson	1.93	use Subsystem;
53 :	olson	1.162	use SeedDas;
54 :	olson	1.183	use Construct;
55 :	parrello	1.200	use FIGRules;
56 :	parrello	1.210	use Tracer;
57 :	olson	1.297	use GenomeIDMap;
58 :	parrello	1.539	use RemoteCustomAttributes;
59 :	olson	1.260
60 :	olson	1.356	our $haveDateParse;
61 :			eval {
62 :			require Date::Parse;
63 :			import Date::Parse;
64 :			$haveDateParse = 1;
65 :	parrello	1.540	require CustomAttributes;
66 :			import CustomAttributes;
67 :	olson	1.356	};
68 :
69 :	olson	1.245	eval { require FigGFF; };
70 :	parrello	1.390	if ($@ and T(1)) {
71 :	olson	1.260	warn $@;
72 :			}
73 :	olson	1.79
74 :			#
75 :			# Conditionally evaluate this in case its prerequisites are not available.
76 :			#
77 :
78 :	olson	1.356	our $ClearinghouseOK;
79 :			eval {
80 :	olson	1.79	require Clearinghouse;
81 :	olson	1.356	$ClearinghouseOK = 1;
82 :	olson	1.79	};
83 :	efrank	1.1
84 :	olson	1.10	use IO::Socket;
85 :
86 :	efrank	1.1	use FileHandle;
87 :
88 :	olson	1.530	use Carp qw(confess croak carp cluck);
89 :	efrank	1.1	use Data::Dumper;
90 :	overbeek	1.25	use Time::Local;
91 :	olson	1.93	use File::Spec;
92 :	olson	1.123	use File::Copy;
93 :	olson	1.112	#
94 :			# Try to load the RPC stuff; it might fail on older versions of the software.
95 :			#
96 :			eval {
97 :			require FIGrpc;
98 :			};
99 :
100 :			my $xmlrpc_available = 1;
101 :	parrello	1.287	if ($@ ne "") {
102 :	olson	1.112	$xmlrpc_available = 0;
103 :			}
104 :
105 :	efrank	1.1
106 :	olson	1.111	use FIGAttributes;
107 :			use base 'FIGAttributes';
108 :
109 :			use vars qw(%_FunctionAttributes);
110 :
111 :			use Data::Dumper;
112 :
113 :	olson	1.124	#
114 :			# Force all new files to be all-writable.
115 :			#
116 :
117 :			umask 0;
118 :
119 :	parrello	1.210	=head1 FIG Genome Annotation System
120 :
121 :			=head2 Introduction
122 :
123 :			This is the main object for access to the SEED data store. The data store
124 :			itself is a combination of flat files and a database. The flat files can
125 :			be moved easily between systems and the database rebuilt as needed.
126 :
127 :			A reduced set of this object's functions are available via the B<SFXlate>
128 :			object. The SFXlate object uses a single database to represent all its
129 :			genomic information. It provides a much smaller capability for updating
130 :			the data, and eliminates all similarities except for bidirectional best
131 :			hits.
132 :
133 :			The key to making the FIG system work is proper configuration of the
134 :			C<FIG_Config.pm> file. This file contains names and URLs for the key
135 :			directories as well as the type and login information for the database.
136 :
137 :	parrello	1.287	FIG was designed to operate as a series of peer instances. Each instance is
138 :			updated independently by its owner, and the instances can be synchronized
139 :			using a process called a I<peer-to-peer update>. The terms
140 :			I<SEED instance> and I<peer> are used more-or-less interchangeably.
141 :
142 :			The POD documentation for this module is still in progress, and is provided
143 :			on an AS IS basis without warranty. If you have a correction and you're
144 :			not a developer, EMAIL the details to B<bruce@gigabarb.com> and I'll fold
145 :			it in.
146 :
147 :			B<NOTE>: The usage example for each method specifies whether it is static
148 :
149 :			FIG::something
150 :
151 :			or dynamic
152 :
153 :			$fig->something
154 :
155 :			If the method is static and has no parameters (C<FIG::something()>) it can
156 :	parrello	1.298	also be invoked dynamically. This is a general artifact of the
157 :	parrello	1.287	way PERL implements object-oriented programming.
158 :
159 :			=head2 Hiding/Caching in a FIG object
160 :
161 :			We save the DB handle, cache taxonomies, and put a few other odds and ends in the
162 :			FIG object. We expect users to invoke these services using the object $fig constructed
163 :			using:
164 :
165 :			use FIG;
166 :			my $fig = new FIG;
167 :
168 :			$fig is then used as the basic mechanism for accessing FIG services. It is, of course,
169 :			just a hash that is used to retain/cache data. The most commonly accessed item is the
170 :			DB filehandle, which is accessed via $self->db_handle.
171 :
172 :			We cache genus/species expansions, taxonomies, distances (very crudely estimated) estimated
173 :			between genomes, and a variety of other things.
174 :
175 :	parrello	1.210	=cut
176 :
177 :	parrello	1.287
178 :	parrello	1.210	#: Constructor FIG->new();
179 :
180 :			=head2 Public Methods
181 :
182 :			=head3 new
183 :
184 :			C<< my $fig = FIG->new(); >>
185 :
186 :	parrello	1.298	This is the constructor for a FIG object. It uses no parameters. If tracing
187 :			has not yet been turned on, it will be turned on here. The tracing type and
188 :			level are specified by the configuration variables C<$FIG_Config::trace_levels>
189 :	parrello	1.301	and C<$FIG_Config::trace_type>. These defaults can be overridden using the
190 :			environment variables C<Trace> and C<TraceType>, respectively.
191 :	parrello	1.210
192 :			=cut
193 :
194 :	efrank	1.1	sub new {
195 :			my($class) = @_;
196 :
197 :	olson	1.102	#
198 :			# Check to see if we have a FIG_URL environment variable set.
199 :			# If we do, don't actually create a FIG object, but rather
200 :			# create a FIGrpc and return that as the return from this constructor.
201 :			#
202 :	parrello	1.390	if ($ENV{FIG_URL} && $xmlrpc_available) {
203 :	parrello	1.210	my $figrpc = new FIGrpc($ENV{FIG_URL});
204 :			return $figrpc;
205 :	olson	1.102	}
206 :	parrello	1.355	Trace("Connecting to the database.") if T(2);
207 :	parrello	1.287	# Connect to the database, then return ourselves.
208 :	efrank	1.1	my $rdbH = new DBrtns;
209 :	overbeek	1.453
210 :			my $self = {
211 :	parrello	1.210	_dbf => $rdbH,
212 :	overbeek	1.453	};
213 :	parrello	1.542	if ($FIG_Config::attrOld) {
214 :			# Use the old attribute system. This is normally only done if we
215 :			# need to reload.
216 :	parrello	1.563	Trace("Legacy attribute system chosen using the override feature.") if T(3);
217 :	parrello	1.542	} elsif ($FIG_Config::attrURL) {
218 :	parrello	1.563	Trace("Remote attribute server $FIG_Config::attrURL chosen.") if T(3);
219 :	parrello	1.539	$self->{_ca} = RemoteCustomAttributes->new($FIG_Config::attrURL);
220 :			} elsif ($FIG_Config::attrDbName) {
221 :	parrello	1.563	Trace("Local attribute database $FIG_Config::attrDbName chosen.") if T(3);
222 :	parrello	1.570	my $user = ($FIG_Config::arch eq 'win' ? 'self' : scalar(getpwent()));
223 :			$self->{_ca} = CustomAttributes->new(user => $user);
224 :	parrello	1.538	}
225 :	overbeek	1.453
226 :			#
227 :			# If we have a readonly-database defined in the config,
228 :			# create a handle for that as well.
229 :			#
230 :
231 :			if (defined($FIG_Config::readonly_dbhost))
232 :			{
233 :	parrello	1.485	my $ro = new DBrtns($FIG_Config::dbms, $FIG_Config::readonly_db, $FIG_Config::readonly_dbuser,
234 :			$FIG_Config::readonly_dbpass, $FIG_Config::readonly_dbport, $FIG_Config::readonly_dbhost,
235 :			$FIG_Config::readonly_dbsock);
236 :			$self->{_ro_dbf} = $ro;
237 :	overbeek	1.453
238 :	parrello	1.485	#
239 :			# Oh ick. All of the queries made go through the one dbf that a FIG holds. We want
240 :			# to redirect the select queries through this readonly object. We'll need
241 :			# to tell the main handle about the readonly one, and let it decide.
242 :			#
243 :
244 :			$rdbH->set_readonly_handle($ro);
245 :	overbeek	1.453	}
246 :
247 :			return bless $self, $class;
248 :	efrank	1.1	}
249 :
250 :	parrello	1.606	=head3 CacheTrick
251 :
252 :			C<< my $value = $fig->CacheTrick($self, $field => $evalString); >>
253 :
254 :			This is a helper method used to create simple field caching in another object. If the
255 :			named field is found in $self, then it will be returned directly. Otherwise, the eval
256 :			string will be executed to compute the value. The value is then cahced in the $self
257 :			object so it can be retrieved easily when needed. Use this method to make a FIG
258 :			data-access object more like an object created by PPO or ERDB.
259 :
260 :			=over 4
261 :
262 :			=item self
263 :
264 :			Hash or blessed object containing the cached fields.
265 :
266 :			=item field
267 :
268 :			Name of the field desired.
269 :
270 :			=item evalString
271 :
272 :			String that can be evaluated to compute the field value.
273 :
274 :			=item RETURN
275 :
276 :			Returns the value of the desired field.
277 :
278 :			=back
279 :
280 :			=cut
281 :
282 :			sub CacheTrick {
283 :			# Get the parameters. Note that we get this object under the name "$fig" rather than
284 :			# "$self", because $self represents the caller's object.
285 :			my ($fig, $self, $field, $evalString) = @_;
286 :			# Declare the return variable.
287 :			my $retVal;
288 :			# Check the cache.
289 :			if (exists $self->{$field}) {
290 :			# Return the cached data.
291 :			$retVal = $self->{$field};
292 :			} else {
293 :			# Compute the field value.
294 :			Trace("Retrieving data for $field using formula: $evalString") if T(4);
295 :			$retVal = eval($evalString);
296 :			# Cache it for future use.
297 :			$self->{$field} = $retVal;
298 :			}
299 :			# Return the field value.
300 :			return $retVal;
301 :			}
302 :
303 :	mkubal	1.546	=head3 go_number_to_term
304 :
305 :			Returns GO term for GO number from go_number_to_term table in database
306 :
307 :			=cut
308 :
309 :			sub go_number_to_term {
310 :			my($self,$id) = @_;
311 :			my $rdbH = $self->db_handle;
312 :	overbeek	1.548	my $relational_db_response = $rdbH->SQL("SELECT go_desc FROM go_terms where go_id = \'$id\'");
313 :	mkubal	1.546	return (@$relational_db_response == 1) ? $relational_db_response->[0]->[0] : "";
314 :			return "";
315 :			}
316 :	overbeek	1.454
317 :	overbeek	1.548	sub go_number_to_info {
318 :			my($self,$id) = @_;
319 :			my $rdbH = $self->db_handle;
320 :			my $relational_db_response = $rdbH->SQL("SELECT go_desc,go_type,obsolete FROM go_terms where go_id = \'$id\'");
321 :			return (@$relational_db_response == 1) ? $relational_db_response->[0] : "";
322 :			return "";
323 :			}
324 :
325 :
326 :	parrello	1.287	=head3 db_handle
327 :
328 :			C<< my $dbh = $fig->db_handle; >>
329 :
330 :			Return the handle to the internal B<DBrtns> object. This allows direct access to
331 :			the database methods.
332 :
333 :			=cut
334 :
335 :			sub db_handle {
336 :			my($self) = @_;
337 :			return $self->{_dbf};
338 :			}
339 :
340 :	overbeek	1.293	sub table_exists {
341 :			my($self,$table) = @_;
342 :
343 :			my $rdbH = $self->db_handle;
344 :			return $rdbH->table_exists($table);
345 :			}
346 :	parrello	1.292
347 :	parrello	1.287	=head3 cached
348 :
349 :			C<< my $x = $fig->cached($name); >>
350 :
351 :			Return a reference to a hash containing transient data. If no hash exists with the
352 :			specified name, create an empty one under that name and return it.
353 :
354 :			The idea behind this method is to allow clients to cache data in the FIG object for
355 :			later use. (For example, a method might cache feature data so that it can be
356 :			retrieved later without using the database.) This facility should be used sparingly,
357 :			since different clients may destroy each other's data if they use the same name.
358 :
359 :			=over 4
360 :
361 :			=item name
362 :
363 :			Name assigned to the cached data.
364 :
365 :			=item RETURN
366 :
367 :			Returns a reference to a hash that is permanently associated with the specified name.
368 :			If no such hash exists, an empty one will be created for the purpose.
369 :
370 :			=back
371 :
372 :			=cut
373 :
374 :			sub cached {
375 :			my($self,$what) = @_;
376 :
377 :			my $x = $self->{$what};
378 :			if (! $x) {
379 :			$x = $self->{$what} = {};
380 :			}
381 :			return $x;
382 :			}
383 :	parrello	1.210
384 :			=head3 get_system_name
385 :
386 :			C<< my $name = $fig->get_system_name; >>
387 :
388 :			Returns C<seed>, indicating that this is object is using the SEED
389 :			database. The same method on an SFXlate object will return C<sprout>.
390 :
391 :			=cut
392 :			#: Return Type $;
393 :			sub get_system_name {
394 :	olson	1.207	return "seed";
395 :	olson	1.205	}
396 :	parrello	1.210
397 :	parrello	1.287	=head3 DESTROY
398 :
399 :			The destructor releases the database handle.
400 :
401 :			=cut
402 :	olson	1.205
403 :	parrello	1.287	sub DESTROY {
404 :	efrank	1.1	my($self) = @_;
405 :			my($rdbH);
406 :
407 :	parrello	1.210	if ($rdbH = $self->db_handle) {
408 :			$rdbH->DESTROY;
409 :	efrank	1.1	}
410 :			}
411 :
412 :	parrello	1.355	=head3 same_seqs
413 :
414 :			C<< my $sameFlag = FIG::same_seqs($s1, $s2); >>
415 :
416 :			Return TRUE if the specified protein sequences are considered equivalent and FALSE
417 :			otherwise. The sequences should be presented in I<nr-analysis> form, which is in
418 :			reverse order and upper case with the stop codon omitted.
419 :
420 :			The sequences will be considered equivalent if the shorter matches the initial
421 :			portion of the long one and is no more than 30% smaller. Since the sequences are
422 :			in nr-analysis form, the equivalent start potions means that the sequences
423 :			have the same tail. The importance of the tail is that the stop point of a PEG
424 :			is easier to find than the start point, so a same tail means that the two
425 :			sequences are equivalent except for the choice of start point.
426 :
427 :			=over 4
428 :
429 :			=item s1
430 :
431 :			First protein sequence, reversed and with the stop codon removed.
432 :
433 :			=item s2
434 :
435 :			Second protein sequence, reversed and with the stop codon removed.
436 :
437 :			=item RETURN
438 :
439 :			Returns TRUE if the two protein sequences are equivalent, else FALSE.
440 :
441 :			=back
442 :
443 :			=cut
444 :
445 :			sub same_seqs {
446 :			my ($s1,$s2) = @_;
447 :
448 :			my $ln1 = length($s1);
449 :			my $ln2 = length($s2);
450 :
451 :			return ((abs($ln1-$ln2) < (0.3 * (($ln1 < $ln2) ? $ln1 : $ln2))) &&
452 :			((($ln1 <= $ln2) && (index($s2,$s1) == 0)) \|\|
453 :			(($ln1 > $ln2) && (index($s1,$s2) == 0))));
454 :			}
455 :
456 :	overbeek	1.520	=head3 is_locked_fid
457 :
458 :			C<< $fig->is_locked_fid($fid); >>
459 :
460 :			returns 1 iff $fid is locked
461 :
462 :			=cut
463 :
464 :			sub is_locked_fid {
465 :			my($self,$fid) = @_;
466 :
467 :	overbeek	1.523	if (! $self->table_exists('fid_locks')) { return 0 }
468 :	overbeek	1.520	my $rdbH = $self->db_handle;
469 :			my $relational_db_response = $rdbH->SQL("SELECT fid FROM fid_locks WHERE fid = \'$fid\' ");
470 :			return (@$relational_db_response > 0) ? 1 : 0;
471 :			}
472 :
473 :			=head3 lock_fid
474 :
475 :			C<< $fig->lock_fid($user,$fid); >>
476 :
477 :			Sets a lock on annotations for $fid.
478 :
479 :			=cut
480 :
481 :			sub lock_fid {
482 :			my($self,$user,$fid) = @_;
483 :
484 :	overbeek	1.523	if (! $self->table_exists('fid_locks')) { return 0 }
485 :	overbeek	1.521	if ((! $user) \|\| ($fid !~ /^fig\\|\d+\.\d+/)) { return 0 }
486 :	overbeek	1.553	if ($self->is_locked_fid($fid)) { return 1 }
487 :	overbeek	1.521
488 :	overbeek	1.520	my $func = $self->function_of($fid);
489 :			$self->add_annotation($fid,$user,"locked assignments to '$func'");
490 :
491 :			my $rdbH = $self->db_handle;
492 :			my $relational_db_response = $rdbH->SQL("SELECT fid FROM fid_locks WHERE fid = \'$fid\' ");
493 :			if (! (@$relational_db_response > 0))
494 :			{
495 :			$rdbH->SQL("INSERT INTO fid_locks ( fid ) VALUES ( '$fid' )");
496 :			if ($fid =~ /^fig\\|(\d+\.\d+)\.([^\.]+)/)
497 :			{
498 :			my $genome = $1;
499 :			my $type = $2;
500 :			if (open(TMP,">>$FIG_Config::organisms/$genome/Features/$type/locks"))
501 :			{
502 :			print TMP "$fid\t1\n";
503 :			}
504 :			close(TMP);
505 :			}
506 :			}
507 :			}
508 :
509 :			=head3 unlock_fid
510 :
511 :			C<< $fig->unlock_fid($user,$fid); >>
512 :
513 :			Sets a unlock on annotations for $fid.
514 :
515 :			=cut
516 :
517 :			sub unlock_fid {
518 :			my($self,$user,$fid) = @_;
519 :
520 :	overbeek	1.523	if (! $self->table_exists('fid_locks')) { return 0 }
521 :	overbeek	1.521	if ((! $user) \|\| ($fid !~ /^fig\\|\d+\.\d+/)) { return 0 }
522 :	overbeek	1.553	if (! $self->is_locked_fid($fid)) { return 1 }
523 :	overbeek	1.521
524 :	overbeek	1.520	$self->add_annotation($fid,$user,"unlocked assignments");
525 :			my $rdbH = $self->db_handle;
526 :			my $relational_db_response = $rdbH->SQL("SELECT fid FROM fid_locks WHERE fid = '$fid' ");
527 :			$rdbH->SQL("DELETE FROM fid_locks WHERE ( fid = '$fid' )");
528 :			if ($fid =~ /^fig\\|(\d+\.\d+)\.([^\.]+)/)
529 :			{
530 :			my $genome = $1;
531 :			my $type = $2;
532 :			if (open(TMP,">>$FIG_Config::organisms/$genome/Features/$type/locks"))
533 :			{
534 :			print TMP "$fid\t0\n";
535 :			}
536 :			close(TMP);
537 :			}
538 :			}
539 :
540 :	parrello	1.210	=head3 delete_genomes
541 :
542 :			C<< $fig->delete_genomes(\@genomes); >>
543 :
544 :			Delete the specified genomes from the data store. This requires making
545 :			system calls to move and delete files.
546 :
547 :			=cut
548 :			#: Return Type ;
549 :	overbeek	1.429	################################# make damn sure that you have enough disk ######################
550 :			### The following code represents a serious, major update. Normally, one simply "marks" deleted
551 :			### genomes, which is quick and does not require halting the system.
552 :	overbeek	1.7	sub delete_genomes {
553 :			my($self,$genomes) = @_;
554 :			my $tmpD = "$FIG_Config::temp/tmp.deleted.$$";
555 :			my $tmp_Data = "$FIG_Config::temp/Data.$$";
556 :
557 :			my %to_del = map { $_ => 1 } @$genomes;
558 :			open(TMP,">$tmpD") \|\| die "could not open $tmpD";
559 :
560 :			my $genome;
561 :	parrello	1.287	foreach $genome ($self->genomes) {
562 :			if (! $to_del{$genome}) {
563 :			print TMP "$genome\n";
564 :			}
565 :	overbeek	1.7	}
566 :			close(TMP);
567 :
568 :			&run("extract_genomes $tmpD $FIG_Config::data $tmp_Data");
569 :	overbeek	1.429	print STDERR "Please bring the system down for a bit\n";
570 :			system "echo \"System down due to update of genomes\n\" >> $tmp_Data/Global/why_down";
571 :	parrello	1.200	&run("mv $FIG_Config::data $FIG_Config::data.deleted");
572 :	overbeek	1.47	&run("mv $tmp_Data $FIG_Config::data");
573 :			&run("fig load_all");
574 :	overbeek	1.429	print STDERR "Now, you should think about deleting $FIG_Config::data.deleted\n";
575 :			unlink("$FIG_Config::global/why_down"); ### start allowing CGIs to run
576 :			# &run("rm -rf $FIG_Config::data.deleted");
577 :			}
578 :
579 :			### Mark a genome as deleted, but do not actually clean up anything. That whole event
580 :			### requires "delete_genomes"
581 :			###
582 :			sub mark_deleted_genomes {
583 :	overbeek	1.466	my($self,$user,$genomes) = @_;
584 :	overbeek	1.429	my($genome);
585 :
586 :	overbeek	1.466	foreach $genome (@$genomes)
587 :			{
588 :	parrello	1.485	$self->log_update($user,$genome,$self->genus_species($genome),"Marked Deleted Genome $genome");
589 :	overbeek	1.466	}
590 :			return $self->mark_deleted_genomes_body($user,$genomes);
591 :			}
592 :
593 :			sub mark_deleted_genomes_body {
594 :			my($self,$user,$genomes) = @_;
595 :			my($genome);
596 :	overbeek	1.440
597 :	overbeek	1.429	my $rdbH = $self->db_handle;
598 :
599 :			my $n = 0;
600 :			foreach $genome (@$genomes)
601 :			{
602 :	parrello	1.485	if ($self->is_genome($genome) && open(DEL,">$FIG_Config::organisms/$genome/DELETED"))
603 :	parrello	1.518	{
604 :	parrello	1.485	print DEL "deleted\n";
605 :			$rdbH->SQL("DELETE FROM genome WHERE ( genome = '$genome' )");
606 :			$n++;
607 :			}
608 :			close(DEL);
609 :	overbeek	1.429	}
610 :	overbeek	1.466	$self->{_is_genome} = {};
611 :	overbeek	1.429	return $n;
612 :			}
613 :	parrello	1.518
614 :	overbeek	1.429	sub unmark_deleted_genomes {
615 :	overbeek	1.466	my($self,$user,$genomes) = @_;
616 :	overbeek	1.429	my($genome);
617 :
618 :	overbeek	1.466	foreach $genome (@$genomes)
619 :			{
620 :	parrello	1.485	$self->log_update($user,$genome,$self->genus_species($genome),"Unmarked Deleted Genome $genome");
621 :	overbeek	1.466	}
622 :
623 :	overbeek	1.429	my $rdbH = $self->db_handle;
624 :
625 :			my $n = 0;
626 :			foreach $genome (@$genomes)
627 :			{
628 :	parrello	1.485	if (-s "$FIG_Config::organisms/$genome/DELETED")
629 :			{
630 :			unlink("$FIG_Config::organisms/$genome/DELETED");
631 :			&run("compute_genome_counts $genome");
632 :			$n++;
633 :			}
634 :	overbeek	1.429	}
635 :	overbeek	1.466	$self->{_is_genome} = {};
636 :	overbeek	1.429	return $n;
637 :	overbeek	1.7	}
638 :	parrello	1.200
639 :	overbeek	1.469	sub log_corr {
640 :	overbeek	1.470	my($self,$user,$genome, $mapping,$msg) = @_;
641 :	overbeek	1.469
642 :			my $gs = $self->genus_species($genome);
643 :	overbeek	1.470	$self->log_update($user,$genome,$gs,"Logged correspondence for $genome [$msg]",$mapping);
644 :	overbeek	1.469	}
645 :
646 :	overbeek	1.466	sub replace_genome {
647 :			my($self,$user,$old_genome,$genomeF, $mapping, $force, $skipnr) = @_;
648 :
649 :	parrello	1.518	($genomeF =~ /(\d+\.\d+)$/)
650 :	parrello	1.485	\|\| die "$genomeF must have a valid genome ID as the last part of the path";
651 :	overbeek	1.466	my $genome = $1;
652 :
653 :			open(TMP,"<$genomeF/GENOME") \|\| die "could not open $genome/GENOME";
654 :			my $gs = <TMP>;
655 :			chomp $gs;
656 :			close(TMP);
657 :
658 :			$self->log_update($user,$genome,$gs,"Replaced genome $old_genome with $genome\n$genomeF $force $skipnr",$genomeF,$mapping);
659 :	parrello	1.518
660 :	overbeek	1.466	$self->mark_deleted_genomes($user,[$old_genome]);
661 :			return $self->add_genome_body($user,$genomeF,$force,$skipnr);
662 :			}
663 :
664 :	parrello	1.210	=head3 add_genome
665 :
666 :	overbeek	1.335	C<< my $ok = $fig->add_genome($genomeF, $force, $skipnr); >>
667 :	parrello	1.210
668 :			Add a new genome to the data store. A genome's data is kept in a directory
669 :	parrello	1.287	by itself, underneath the main organism directory. This method essentially
670 :			moves genome data from an external directory to the main directory and
671 :			performs some indexing tasks to integrate it.
672 :	parrello	1.210
673 :			=over 4
674 :
675 :			=item genomeF
676 :
677 :	parrello	1.287	Name of the directory containing the genome files. This should be a
678 :			fully-qualified directory name. The last segment of the directory
679 :			name should be the genome ID.
680 :	parrello	1.210
681 :	overbeek	1.331	=item force
682 :
683 :			This will ignore errors thrown by verify_genome_directory. This is bad, and you should
684 :			never do it, but I am in the situation where I need to move a genome from one machine
685 :			to another, and although I trust the genome I can't.
686 :
687 :	overbeek	1.335	=item skipnr
688 :
689 :	olson	1.478	We don't always want to add the proteins 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.
690 :	overbeek	1.335
691 :	parrello	1.210	=item RETURN
692 :
693 :			Returns TRUE if successful, else FALSE.
694 :
695 :			=back
696 :
697 :			=cut
698 :			#: Return Type $;
699 :	efrank	1.1	sub add_genome {
700 :	overbeek	1.466	my($self,$user,$genomeF, $force, $skipnr, $dont_mark_complete) = @_;
701 :
702 :	parrello	1.518	($genomeF =~ /(\d+\.\d+)$/)
703 :	parrello	1.485	\|\| die "$genomeF must have a valid genome ID as the last part of the path";
704 :	overbeek	1.466	my $genome = $1;
705 :
706 :			open(TMP,"<$genomeF/GENOME") \|\| die "could not open $genome/GENOME";
707 :			my $gs = <TMP>;
708 :			chomp $gs;
709 :			close(TMP);
710 :
711 :	olson	1.478	my $rc = $self->add_genome_body($user,$genomeF,$force,$skipnr,$dont_mark_complete);
712 :	overbeek	1.466
713 :	olson	1.478	if ($rc)
714 :			{
715 :	parrello	1.485	$self->log_update($user,$genome,$gs,"Added genome $genome\n$genomeF $force $skipnr",$genomeF);
716 :	olson	1.478	}
717 :	parrello	1.518
718 :	olson	1.478	return $rc;
719 :	overbeek	1.466	}
720 :	efrank	1.1
721 :	overbeek	1.466	sub add_genome_body {
722 :			my($self,$user,$genomeF, $force, $skipnr,$dont_mark_complete) = @_;
723 :	overbeek	1.440
724 :	efrank	1.1	my $rc = 0;
725 :	olson	1.93
726 :			my(undef, $path, $genome) = File::Spec->splitpath($genomeF);
727 :
728 :	parrello	1.287	if ($genome !~ /^\d+\.\d+$/) {
729 :			warn "Invalid genome filename $genomeF\n";
730 :			return $rc;
731 :	olson	1.93	}
732 :
733 :	parrello	1.287	if (-d $FIG_Config::organisms/$genome) {
734 :			warn "Organism already exists for $genome\n";
735 :			return $rc;
736 :	olson	1.93	}
737 :	parrello	1.200
738 :	olson	1.93
739 :			#
740 :			# We're okay, it doesn't exist.
741 :			#
742 :
743 :			my @errors = `$FIG_Config::bin/verify_genome_directory $genomeF`;
744 :
745 :	parrello	1.287	if (@errors) {
746 :	olson	1.478	print STDERR "Errors found while verifying genome directory $genomeF:\n";
747 :			print STDERR join("", @errors);
748 :
749 :			if (!$force)
750 :	parrello	1.485	{
751 :			return $rc;
752 :			}
753 :	olson	1.478	else
754 :	parrello	1.485	{
755 :			warn "Skipped these errors and continued. You should not do this";
756 :			}
757 :	olson	1.93	}
758 :	parrello	1.200
759 :	olson	1.478	my $sysrc = system("cp -r $genomeF $FIG_Config::organisms");
760 :			if ($sysrc != 0)
761 :			{
762 :	parrello	1.485	warn "Failure copying $genomeF to $FIG_Config::organisms\n";
763 :			return $rc;
764 :	olson	1.478	}
765 :	olson	1.617
766 :			my $genome_dir = "$FIG_Config::organisms/$genome";
767 :
768 :			$sysrc = system("chmod -R 777 $genome_dir");
769 :	olson	1.478	if ($sysrc != 0)
770 :			{
771 :	olson	1.617	warn "Command failed: chmod -R 777 $genome_dir\n";
772 :	parrello	1.485	return $rc;
773 :	olson	1.478	}
774 :	parrello	1.379
775 :	olson	1.617	if (-s "$genome_dir/COMPLETE")
776 :	overbeek	1.353	{
777 :	parrello	1.485	if ($dont_mark_complete)
778 :			{
779 :			print STDERR "$genome was marked as \"complete\", but moving to WAS_MARKED_COMPLETE\n";
780 :	olson	1.617	rename("$genome_dir/COMPLETE", "$genome_dir/WAS_MARKED_COMPLETE");
781 :	parrello	1.485	}
782 :			else
783 :			{
784 :			print STDERR "$genome was marked as \"complete\"\n";
785 :			}
786 :	overbeek	1.353	}
787 :			else
788 :			{
789 :	parrello	1.485	#
790 :			# Not marked complete; assess completeness.
791 :			#
792 :	parrello	1.518
793 :	olson	1.617	my $sysrc = system("$FIG_Config::bin/assess_completeness $genome_dir > $genome_dir/assess_completeness.out 2>&1");
794 :	parrello	1.485	if ($sysrc != 0)
795 :			{
796 :	olson	1.617	warn "assess_completeness $genome_dir failed; continuing with installation.\n";
797 :	parrello	1.485	}
798 :			else
799 :			{
800 :	olson	1.617	if (-s "$genome_dir/PROBABLY_COMPLETE")
801 :	parrello	1.485	{
802 :			print STDERR "Assessed $genome to be probably complete\n";
803 :			if ($dont_mark_complete)
804 :			{
805 :			print STDERR "Not copying PROBABLY_COMPLETE to COMPLETE; this will need to be done later\n";
806 :			}
807 :			else
808 :			{
809 :	olson	1.617	my $cp = "cp -p $genome_dir/PROBABLY_COMPLETE $genome_dir/COMPLETE";
810 :	parrello	1.485	$sysrc = system($cp);
811 :			$sysrc == 0 or warn "Command failed, continuing: $cp\n";
812 :			}
813 :			}
814 :			else
815 :			{
816 :			print STDERR "Assessed $genome to not be probably complete\n";
817 :			}
818 :			}
819 :	overbeek	1.353	}
820 :	parrello	1.379
821 :	olson	1.617	#
822 :			# If this was a RAST genome that has imp_annotations and imp_assigned_functions files,
823 :			# rename any existing annotations/assigned_functions files to rast_XX and copy
824 :			# imp_XX to XX.
825 :			#
826 :
827 :			if (-f "$genome_dir/RAST")
828 :			{
829 :			for my $base ('annotations', 'assigned_functions')
830 :			{
831 :			my $imp = "$genome_dir/imp_$base";
832 :			my $file = "$genome_dir/$base";
833 :			my $rast = "$genome_dir/rast_$base";
834 :
835 :	olson	1.618	if (-f $file)
836 :	olson	1.617	{
837 :	olson	1.618	print "Rename $file to $rast\n";
838 :			rename($file, $rast);
839 :	olson	1.617	}
840 :			if (-f $imp)
841 :			{
842 :	olson	1.618	print "Copy $imp to $file\n";
843 :			copy($imp, $file);
844 :	olson	1.617	}
845 :			}
846 :			}
847 :
848 :	olson	1.478	$sysrc = system("index_contigs $genome");
849 :			$sysrc == 0 or
850 :	parrello	1.485	warn "index_contigs $genome failed; continuing with installation\n";
851 :	olson	1.478
852 :			$sysrc = system("compute_genome_counts $genome");
853 :			$sysrc == 0 or
854 :	parrello	1.485	warn "compute_genome_counts $genome failed; continuing with installation\n";
855 :	olson	1.478
856 :			$sysrc = system("load_features $genome");
857 :			$sysrc == 0 or
858 :	parrello	1.485	warn "load_features $genome failed; continuing with installation\n";
859 :	parrello	1.379
860 :	olson	1.93	$rc = 1;
861 :	olson	1.617	if (-s "$genome_dir/Features/peg/fasta")
862 :	olson	1.478	{
863 :	parrello	1.518
864 :	parrello	1.485	$sysrc = system("index_translations $genome");
865 :			$sysrc == 0 or
866 :			warn "index_translations $genome failed; continuing with installation\n";
867 :	parrello	1.518
868 :	olson	1.615	if (0)
869 :			{
870 :			#
871 :			# We don't do anything with the NR now; that update process is handled externally.
872 :			# The same applies to sims; we plan to optimize the genome installation process
873 :			# for genomes that were processed with the RAST server. For these, a completely
874 :			# new NR and sims set will be computed, OR the sims will be installed from the
875 :			# RAST installation and used locally from the genome direcotry (code still to be
876 :			# added).
877 :			# RDO 2007-09-06
878 :			#
879 :
880 :	olson	1.617	my @tmp = `cut -f1 $genome_dir/Features/peg/tbl`;
881 :	olson	1.615	if (@tmp == 0)
882 :			{
883 :	olson	1.617	warn "Did not find any features in $genome_dir/Features/peg/tbl\n";
884 :	olson	1.615	}
885 :			chomp @tmp;
886 :			if (!$skipnr)
887 :			{
888 :	olson	1.617	$sysrc = system("cat $genome_dir/Features/peg/fasta >> $FIG_Config::data/Global/nr");
889 :	olson	1.615	$sysrc == 0 or warn "error concatenating features ot NR; continuing with installation\n";
890 :
891 :			# &run("formatdb -i $FIG_Config::data/Global/nr -p T");
892 :			}
893 :			&enqueue_similarities(\@tmp);
894 :			}
895 :	olson	1.93	}
896 :	olson	1.478
897 :	olson	1.617	if ((-s "$genome_dir/assigned_functions") \|\|
898 :			(-d "$genome_dir/UserModels"))
899 :	olson	1.478	{
900 :			$sysrc = system("add_assertions_of_function $genome");
901 :	parrello	1.485	$sysrc == 0 or warn "add_assertions_of_function $genome failed; continuing with installation\n";
902 :	efrank	1.1	}
903 :	parrello	1.200
904 :	olson	1.622	if (-s "$genome_dir/annotations")
905 :			{
906 :			$sysrc = system("index_annotations $genome");
907 :			$sysrc == 0 or warn "index_annoations $genome failed; continuing with installation\n";
908 :			}
909 :
910 :	olson	1.615	#
911 :			# New support for installing precomputed data coming out of the RAST runs.
912 :			#
913 :			# PCHs are installed with install_new_coupling_data.
914 :			#
915 :
916 :	olson	1.617	my $pchs = "$genome_dir/pchs";
917 :			my $pch_scores = "$genome_dir/pchs.scored";
918 :	olson	1.615
919 :			if (-f $pchs and -f $pch_scores)
920 :			{
921 :			$sysrc = system("$FIG_Config::bin/install_new_coupling_data",
922 :			$genome,
923 :			$pchs,
924 :			$pch_scores);
925 :			if ($sysrc == 0)
926 :			{
927 :			print "PCHs installed, indexing.\n";
928 :			$sysrc = system("$FIG_Config::bin/load_coupling", $genome);
929 :			if ($sysrc != 0)
930 :			{
931 :			warn "load_coupling $genome failed with rc=$sysrc\n";
932 :			}
933 :			}
934 :			else
935 :			{
936 :			warn "Error $sysrc installing coupling data";
937 :			}
938 :			}
939 :
940 :	olson	1.621	#
941 :			# If this is a RAST replacement genome, perform subsystem salvage.
942 :			#
943 :			my $replaces = &FIG::file_head("$genome_dir/REPLACES", 1);
944 :			chomp $replaces;
945 :			if (-f "$genome_dir/RAST" and $replaces ne '')
946 :			{
947 :			if (open(MAP, "$genome_dir/peg_maps"))
948 :			{
949 :			my %map;
950 :			while (<MAP>)
951 :			{
952 :			chomp;
953 :			my($f, $t) = split(/\t/);
954 :			$map{$f} = $t;
955 :			}
956 :			close(MAP);
957 :
958 :			$self->perform_subsystem_salvage([[$replaces, $genome]], \%map);
959 :			}
960 :			else
961 :			{
962 :			warn "Genome $genome that replaces $replaces is missing a peg_maps file: $!";
963 :			}
964 :			}
965 :
966 :	efrank	1.1	return $rc;
967 :			}
968 :
969 :	overbeek	1.466	sub get_index {
970 :			my($self,$gs) = @_;
971 :
972 :			my($index,$max);
973 :			$gs \|\| confess "MISSING GS";
974 :
975 :	overbeek	1.467	my $indexF = "$FIG_Config::data/Logs/GenomeLog/index";
976 :	overbeek	1.466	if (open(INDEX,"<$indexF"))
977 :			{
978 :	parrello	1.485	while ((! $index) && ($_ = <INDEX>))
979 :			{
980 :			if ($_ =~ /^(\d+)/)
981 :			{
982 :			$max = $1;
983 :			if (($_ =~ /^(\d+)\t(\S.*\S)/) && ($2 eq $gs))
984 :			{
985 :			$index = $1;
986 :			}
987 :			}
988 :			}
989 :			close(INDEX);
990 :	overbeek	1.466	}
991 :
992 :			if (! $index)
993 :			{
994 :	parrello	1.485	open(INDEX,">>$indexF") \|\| die "could not open $indexF";
995 :			$index = defined($max) ? $max+1 : 1;
996 :			print INDEX "$index\t$gs\n";
997 :			close(INDEX);
998 :			&verify_dir("$FIG_Config::data/Logs/GenomeLog/Entries/$index");
999 :	overbeek	1.466	}
1000 :			return $index;
1001 :			}
1002 :	parrello	1.518
1003 :	overbeek	1.440	sub log_update {
1004 :	overbeek	1.466	my($self,$user,$genome,$gs,$msg,@data) = @_;
1005 :	overbeek	1.440
1006 :			my $time_made = time;
1007 :	overbeek	1.471	&verify_dir("$FIG_Config::data/Logs/GenomeLog");
1008 :	overbeek	1.466	my $index_id = $self->get_index($gs);
1009 :			$index_id \|\| die "could not make an index entry for $gs";
1010 :	overbeek	1.471	my $gs_dir = "$FIG_Config::data/Logs/GenomeLog/Entries/$index_id";
1011 :	overbeek	1.466
1012 :	overbeek	1.440	my($i,$file_or_dir,@tars);
1013 :			for ($i=0; ($i < @data); $i++)
1014 :			{
1015 :	parrello	1.485	$file_or_dir = $data[$i];
1016 :			my($dir,$file);
1017 :			if ($file_or_dir =~ /^(.*)\/([^\/]+)$/)
1018 :			{
1019 :			($dir,$file) = ($1,$2);
1020 :			}
1021 :			else
1022 :			{
1023 :			($dir,$file) = (".",$file_or_dir);
1024 :			}
1025 :			my $tar = "$gs_dir/$time_made.$i.tgz";
1026 :			&run("cd $dir; tar czf $tar $file");
1027 :			push(@tars,$tar);
1028 :	overbeek	1.440	}
1029 :	overbeek	1.466	open(LOG,">>$gs_dir/log")
1030 :	parrello	1.485	\|\| die "could not open $gs_dir/log";
1031 :	overbeek	1.466	print LOG "$time_made\n$user\n$genome\n$msg\n";
1032 :	parrello	1.518	if (@tars > 0)
1033 :	overbeek	1.466	{
1034 :	parrello	1.485	print LOG join(",",@tars),"\n";
1035 :	overbeek	1.466	}
1036 :			print LOG "//\n";
1037 :	overbeek	1.440	close(LOG);
1038 :			}
1039 :
1040 :	parrello	1.287	=head3 parse_genome_args
1041 :
1042 :			C<< my ($mode, @genomes) = FIG::parse_genome_args(@args); >>
1043 :
1044 :			Extract a list of genome IDs from an argument list. If the argument list is empty,
1045 :			return all the genomes in the data store.
1046 :
1047 :			This is a function that is performed by many of the FIG command-line utilities. The
1048 :			user has the option of specifying a list of specific genome IDs or specifying none
1049 :			in order to get all of them. If your command requires additional arguments in the
1050 :			command line, you can still use this method if you shift them out of the argument list
1051 :			before calling. The $mode return value will be C<all> if the user asked for all of
1052 :			the genomes or C<some> if he specified a list of IDs. This is useful to know if,
1053 :			for example, we are loading a table. If we're loading everything, we can delete the
1054 :			entire table; if we're only loading some genomes, we must delete them individually.
1055 :
1056 :			This method uses the genome directory rather than the database because it may be used
1057 :			before the database is ready.
1058 :
1059 :			=over 4
1060 :
1061 :			=item args1, args2, ... argsN
1062 :
1063 :			List of genome IDs. If all genome IDs are to be processed, then this list should be
1064 :			empty.
1065 :
1066 :			=item RETURN
1067 :
1068 :			Returns a list. The first element of the list is C<all> if the user is asking for all
1069 :			the genome IDs and C<some> otherwise. The remaining elements of the list are the
1070 :			desired genome IDs.
1071 :
1072 :			=back
1073 :
1074 :			=cut
1075 :
1076 :			sub parse_genome_args {
1077 :			# Get the parameters.
1078 :			my @args = @_;
1079 :			# Check the mode.
1080 :			my $mode = (@args > 0 ? 'some' : 'all');
1081 :			# Build the return list.
1082 :			my @retVal = ($mode);
1083 :			# Process according to the mode.
1084 :			if ($mode eq 'all') {
1085 :			# We want all the genomes, so we get them from the organism directory.
1086 :			my $orgdir = "$FIG_Config::organisms";
1087 :			opendir( GENOMES, $orgdir ) \|\| Confess("Could not open directory $orgdir");
1088 :			push @retVal, grep { $_ =~ /^\d/ } readdir( GENOMES );
1089 :			closedir( GENOMES );
1090 :			} else {
1091 :			# We want only the genomes specified by the user.
1092 :			push @retVal, @args;
1093 :			}
1094 :			# Return the result.
1095 :			return @retVal;
1096 :			}
1097 :
1098 :			=head3 reload_table
1099 :
1100 :			C<< $fig->reload_table($mode, $table, $flds, $xflds, $fileName, $keyList, $keyName); >>
1101 :
1102 :			Reload a database table from a sequential file. If I<$mode> is C<all>, the table
1103 :			will be dropped and re-created. If I<$mode> is C<some>, the data for the individual
1104 :			items in I<$keyList> will be deleted before the table is loaded. Thus, the load
1105 :			process is optimized for the type of reload.
1106 :
1107 :			=over 4
1108 :
1109 :			=item mode
1110 :
1111 :			C<all> if we are reloading the entire table, C<some> if we are only reloading
1112 :			specific entries.
1113 :
1114 :			=item table
1115 :
1116 :			Name of the table to reload.
1117 :
1118 :			=item flds
1119 :
1120 :			String defining the table columns, in SQL format. In general, this is a
1121 :			comma-delimited set of field specifiers, each specifier consisting of the
1122 :			field name followed by the field type and any optional qualifiers (such as
1123 :			C<NOT NULL> or C<DEFAULT>); however, it can be anything that would appear
1124 :			between the parentheses in a C<CREATE TABLE> statement. The order in which
1125 :			the fields are specified is important, since it is presumed that is the
1126 :			order in which they are appearing in the load file.
1127 :
1128 :			=item xflds
1129 :
1130 :			Reference to a hash that describes the indexes. The hash is keyed by index name.
1131 :			The value is the index's field list. This is a comma-delimited list of field names
1132 :			in order from most significant to least significant. If a field is to be indexed
1133 :			in descending order, its name should be followed by the qualifier C<DESC>. For
1134 :			example, the following I<$xflds> value will create two indexes, one for name followed
1135 :			by creation date in reverse chronological order, and one for ID.
1136 :
1137 :			{ name_index => "name, createDate DESC", id_index => "id" }
1138 :
1139 :			=item fileName
1140 :
1141 :			Fully-qualified name of the file containing the data to load. Each line of the
1142 :			file must correspond to a record, and the fields must be arranged in order and
1143 :	parrello	1.298	tab-delimited. If the file name is omitted, the table is dropped and re-created
1144 :			but not loaded.
1145 :	parrello	1.287
1146 :			=item keyList
1147 :
1148 :			Reference to a list of the IDs for the objects being reloaded. This parameter is
1149 :			only used if I<$mode> is C<some>.
1150 :
1151 :			=item keyName (optional)
1152 :
1153 :			Name of the key field containing the IDs in the keylist. If omitted, C<genome> is
1154 :			assumed.
1155 :
1156 :			=back
1157 :
1158 :			=cut
1159 :
1160 :			sub reload_table {
1161 :	parrello	1.298	# Get the parameters.
1162 :			my ($self, $mode, $table, $flds, $xflds, $fileName, $keyList, $keyName) = @_;
1163 :	parrello	1.287	if (!defined $keyName) {
1164 :			$keyName = 'genome';
1165 :			}
1166 :			# Get the database handler.
1167 :			my $dbf = $self->{_dbf};
1168 :	parrello	1.298	# Call the DBKernel method.
1169 :			$dbf->reload_table($mode, $table, $flds, $xflds, $fileName, $keyList, $keyName);
1170 :	parrello	1.287	}
1171 :
1172 :	parrello	1.210	=head3 enqueue_similarities
1173 :	olson	1.93
1174 :	parrello	1.287	C<< FIG::enqueue_similarities(\@fids); >>
1175 :
1176 :			Queue the passed Feature IDs for similarity computation. The actual
1177 :			computation is performed by L</create_sim_askfor_pool>. The queue is a
1178 :			persistent text file in the global data directory, and this method
1179 :			essentially writes new IDs on the end of it.
1180 :
1181 :			=over 4
1182 :
1183 :			=item fids
1184 :
1185 :			Reference to a list of feature IDs.
1186 :	olson	1.93
1187 :	parrello	1.287	=back
1188 :	olson	1.93
1189 :			=cut
1190 :	parrello	1.210	#: Return Type ;
1191 :	olson	1.93	sub enqueue_similarities {
1192 :	olson	1.334	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1193 :	efrank	1.1	my($fids) = @_;
1194 :			my $fid;
1195 :
1196 :	olson	1.93	my $sim_q = "$FIG_Config::global/queued_similarities";
1197 :
1198 :			open(TMP,">>$sim_q")
1199 :	parrello	1.287	\|\| die "could not open $sim_q";
1200 :	olson	1.93
1201 :			#
1202 :			# We need to lock here so that if a computation is creating a snapshot of the
1203 :			# queue, we block until it's done.
1204 :			#
1205 :
1206 :			flock(TMP, LOCK_EX) or die "Cannot lock $sim_q\n";
1207 :	overbeek	1.442	seek(TMP, 0, 2);
1208 :	olson	1.93
1209 :	parrello	1.287	foreach $fid (@$fids) {
1210 :			print TMP "$fid\n";
1211 :	efrank	1.1	}
1212 :			close(TMP);
1213 :	olson	1.10	}
1214 :
1215 :	olson	1.281	=head3 export_similarity_request
1216 :
1217 :			Creates a similarity computation request from the queued similarities and
1218 :	parrello	1.287	the current NR.
1219 :	olson	1.281
1220 :			We keep track of the exported requests in case one gets lost.
1221 :
1222 :			=cut
1223 :
1224 :	parrello	1.287	sub export_similarity_request {
1225 :	overbeek	1.439	my($self, $user_req_dir) = @_;
1226 :
1227 :			my $nr_file = "$user_req_dir/nr";
1228 :			my $fasta_file = "$user_req_dir/fasta";
1229 :			my $peg_syn_file = "$user_req_dir/peg.synonyms";
1230 :	olson	1.281
1231 :			my $req_dir = "$FIG_Config::fig/var/sim_requests";
1232 :			&verify_dir("$FIG_Config::fig/var");
1233 :			&verify_dir($req_dir);
1234 :
1235 :			$req_dir = "$req_dir/" . time;
1236 :			&verify_dir($req_dir);
1237 :
1238 :			#
1239 :			# Open all of our output files before zeroing out the sim queue, in case
1240 :			# there is a problem.
1241 :			#
1242 :
1243 :			open(my $user_fasta_fh, ">$fasta_file") or confess "Cannot open $fasta_file for writing: $!";
1244 :			open(my $fasta_fh, ">$req_dir/fasta.in");
1245 :
1246 :			open(my $user_nr_fh, ">$nr_file") or confess "Cannot open $nr_file for writing: $!";
1247 :			open(my $nr_fh, ">$req_dir/nr") or confess "Cannot open $req_dir/nr for writing: $!";
1248 :
1249 :	overbeek	1.439	open(my $user_peg_syn_fh, ">$peg_syn_file") or confess "Cannot open $peg_syn_file for writing: $!";
1250 :			open(my $peg_syn_fh, ">$req_dir/peg.synonyms") or confess "Cannot open $req_dir/peg.synonyms for writing: $!";
1251 :
1252 :	olson	1.281	open(my $nr_read_fh, "<$FIG_Config::data/Global/nr") or die "Cannot open $FIG_Config::data/Global/nr for reading: $!";
1253 :	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: $!";
1254 :	parrello	1.287
1255 :	olson	1.281	my $sim_q = "$FIG_Config::global/queued_similarities";
1256 :
1257 :			#
1258 :			# We need to lock here so that if a computation is creating a snapshot of the
1259 :			# queue, we block until it's done.
1260 :			#
1261 :
1262 :			open(my $sim_q_lock, ">>$sim_q") or confess "could not open $sim_q";
1263 :			flock($sim_q_lock, LOCK_EX) or confess "Cannot lock $sim_q\n";
1264 :
1265 :			#
1266 :			# Everything open & locked, start copying.
1267 :			#
1268 :	parrello	1.287
1269 :	olson	1.281	copy("$sim_q", "$req_dir/q") or confess "Copy $sim_q $req_dir/q failed: $!";
1270 :	overbeek	1.439	copy("$sim_q", "$user_req_dir/q") or confess "Copy $sim_q $user_req_dir/q failed: $!";
1271 :	parrello	1.287
1272 :	overbeek	1.442	#
1273 :			# Copy the contents of the sim queue to the "expected import" queue;
1274 :			# this is a list of pegs for which we expect sims to be computed and installed
1275 :			# at some point.
1276 :			#
1277 :			# We also lock on the pending queue file.
1278 :			#
1279 :	parrello	1.518
1280 :	overbeek	1.442	if (not(open(SQ, "<$sim_q")))
1281 :			{
1282 :	parrello	1.485	warn "Cannot open $sim_q for reading: $!\n";
1283 :	overbeek	1.442	}
1284 :			else
1285 :			{
1286 :	parrello	1.485	if (open(AW, ">>$FIG_Config::global/pending_similarities"))
1287 :			{
1288 :			flock(AW, LOCK_EX);
1289 :			seek(AW, 0, 2);
1290 :
1291 :			while (<SQ>)
1292 :			{
1293 :			print AW @_;
1294 :			}
1295 :			close(AW);
1296 :			}
1297 :			else
1298 :			{
1299 :			warn "Could not open $FIG_Config::global/pending_similarities: $!\n";
1300 :			}
1301 :			close(SQ);
1302 :	overbeek	1.442	}
1303 :	parrello	1.518
1304 :	olson	1.281	my($buf);
1305 :	parrello	1.287	while (1) {
1306 :			my $n = read($nr_read_fh, $buf, 4096);
1307 :			defined($n) or confess "Error reading nr: $!";
1308 :			last unless $n;
1309 :			syswrite($user_nr_fh, $buf) or confess "Error writing $nr_file: $!";
1310 :			syswrite($nr_fh, $buf) or confess "Error writing $req_dir/nr: $!";
1311 :	olson	1.281	}
1312 :
1313 :			close($nr_read_fh);
1314 :			close($nr_fh);
1315 :			close($user_nr_fh);
1316 :
1317 :	overbeek	1.439	while (1) {
1318 :			my $n = read($peg_syn_read_fh, $buf, 4096);
1319 :			defined($n) or confess "Error reading peg.synonyms: $!";
1320 :			last unless $n;
1321 :			syswrite($user_peg_syn_fh, $buf) or confess "Error writing $peg_syn_file: $!";
1322 :			syswrite($peg_syn_fh, $buf) or confess "Error writing $req_dir/peg.synonyms: $!";
1323 :			}
1324 :
1325 :			close($peg_syn_read_fh);
1326 :			close($peg_syn_fh);
1327 :			close($user_peg_syn_fh);
1328 :	parrello	1.518
1329 :	olson	1.281	#
1330 :			# We can zero out the queue and unlock now.
1331 :			#
1332 :
1333 :			open(F, ">$sim_q") or die "Cannot open $sim_q to truncate it: $!\n";
1334 :			close(F);
1335 :	parrello	1.287
1336 :	olson	1.281	close($sim_q_lock);
1337 :
1338 :			#
1339 :			# Generate the fasta input from the queued ids.
1340 :			#
1341 :
1342 :			open(my $q_fh, "<$req_dir/q");
1343 :	parrello	1.287	while (my $id = <$q_fh>) {
1344 :			chomp $id;
1345 :	olson	1.281
1346 :	parrello	1.287	my $seq = $self->get_translation($id);
1347 :	olson	1.281
1348 :	parrello	1.287	display_id_and_seq($id, \$seq, $user_fasta_fh);
1349 :			display_id_and_seq($id, \$seq, $fasta_fh);
1350 :	olson	1.281	}
1351 :			close($q_fh);
1352 :
1353 :			close($user_fasta_fh);
1354 :			close($fasta_fh);
1355 :			}
1356 :
1357 :	parrello	1.210	=head3 create_sim_askfor_pool
1358 :	olson	1.93
1359 :	parrello	1.287	C<< $fig->create_sim_askfor_pool($chunk_size); >>
1360 :	olson	1.93
1361 :	parrello	1.287	Creates an askfor pool, which a snapshot of the current NR and similarity
1362 :			queue. This process clears the old queue.
1363 :	olson	1.123
1364 :			The askfor pool needs to keep track of which sequences need to be
1365 :			calculated, which have been handed out, etc. To simplify this task we
1366 :	olson	1.279	chunk the sequences into fairly small numbers (20k characters) and
1367 :	olson	1.123	allocate work on a per-chunk basis. We make use of the relational
1368 :			database to keep track of chunk status as well as the seek locations
1369 :			into the file of sequence data. The initial creation of the pool
1370 :			involves indexing the sequence data with seek offsets and lengths and
1371 :			populating the sim_askfor_index table with this information and with
1372 :			initial status information.
1373 :	olson	1.93
1374 :	parrello	1.287	=over 4
1375 :
1376 :			=item chunk_size
1377 :
1378 :			Number of features to put into a processing chunk. The default is 15.
1379 :
1380 :			=back
1381 :
1382 :	parrello	1.200	=cut
1383 :	parrello	1.210	#: Return Type $;
1384 :	parrello	1.287	sub create_sim_askfor_pool {
1385 :	olson	1.123	my($self, $chunk_size) = @_;
1386 :
1387 :	olson	1.279	$chunk_size = 20000 unless $chunk_size =~ /^\d+$/;
1388 :	olson	1.93
1389 :	olson	1.279	my $pool_dir = "$FIG_Config::fig/var/sim_pools";
1390 :	olson	1.93	&verify_dir($pool_dir);
1391 :
1392 :			#
1393 :			# Lock the pool directory.
1394 :			#
1395 :			open(my $lock, ">$pool_dir/lockfile");
1396 :
1397 :			flock($lock, LOCK_EX);
1398 :
1399 :			my $num = 0;
1400 :	parrello	1.287	if (open(my $toc, "<$pool_dir/TOC")) {
1401 :			while (<$toc>) {
1402 :			chomp;
1403 :			# print STDERR "Have toc entry $_\n";
1404 :			my ($idx, $time, $str) = split(/\s+/, $_, 3);
1405 :	olson	1.93
1406 :	parrello	1.287	$num = max($num, $idx);
1407 :			}
1408 :			close($toc);
1409 :	olson	1.93	}
1410 :			$num++;
1411 :			open(my $toc, ">>$pool_dir/TOC") or die "Cannot write $pool_dir/TOC: $!\n";
1412 :
1413 :			print $toc "$num ", time(), " New toc entry\n";
1414 :			close($toc);
1415 :
1416 :	olson	1.123	my $cpool_id = sprintf "%04d", $num;
1417 :			my $cpool_dir = "$pool_dir/$cpool_id";
1418 :	olson	1.93
1419 :			#
1420 :			# All set, create the directory for this pool.
1421 :			#
1422 :
1423 :			&verify_dir($cpool_dir);
1424 :
1425 :			#
1426 :			# Now we can copy the nr and sim queue here.
1427 :			# Do this stuff inside an eval so we can clean up
1428 :			# the lockfile.
1429 :			#
1430 :
1431 :			eval {
1432 :	parrello	1.287	my $sim_q = "$FIG_Config::global/queued_similarities";
1433 :	olson	1.93
1434 :	parrello	1.287	copy("$sim_q", "$cpool_dir/q");
1435 :			copy("$FIG_Config::data/Global/nr", "$cpool_dir/nr");
1436 :	olson	1.93
1437 :	parrello	1.287	open(F, ">$sim_q") or die "Cannot open $sim_q to truncate it: $!\n";
1438 :			close(F);
1439 :	olson	1.93	};
1440 :	parrello	1.200
1441 :	olson	1.93	unlink("$pool_dir/lockfile");
1442 :			close($lock);
1443 :	olson	1.123
1444 :			#
1445 :			# We've created our pool; we can now run the formatdb and
1446 :			# extract the sequences for the blast run.
1447 :			#
1448 :	parrello	1.287	my $child_pid = $self->run_in_background(
1449 :			sub {
1450 :			#
1451 :			# Need to close db or there's all sorts of trouble.
1452 :			#
1453 :
1454 :			my $cmd = "$FIG_Config::ext_bin/formatdb -i $cpool_dir/nr -p T -l $cpool_dir/formatdb.log";
1455 :			print "Will run '$cmd'\n";
1456 :			&run($cmd);
1457 :			print "finished. Logfile:\n";
1458 :			print &FIG::file_read("$cpool_dir/formatdb.log");
1459 :			unlink("$cpool_dir/formatdb.pid");
1460 :			});
1461 :	olson	1.279	warn "Running formatdb in background job $child_pid\n";
1462 :	olson	1.123	open(FPID, ">$cpool_dir/formatdb.pid");
1463 :			print FPID "$child_pid\n";
1464 :			close(FPID);
1465 :
1466 :			my $db = $self->db_handle();
1467 :	parrello	1.287	if (!$db->table_exists("sim_queue")) {
1468 :			$db->create_table(tbl => "sim_queue",
1469 :			flds => "qid varchar(32), chunk_id INTEGER, seek INTEGER, len INTEGER, " .
1470 :			"assigned BOOL, finished BOOL, output_file varchar(255), " .
1471 :	parrello	1.485	"worker_pid INTEGER, start_time timestamp, " .
1472 :	parrello	1.287	"assignment_expires INTEGER, worker_info varchar(255)"
1473 :			);
1474 :	olson	1.123	}
1475 :
1476 :			#
1477 :			# Write the fasta input file. Keep track of how many have been written,
1478 :			# and write seek info into the database as appropriate.
1479 :			#
1480 :
1481 :			open(my $seq_fh, ">$cpool_dir/fasta.in");
1482 :
1483 :			my($chunk_idx, $chunk_begin, $seq_idx);
1484 :
1485 :	olson	1.279	my $cur_size = 0;
1486 :
1487 :	olson	1.123	$chunk_idx = 0;
1488 :			$chunk_begin = 0;
1489 :			$seq_idx = 0;
1490 :
1491 :	olson	1.279	my $tmpfile = "$FIG_Config::temp/simseek.$$";
1492 :			open(my $tmpfh, ">$tmpfile") or confess "Cannot open tmpfile $tmpfile: $!";
1493 :
1494 :	olson	1.123	open(my $q_fh, "<$cpool_dir/q");
1495 :	parrello	1.287	while (my $id = <$q_fh>) {
1496 :			chomp $id;
1497 :	olson	1.123
1498 :	parrello	1.287	my $seq = $self->get_translation($id);
1499 :	olson	1.123
1500 :	parrello	1.287	#
1501 :			# check if we're at the beginning of a chunk
1502 :			#
1503 :
1504 :			print $seq_fh ">$id\n$seq\n";
1505 :
1506 :			#
1507 :			# Check if we're at the end of a chunk
1508 :			#
1509 :
1510 :			$cur_size += length($seq);
1511 :			if ($cur_size >= $chunk_size) {
1512 :			my $chunk_end = tell($seq_fh);
1513 :			my $chunk_len = $chunk_end - $chunk_begin;
1514 :
1515 :	olson	1.430	print $tmpfh join("\t", $cpool_id, $chunk_idx, $chunk_begin, $chunk_len, 'FALSE', 'FALSE',
1516 :	parrello	1.485	'\N', '\N', '\N', '\N', '\N'), "\n";
1517 :	parrello	1.287	$chunk_idx++;
1518 :			$chunk_begin = $chunk_end;
1519 :			$cur_size = 0;
1520 :			}
1521 :			$seq_idx++;
1522 :	olson	1.123	}
1523 :
1524 :	parrello	1.287	if ($cur_size > 0) {
1525 :			my $chunk_end = tell($seq_fh);
1526 :			my $chunk_len = $chunk_end - $chunk_begin;
1527 :	olson	1.123
1528 :	olson	1.430	print $tmpfh join("\t", $cpool_id, $chunk_idx, $chunk_begin, $chunk_len, 'FALSE', 'FALSE',
1529 :	parrello	1.485	'\N', '\N', '\N', '\N', '\N'), "\n";
1530 :	olson	1.123	}
1531 :
1532 :			close($q_fh);
1533 :			close($seq_fh);
1534 :	olson	1.279	close($tmpfh);
1535 :	olson	1.123
1536 :	olson	1.279	warn "Write seqs from $tmpfile\n";
1537 :	olson	1.123
1538 :	olson	1.279	$self->db_handle->load_table(tbl => 'sim_queue',
1539 :	parrello	1.298	file => $tmpfile);
1540 :	parrello	1.200
1541 :	olson	1.430	# unlink($tmpfile);
1542 :	parrello	1.287
1543 :	olson	1.279	# for my $seek (@seeks)
1544 :			# {
1545 :	parrello	1.298	# my($cpool_id, $chunk_idx, $chunk_begin, $chunk_len) = @$seek;
1546 :	olson	1.279
1547 :	parrello	1.298	# $db->SQL("insert into sim_queue (qid, chunk_id, seek, len, assigned, finished) " .
1548 :			# "values('$cpool_id', $chunk_idx, $chunk_begin, $chunk_len, FALSE, FALSE)");
1549 :	olson	1.279	# }
1550 :	parrello	1.200
1551 :	olson	1.123	return $cpool_id;
1552 :			}
1553 :
1554 :	parrello	1.210	#=head3 get_sim_queue
1555 :			#
1556 :			#usage: get_sim_queue($pool_id, $all_sims)
1557 :			#
1558 :			#Returns the sims in the given pool. If $all_sims is true, return the entire queue. Otherwise,
1559 :			#just return the sims awaiting processing.
1560 :			#
1561 :			#=cut
1562 :	olson	1.123
1563 :	parrello	1.287	sub get_sim_queue {
1564 :	olson	1.123	my($self, $pool_id, $all_sims) = @_;
1565 :	olson	1.279	}
1566 :
1567 :	parrello	1.287	=head3 get_sim_work
1568 :	olson	1.279
1569 :	parrello	1.287	C<< my ($nrPath, $fasta) = $fig->get_sim_work(); >>
1570 :	olson	1.279
1571 :			Get the next piece of sim computation work to be performed. Returned are
1572 :			the path to the NR and a string containing the fasta data.
1573 :
1574 :			=cut
1575 :
1576 :	parrello	1.287	sub get_sim_work {
1577 :
1578 :			my ($self) = @_;
1579 :	olson	1.279
1580 :			#
1581 :			# For now, just don't care about order of data that we get back.
1582 :			#
1583 :
1584 :			my $db = $self->db_handle();
1585 :			my $lock = FIG::SimLock->new;
1586 :
1587 :			my $work = $db->SQL(qq(SELECT qid, chunk_id, seek, len
1588 :	parrello	1.298	FROM sim_queue
1589 :	olson	1.430	WHERE not finished AND not assigned
1590 :	parrello	1.298	LIMIT 1));
1591 :	olson	1.279	print "Got work ", Dumper($work), "\n";
1592 :
1593 :	parrello	1.287	if (not $work or @$work == 0) {
1594 :			return undef;
1595 :	olson	1.279	}
1596 :
1597 :			my($cpool_id, $chunk_id, $seek, $len) = @{$work->[0]};
1598 :	parrello	1.287
1599 :	olson	1.279	my $pool_dir = "$FIG_Config::fig/var/sim_pools";
1600 :			my $cpool_dir = "$pool_dir/$cpool_id";
1601 :
1602 :			my $nr = "$cpool_dir/nr";
1603 :			open(my $fh, "<$cpool_dir/fasta.in");
1604 :			seek($fh, $seek, 0);
1605 :			my $fasta;
1606 :			read($fh, $fasta, $len);
1607 :
1608 :	olson	1.430	$db->SQL(qq(UPDATE sim_queue
1609 :	parrello	1.485	SET assigned = true
1610 :			WHERE qid = ? AND chunk_id = ?), undef,
1611 :			$cpool_id, $chunk_id);
1612 :	olson	1.430
1613 :	olson	1.279	return($cpool_id, $chunk_id, $nr, $fasta, "$cpool_dir/out.$chunk_id");
1614 :			}
1615 :
1616 :	olson	1.430	sub sim_work_working
1617 :			{
1618 :			my($self, $pool, $chunk, $host, $pid) = @_;
1619 :
1620 :			my $db = $self->db_handle();
1621 :			my $lock = FIG::SimLock->new;
1622 :
1623 :			my $res = $db->SQL(qq(UPDATE sim_queue
1624 :	parrello	1.485	SET worker_pid = ?, start_time = NOW(), worker_info = ?
1625 :			WHERE qid = ? AND chunk_id = ?),
1626 :	parrello	1.518	undef,
1627 :	parrello	1.485	$pid, $host, $pool, $chunk);
1628 :	olson	1.430	}
1629 :
1630 :	olson	1.279	=head3 sim_work_done
1631 :
1632 :	parrello	1.287	C<< $fig->sim_work_done($pool_id, $chunk_id, $out_file); >>
1633 :
1634 :	olson	1.279	Declare that the work in pool_id/chunk_id has been completed, and output written
1635 :			to the pool directory (get_sim_work gave it the path).
1636 :
1637 :	parrello	1.287	=over 4
1638 :
1639 :			=item pool_id
1640 :
1641 :			The ID number of the pool containing the work that just completed.
1642 :
1643 :			=item chunk_id
1644 :
1645 :			The ID number of the chunk completed.
1646 :
1647 :			=item out_file
1648 :
1649 :			The file into which the work was placed.
1650 :
1651 :			=back
1652 :
1653 :	olson	1.279	=cut
1654 :
1655 :	parrello	1.287	sub sim_work_done {
1656 :			my ($self, $pool_id, $chunk_id, $out_file) = @_;
1657 :	olson	1.279
1658 :	parrello	1.287	if (! -f $out_file) {
1659 :			Confess("sim_work_done: output file $out_file does not exist");
1660 :	olson	1.279	}
1661 :
1662 :			my $db = $self->db_handle();
1663 :			my $lock = FIG::SimLock->new;
1664 :
1665 :			my $dbh = $db->{_dbh};
1666 :
1667 :			my $rows = $dbh->do(qq(UPDATE sim_queue
1668 :	parrello	1.298	SET finished = TRUE, output_file = ?
1669 :			WHERE qid = ? and chunk_id = ?), undef, $out_file, $pool_id, $chunk_id);
1670 :	parrello	1.287	if ($rows != 1) {
1671 :			if ($dbh->errstr) {
1672 :			Confess("Update not able to set finished=TRUE: ", $dbh->errstr);
1673 :			} else {
1674 :			Confess("Update not able to set finished=TRUE");
1675 :			}
1676 :	olson	1.279	}
1677 :			#
1678 :			# Determine if this was the last piece of work for this pool. If so, we can
1679 :	parrello	1.287	# schedule the postprocessing work.
1680 :	olson	1.279	#
1681 :			# Note we're still holding the lock.
1682 :			#
1683 :
1684 :			my $out = $db->SQL(qq(SELECT chunk_id
1685 :	parrello	1.298	FROM sim_queue
1686 :			WHERE qid = ? AND not finished), undef, $pool_id);
1687 :	parrello	1.287	if (@$out == 0) {
1688 :			#
1689 :			# Pool is done.
1690 :			#
1691 :			$self->schedule_sim_pool_postprocessing($pool_id);
1692 :	olson	1.279	}
1693 :	olson	1.123	}
1694 :
1695 :	olson	1.279	=head3 schedule_sim_pool_postprocessing
1696 :
1697 :	parrello	1.287	C<< $fig->schedule_sim_pool_postprocessing($pool_id); >>
1698 :
1699 :			Schedule a job to do the similarity postprocessing for the specified pool.
1700 :
1701 :			=over 4
1702 :
1703 :			=item pool_id
1704 :
1705 :			ID of the pool whose similarity postprocessing needs to be scheduled.
1706 :	olson	1.279
1707 :	parrello	1.287	=back
1708 :	olson	1.279
1709 :			=cut
1710 :
1711 :	parrello	1.287	sub schedule_sim_pool_postprocessing {
1712 :
1713 :	olson	1.279	my($self, $pool_id) = @_;
1714 :
1715 :			my $pool_dir = "$FIG_Config::fig/var/sim_pools";
1716 :			my $cpool_dir = "$pool_dir/$pool_id";
1717 :
1718 :			my $js = JobScheduler->new();
1719 :			my $job = $js->job_create();
1720 :
1721 :			my $spath = $job->get_script_path();
1722 :			open(my $sfh, ">$spath");
1723 :			print $sfh <<END;
1724 :			#!/bin/sh
1725 :			. $FIG_Config::fig_disk/config/fig-user-env.sh
1726 :			$FIG_Config::bin/postprocess_computed_sims $pool_id
1727 :			END
1728 :
1729 :			close($sfh);
1730 :			chmod(0775, $spath);
1731 :
1732 :			#
1733 :			# Write the job ID to the subsystem queue dir.
1734 :			#
1735 :
1736 :			open(J, ">$cpool_dir/postprocess_jobid");
1737 :			print J $job->get_id(), "\n";
1738 :			close(J);
1739 :
1740 :			$job->enqueue();
1741 :			}
1742 :
1743 :			=head3 postprocess_computed_sims
1744 :
1745 :	parrello	1.287	C<< $fig->postprocess_computed_sims($pool_id); >>
1746 :
1747 :			Set up to reduce, reformat, and split the similarities in a given pool. We build
1748 :			a pipe to this pipeline:
1749 :	olson	1.279
1750 :			reduce_sims peg.synonyms 300 \| reformat_sims nr \| split_sims dest prefix
1751 :
1752 :	parrello	1.287	Then we put the new sims in the pool directory, and then copy to NewSims.
1753 :
1754 :			=over 4
1755 :
1756 :			=item pool_id
1757 :
1758 :			ID of the pool whose similarities are to be post-processed.
1759 :
1760 :			=back
1761 :	olson	1.279
1762 :			=cut
1763 :
1764 :	parrello	1.287	sub postprocess_computed_sims {
1765 :	olson	1.279	my($self, $pool_id) = @_;
1766 :
1767 :			#
1768 :			# We don't lock here because the job is already done, and we
1769 :			# shouldn't (ha, ha) ever postprocess twice.
1770 :			#
1771 :
1772 :			my $pool_dir = "$FIG_Config::fig/var/sim_pools";
1773 :			my $cpool_dir = "$pool_dir/$pool_id";
1774 :
1775 :			my $sim_dir = "$cpool_dir/NewSims";
1776 :			&verify_dir($sim_dir);
1777 :
1778 :			#
1779 :			# Open the processing pipeline.
1780 :			#
1781 :
1782 :			my $reduce = "$FIG_Config::bin/reduce_sims $FIG_Config::global/peg.synonyms 300";
1783 :			my $reformat = "$FIG_Config::bin/reformat_sims $cpool_dir/nr";
1784 :			my $split = "$FIG_Config::bin/split_sims $sim_dir sims.$pool_id";
1785 :			open(my $process, "\| $reduce \| $reformat \| $split");
1786 :
1787 :			#
1788 :			# Iterate over all the sims files, taken from the database.
1789 :			#
1790 :
1791 :			my $dbh = $self->db_handle()->{_dbh};
1792 :			my $files = $dbh->selectcol_arrayref(qq(SELECT output_file
1793 :	parrello	1.298	FROM sim_queue
1794 :			WHERE qid = ? and output_file IS NOT NULL
1795 :			ORDER BY chunk_id), undef, $pool_id);
1796 :	parrello	1.287	for my $file (@$files) {
1797 :			my $buf;
1798 :			open(my $fh, "<$file") or confess "Cannot sim input file $file: $!";
1799 :			while (read($fh, $buf, 4096)) {
1800 :			print $process $buf;
1801 :			}
1802 :			close($fh);
1803 :	olson	1.279	}
1804 :			my $res = close($process);
1805 :	parrello	1.287	if (!$res) {
1806 :			if ($!) {
1807 :			confess "Error closing process pipeline: $!";
1808 :			} else {
1809 :			confess "Process pipeline exited with status $?";
1810 :			}
1811 :	olson	1.279	}
1812 :
1813 :			#
1814 :			# If we got here, it worked. Copy the new sims files over to NewSims.
1815 :			#
1816 :
1817 :			opendir(my $simdh, $sim_dir) or confess "Cannot open $sim_dir: $!";
1818 :			my @new_sims = grep { $_ !~ /^\./ } readdir($simdh);
1819 :			closedir($simdh);
1820 :
1821 :			&verify_dir("$FIG_Config::data/NewSims");
1822 :
1823 :	parrello	1.287	for my $sim_file (@new_sims) {
1824 :			my $target = "$FIG_Config::data/NewSims/$sim_file";
1825 :			if (-s $target) {
1826 :			Confess("$target already exists");
1827 :			}
1828 :			print "copying sim file $sim_file\n";
1829 :			&FIG::run("cp $sim_dir/$sim_file $target");
1830 :			&FIG::run("$FIG_Config::bin/index_sims $target");
1831 :	olson	1.279	}
1832 :			}
1833 :
1834 :	parrello	1.210	=head3 get_active_sim_pools
1835 :	olson	1.123
1836 :	parrello	1.287	C<< @pools = $fig->get_active_sim_pools(); >>
1837 :	olson	1.123
1838 :	parrello	1.287	Return a list of the pool IDs for the sim processing queues that have
1839 :			entries awaiting computation.
1840 :	olson	1.123
1841 :			=cut
1842 :	parrello	1.210	#: Return Type @;
1843 :	parrello	1.287	sub get_active_sim_pools {
1844 :	olson	1.123	my($self) = @_;
1845 :
1846 :			my $dbh = $self->db_handle();
1847 :
1848 :			my $res = $dbh->SQL("select distinct qid from sim_queue where not finished");
1849 :			return undef unless $res;
1850 :
1851 :			return map { $_->[0] } @$res;
1852 :			}
1853 :
1854 :	parrello	1.376	=head3 compute_clusters
1855 :
1856 :			C<< my @clusterList = $fig->compute_clusters(\@pegList, $subsystem, $distance); >>
1857 :
1858 :			Partition a list of PEGs into sections that are clustered close together on
1859 :			the genome. The basic algorithm used builds a graph connecting PEGs to
1860 :			other PEGs close by them on the genome. Each connected subsection of the graph
1861 :			is then separated into a cluster. Singleton clusters are thrown away, and
1862 :			the remaining ones are sorted by length. All PEGs in the incoming list
1863 :			should belong to the same genome, but this is not a requirement. PEGs on
1864 :			different genomes will simply find themselves in different clusters.
1865 :
1866 :			=over 4
1867 :
1868 :			=item pegList
1869 :
1870 :			Reference to a list of PEG IDs.
1871 :
1872 :			=item subsystem
1873 :
1874 :			Subsystem object for the relevant subsystem. This parameter is not used, but is
1875 :			required for compatability with Sprout.
1876 :
1877 :			=item distance (optional)
1878 :
1879 :			The maximum distance between PEGs that makes them considered close. If omitted,
1880 :			the distance is 5000 bases.
1881 :
1882 :			=item RETURN
1883 :
1884 :			Returns a list of lists. Each sub-list is a cluster of PEGs.
1885 :
1886 :			=back
1887 :
1888 :			=cut
1889 :
1890 :			sub compute_clusters {
1891 :			# Get the parameters.
1892 :			my ($self, $pegList, $subsystem, $distance) = @_;
1893 :			if (! defined $distance) {
1894 :			$distance = 5000;
1895 :			}
1896 :	overbeek	1.434
1897 :			my($peg,%by_contig);
1898 :			foreach $peg (@$pegList)
1899 :			{
1900 :	parrello	1.485	my $loc;
1901 :			if ($loc = $self->feature_location($peg))
1902 :			{
1903 :	parrello	1.488	my ($contig,$beg,$end) = $self->boundaries_of($loc);
1904 :	parrello	1.485	my $genome = &FIG::genome_of($peg);
1905 :			push(@{$by_contig{"$genome\t$contig"}},[($beg+$end)/2,$peg]);
1906 :			}
1907 :	overbeek	1.434	}
1908 :
1909 :	parrello	1.376	my @clusters = ();
1910 :	overbeek	1.434	foreach my $tuple (keys(%by_contig))
1911 :			{
1912 :	parrello	1.485	my $x = $by_contig{$tuple};
1913 :			my @pegs = sort { $a->[0] <=> $b->[0] } @$x;
1914 :			while ($x = shift @pegs)
1915 :			{
1916 :			my $clust = [$x->[1]];
1917 :			while ((@pegs > 0) && (abs($pegs[0]->[0] - $x->[0]) <= $distance))
1918 :			{
1919 :			$x = shift @pegs;
1920 :			push(@$clust,$x->[1]);
1921 :			}
1922 :	parrello	1.518
1923 :	parrello	1.485	if (@$clust > 1)
1924 :			{
1925 :			push(@clusters,$clust);
1926 :			}
1927 :			}
1928 :	parrello	1.376	}
1929 :	overbeek	1.434	return sort { @$b <=> @$a } @clusters;
1930 :	parrello	1.376	}
1931 :
1932 :	parrello	1.210	=head3 get_sim_pool_info
1933 :	olson	1.123
1934 :	parrello	1.287	C<< my ($total_entries, $n_finished, $n_assigned, $n_unassigned) = $fig->get_sim_pool_info($pool_id); >>
1935 :
1936 :			Return information about the given sim pool.
1937 :
1938 :			=over 4
1939 :
1940 :			=item pool_id
1941 :
1942 :			Pool ID of the similarity processing queue whose information is desired.
1943 :
1944 :			=item RETURN
1945 :
1946 :			Returns a four-element list. The first is the number of features in the
1947 :			queue; the second is the number of features that have been processed; the
1948 :			third is the number of features that have been assigned to a
1949 :			processor, and the fourth is the number of features left over.
1950 :	olson	1.123
1951 :	parrello	1.287	=back
1952 :	olson	1.123
1953 :			=cut
1954 :	parrello	1.210	#: Return Type @;
1955 :	parrello	1.287	sub get_sim_pool_info {
1956 :
1957 :	olson	1.123	my($self, $pool_id) = @_;
1958 :			my($dbh, $res, $total_entries, $n_finished, $n_assigned, $n_unassigned);
1959 :
1960 :			$dbh = $self->db_handle();
1961 :
1962 :			$res = $dbh->SQL("select count(chunk_id) from sim_queue where qid = '$pool_id'");
1963 :	parrello	1.200	$total_entries = $res->[0]->[0];
1964 :	olson	1.123
1965 :			$res = $dbh->SQL("select count(chunk_id) from sim_queue where qid = '$pool_id' and finished");
1966 :			$n_finished = $res->[0]->[0];
1967 :
1968 :			$res = $dbh->SQL("select count(chunk_id) from sim_queue where qid = '$pool_id' and assigned and not finished");
1969 :			$n_assigned = $res->[0]->[0];
1970 :
1971 :			$res = $dbh->SQL("select count(chunk_id) from sim_queue where qid = '$pool_id' and not finished and not assigned");
1972 :			$n_unassigned = $res->[0]->[0];
1973 :
1974 :			return ($total_entries, $n_finished, $n_assigned, $n_unassigned);
1975 :	olson	1.93	}
1976 :
1977 :	parrello	1.210	#=head3 get_sim_chunk
1978 :			#
1979 :			#usage: get_sim_chunk($n_seqs, $worker_id)
1980 :			#
1981 :			#Returns a chunk of $n_seqs of work.
1982 :			#
1983 :			#From Ross, about how sims are processed:
1984 :			#
1985 :			#Here is how I process them:
1986 :			#
1987 :			#
1988 :			# bash$ cd /Volumes/seed/olson/Sims/June22.out
1989 :			# bash$ for i in really*
1990 :			# > do
1991 :			# > cat < $i >> /Volumes/laptop/new.sims
1992 :			# > done
1993 :			#
1994 :			#
1995 :			#Then, I need to "reformat" them by adding to columns to each one
1996 :			# and split the result into files of about 3M each This I do using
1997 :			#
1998 :			#reduce_sims /Volumes/laptop/NR/NewNR/peg.synonyms.june21 300 < /Volumes/laptop/new.sims \|
1999 :			# reformat_sims /Volumes/laptop/NR/NewNR/checked.nr.june21 > /Volumes/laptop/reformated.sims
2000 :			#rm /Volumes/laptop/new.sims
2001 :			#split_sims /Volumes/laptop/NewSims sims.june24 reformated.sims
2002 :			#rm reformatted.sims
2003 :			#
2004 :			#=cut
2005 :	olson	1.93
2006 :	parrello	1.287	sub get_sim_chunk {
2007 :	parrello	1.210	my($self, $n_seqs, $worker_id) = @_;
2008 :			}
2009 :	olson	1.123
2010 :	parrello	1.210	=head3 get_local_hostname
2011 :	parrello	1.200
2012 :	parrello	1.287	C<< my $result = FIG::get_local_hostname(); >>
2013 :
2014 :			Return the local host name for the current processor. The name may be
2015 :			stored in a configuration file, or we may have to get it from the
2016 :			operating system.
2017 :	olson	1.123
2018 :	olson	1.93	=cut
2019 :	parrello	1.213	#: Return Type $;
2020 :	olson	1.10	sub get_local_hostname {
2021 :	olson	1.52
2022 :			#
2023 :			# See if there is a FIGdisk/config/hostname file. If there
2024 :			# is, force the hostname to be that.
2025 :			#
2026 :
2027 :			my $hostfile = "$FIG_Config::fig_disk/config/hostname";
2028 :	parrello	1.287	if (-f $hostfile) {
2029 :			my $fh;
2030 :			if (open($fh, $hostfile)) {
2031 :			my $hostname = <$fh>;
2032 :			chomp($hostname);
2033 :			return $hostname;
2034 :			}
2035 :	olson	1.52	}
2036 :	parrello	1.200
2037 :	olson	1.10	#
2038 :			# First check to see if we our hostname is correct.
2039 :			#
2040 :			# Map it to an IP address, and try to bind to that ip.
2041 :			#
2042 :
2043 :	overbeek	1.435	local $/ = "\n";
2044 :
2045 :	olson	1.10	my $tcp = getprotobyname('tcp');
2046 :	parrello	1.200
2047 :	olson	1.10	my $hostname = `hostname`;
2048 :	overbeek	1.435	chomp $hostname;
2049 :	olson	1.10
2050 :			my @hostent = gethostbyname($hostname);
2051 :
2052 :	parrello	1.287	if (@hostent > 0) {
2053 :			my $sock;
2054 :			my $ip = $hostent[4];
2055 :
2056 :			socket($sock, PF_INET, SOCK_STREAM, $tcp);
2057 :			if (bind($sock, sockaddr_in(0, $ip))) {
2058 :			#
2059 :			# It worked. Reverse-map back to a hopefully fqdn.
2060 :			#
2061 :
2062 :			my @rev = gethostbyaddr($ip, AF_INET);
2063 :			if (@rev > 0) {
2064 :			my $host = $rev[0];
2065 :			#
2066 :			# Check to see if we have a FQDN.
2067 :			#
2068 :
2069 :			if ($host =~ /\./) {
2070 :			#
2071 :			# Good.
2072 :			#
2073 :			return $host;
2074 :			} else {
2075 :			#
2076 :			# We didn't get a fqdn; bail and return the IP address.
2077 :			#
2078 :			return get_hostname_by_adapter()
2079 :			}
2080 :			} else {
2081 :			return inet_ntoa($ip);
2082 :			}
2083 :			} else {
2084 :			#
2085 :			# Our hostname must be wrong; we can't bind to the IP
2086 :			# address it maps to.
2087 :			# Return the name associated with the adapter.
2088 :			#
2089 :			return get_hostname_by_adapter()
2090 :			}
2091 :			} else {
2092 :			#
2093 :			# Our hostname isn't known to DNS. This isn't good.
2094 :			# Return the name associated with the adapter.
2095 :			#
2096 :			return get_hostname_by_adapter()
2097 :			}
2098 :			}
2099 :
2100 :			=head3 get_hostname_by_adapter
2101 :	parrello	1.200
2102 :	parrello	1.287	C<< my $name = FIG::get_hostname_by_adapter(); >>
2103 :	olson	1.10
2104 :	parrello	1.287	Return the local host name for the current network environment.
2105 :	parrello	1.213
2106 :			=cut
2107 :			#: Return Type $;
2108 :	olson	1.10	sub get_hostname_by_adapter {
2109 :			#
2110 :			# Attempt to determine our local hostname based on the
2111 :			# network environment.
2112 :			#
2113 :			# This implementation reads the routing table for the default route.
2114 :			# We then look at the interface config for the interface that holds the default.
2115 :			#
2116 :			#
2117 :			# Linux routing table:
2118 :			# [olson@yips 0.0.0]$ netstat -rn
2119 :			# Kernel IP routing table
2120 :			# Destination Gateway Genmask Flags MSS Window irtt Iface
2121 :			# 140.221.34.32 0.0.0.0 255.255.255.224 U 0 0 0 eth0
2122 :			# 169.254.0.0 0.0.0.0 255.255.0.0 U 0 0 0 eth0
2123 :			# 127.0.0.0 0.0.0.0 255.0.0.0 U 0 0 0 lo
2124 :			# 0.0.0.0 140.221.34.61 0.0.0.0 UG 0 0 0 eth0
2125 :	parrello	1.200	#
2126 :	olson	1.10	# Mac routing table:
2127 :	parrello	1.200	#
2128 :	olson	1.10	# bash-2.05a$ netstat -rn
2129 :			# Routing tables
2130 :	parrello	1.200	#
2131 :	olson	1.10	# Internet:
2132 :			# Destination Gateway Flags Refs Use Netif Expire
2133 :			# default 140.221.11.253 UGSc 12 120 en0
2134 :			# 127.0.0.1 127.0.0.1 UH 16 8415486 lo0
2135 :			# 140.221.8/22 link#4 UCS 12 0 en0
2136 :			# 140.221.8.78 0:6:5b:f:51:c4 UHLW 0 183 en0 408
2137 :			# 140.221.8.191 0:3:93:84:ab:e8 UHLW 0 92 en0 622
2138 :			# 140.221.8.198 0:e0:98:8e:36:e2 UHLW 0 5 en0 691
2139 :			# 140.221.9.6 0:6:5b:f:51:d6 UHLW 1 63 en0 1197
2140 :			# 140.221.10.135 0:d0:59:34:26:34 UHLW 2 2134 en0 1199
2141 :			# 140.221.10.152 0:30:1b:b0:ec:dd UHLW 1 137 en0 1122
2142 :			# 140.221.10.153 127.0.0.1 UHS 0 0 lo0
2143 :			# 140.221.11.37 0:9:6b:53:4e:4b UHLW 1 624 en0 1136
2144 :			# 140.221.11.103 0:30:48:22:59:e6 UHLW 3 973 en0 1016
2145 :			# 140.221.11.224 0:a:95:6f:7:10 UHLW 1 1 en0 605
2146 :			# 140.221.11.237 0:1:30:b8:80:c0 UHLW 0 0 en0 1158
2147 :			# 140.221.11.250 0:1:30:3:1:0 UHLW 0 0 en0 1141
2148 :			# 140.221.11.253 0:d0:3:e:70:a UHLW 13 0 en0 1199
2149 :			# 169.254 link#4 UCS 0 0 en0
2150 :	parrello	1.200	#
2151 :	olson	1.10	# Internet6:
2152 :			# Destination Gateway Flags Netif Expire
2153 :			# UH lo0
2154 :			# fe80::%lo0/64 Uc lo0
2155 :			# link#1 UHL lo0
2156 :			# fe80::%en0/64 link#4 UC en0
2157 :			# 0:a:95:a8:26:68 UHL lo0
2158 :			# ff01::/32 U lo0
2159 :			# ff02::%lo0/32 UC lo0
2160 :			# ff02::%en0/32 link#4 UC en0
2161 :
2162 :			my($fh);
2163 :
2164 :	parrello	1.287	if (!open($fh, "netstat -rn \|")) {
2165 :			warn "Cannot run netstat to determine local IP address\n";
2166 :			return "localhost";
2167 :	olson	1.10	}
2168 :
2169 :			my $interface_name;
2170 :	parrello	1.200
2171 :	parrello	1.287	while (<$fh>) {
2172 :			my @cols = split();
2173 :	olson	1.10
2174 :	parrello	1.287	if ($cols[0] eq "default" \|\| $cols[0] eq "0.0.0.0") {
2175 :			$interface_name = $cols[$#cols];
2176 :			}
2177 :	olson	1.10	}
2178 :			close($fh);
2179 :	parrello	1.200
2180 :	olson	1.11	# print "Default route on $interface_name\n";
2181 :	olson	1.10
2182 :			#
2183 :			# Find ifconfig.
2184 :			#
2185 :
2186 :			my $ifconfig;
2187 :
2188 :	parrello	1.287	for my $dir ((split(":", $ENV{PATH}), "/sbin", "/usr/sbin")) {
2189 :			if (-x "$dir/ifconfig") {
2190 :			$ifconfig = "$dir/ifconfig";
2191 :			last;
2192 :			}
2193 :	olson	1.10	}
2194 :
2195 :	parrello	1.287	if ($ifconfig eq "") {
2196 :			warn "Ifconfig not found\n";
2197 :			return "localhost";
2198 :	olson	1.10	}
2199 :	olson	1.11	# print "Foudn $ifconfig\n";
2200 :	olson	1.10
2201 :	parrello	1.287	if (!open($fh, "$ifconfig $interface_name \|")) {
2202 :			warn "Could not run $ifconfig: $!\n";
2203 :			return "localhost";
2204 :	olson	1.10	}
2205 :
2206 :			my $ip;
2207 :	parrello	1.287	while (<$fh>) {
2208 :			#
2209 :			# Mac:
2210 :			# inet 140.221.10.153 netmask 0xfffffc00 broadcast 140.221.11.255
2211 :			# Linux:
2212 :			# inet addr:140.221.34.37 Bcast:140.221.34.63 Mask:255.255.255.224
2213 :			#
2214 :
2215 :			chomp;
2216 :			s/^\s*//;
2217 :
2218 :			# print "Have '$_'\n";
2219 :			if (/inet\s+addr:(\d+\.\d+\.\d+\.\d+)\s+/) {
2220 :			#
2221 :			# Linux hit.
2222 :			#
2223 :			$ip = $1;
2224 :			# print "Got linux $ip\n";
2225 :			last;
2226 :			} elsif (/inet\s+(\d+\.\d+\.\d+\.\d+)\s+/) {
2227 :			#
2228 :			# Mac hit.
2229 :			#
2230 :			$ip = $1;
2231 :			# print "Got mac $ip\n";
2232 :			last;
2233 :			}
2234 :	olson	1.10	}
2235 :			close($fh);
2236 :
2237 :	parrello	1.287	if ($ip eq "") {
2238 :			warn "Didn't find an IP\n";
2239 :			return "localhost";
2240 :	olson	1.10	}
2241 :
2242 :			return $ip;
2243 :	efrank	1.1	}
2244 :
2245 :	parrello	1.213	=head3 get_seed_id
2246 :
2247 :	parrello	1.287	C<< my $id = FIG::get_seed_id(); >>
2248 :
2249 :			Return the Universally Unique ID for this SEED instance. If one
2250 :			does not exist, it will be created.
2251 :	parrello	1.213
2252 :			=cut
2253 :			#: Return type $;
2254 :	olson	1.38	sub get_seed_id {
2255 :			#
2256 :			# Retrieve the seed identifer from FIGdisk/config/seed_id.
2257 :			#
2258 :			# If it's not there, create one, and make it readonly.
2259 :			#
2260 :			my $id;
2261 :			my $id_file = "$FIG_Config::fig_disk/config/seed_id";
2262 :	parrello	1.287	if (! -f $id_file) {
2263 :			my $newid = `uuidgen`;
2264 :			if (!$newid) {
2265 :			die "Cannot run uuidgen: $!";
2266 :			}
2267 :	olson	1.38
2268 :	parrello	1.287	chomp($newid);
2269 :			my $fh = new FileHandle(">$id_file");
2270 :			if (!$fh) {
2271 :			die "error creating $id_file: $!";
2272 :			}
2273 :			print $fh "$newid\n";
2274 :			$fh->close();
2275 :			chmod(0444, $id_file);
2276 :	olson	1.38	}
2277 :			my $fh = new FileHandle("<$id_file");
2278 :			$id = <$fh>;
2279 :			chomp($id);
2280 :			return $id;
2281 :			}
2282 :
2283 :	parrello	1.287	=head3 get_release_info
2284 :	olson	1.155
2285 :	parrello	1.287	C<< my ($name, $id, $inst, $email, $parent_id, $description) = FIG::get_release_info(); >>
2286 :	olson	1.155
2287 :	parrello	1.287	Return the current data release information..
2288 :	olson	1.195
2289 :			The release info comes from the file FIG/Data/RELEASE. It is formatted as:
2290 :
2291 :	parrello	1.287	<release-name>
2292 :			<unique id>
2293 :			<institution>
2294 :			<contact email>
2295 :			<unique id of data release this release derived from>
2296 :			<description>
2297 :	olson	1.195
2298 :			For instance:
2299 :
2300 :	parrello	1.287	-----
2301 :			SEED Data Release, 09/15/2004.
2302 :			4148208C-1DF2-11D9-8417-000A95D52EF6
2303 :			ANL/FIG
2304 :			olson@mcs.anl.gov
2305 :
2306 :			Test release.
2307 :			-----
2308 :	olson	1.195
2309 :			If no RELEASE file exists, this routine will create one with a new unique ID. This
2310 :			lets a peer optimize the data transfer by being able to cache ID translations
2311 :			from this instance.
2312 :	olson	1.155
2313 :			=cut
2314 :	parrello	1.213	#: Return Type @;
2315 :	parrello	1.287	sub get_release_info {
2316 :	olson	1.196	my($fig, $no_create) = @_;
2317 :	olson	1.195
2318 :			my $rel_file = "$FIG_Config::data/RELEASE";
2319 :
2320 :	parrello	1.287	if (! -f $rel_file and !$no_create) {
2321 :	parrello	1.298	#
2322 :			# Create a new one.
2323 :			#
2324 :	olson	1.195
2325 :	parrello	1.287	my $newid = `uuidgen`;
2326 :			if (!$newid) {
2327 :			die "Cannot run uuidgen: $!";
2328 :			}
2329 :	olson	1.195
2330 :	parrello	1.287	chomp($newid);
2331 :	olson	1.195
2332 :	parrello	1.287	my $relinfo = "Automatically generated release info " . localtime();
2333 :			my $inst = "Unknown";
2334 :			my $contact = "Unknown";
2335 :			my $parent = "";
2336 :			my( $a, $b, $e, $v, $env ) = $fig->genome_counts;
2337 :			my $description = "Automatically generated release info\n";
2338 :			$description .= "Contains $a archaeal, $b bacterial, $e eukaryal, $v viral and $env environmental genomes.\n";
2339 :
2340 :			my $fh = new FileHandle(">$rel_file");
2341 :			if (!$fh) {
2342 :			warn "error creating $rel_file: $!";
2343 :			return undef;
2344 :			}
2345 :			print $fh "$relinfo\n";
2346 :			print $fh "$newid\n";
2347 :			print $fh "$inst\n";
2348 :			print $fh "$contact\n";
2349 :			print $fh "$parent\n";
2350 :			print $fh $description;
2351 :			$fh->close();
2352 :			chmod(0444, $rel_file);
2353 :	olson	1.195	}
2354 :
2355 :	parrello	1.287	if (open(my $fh, $rel_file)) {
2356 :			my(@lines) = <$fh>;
2357 :			close($fh);
2358 :	parrello	1.200
2359 :	parrello	1.287	chomp(@lines);
2360 :	parrello	1.200
2361 :	parrello	1.287	my($info, $id, $inst, $contact, $parent, @desc) = @lines;
2362 :	olson	1.195
2363 :	parrello	1.287	return ($info, $id, $inst, $contact, $parent, join("\n", @desc));
2364 :	olson	1.195	}
2365 :	olson	1.155
2366 :			return undef;
2367 :			}
2368 :
2369 :	parrello	1.406	=head3 Title
2370 :
2371 :			C<< my $title = $fig->Title(); >>
2372 :
2373 :			Return the title of this database. For SEED, this will return SEED, for Sprout
2374 :			it will return NMPDR, and so forth.
2375 :
2376 :			=cut
2377 :
2378 :			sub Title {
2379 :			return "SEED";
2380 :			}
2381 :
2382 :	parrello	1.376	=head3 FIG
2383 :
2384 :			C<< my $realFig = $fig->FIG(); >>
2385 :
2386 :			Return this object. This method is provided for compatability with SFXlate.
2387 :
2388 :			=cut
2389 :
2390 :			sub FIG {
2391 :			my ($self) = @_;
2392 :			return $self;
2393 :			}
2394 :
2395 :	parrello	1.287	=head3 get_peer_last_update
2396 :	olson	1.155
2397 :	parrello	1.287	C<< my $date = $fig->get_peer_last_update($peer_id); >>
2398 :	parrello	1.213
2399 :	olson	1.155	Return the timestamp from the last successful peer-to-peer update with
2400 :	parrello	1.287	the given peer. If the specified peer has made updates, comparing this
2401 :			timestamp to the timestamp of the updates can tell you whether or not
2402 :			the updates have been integrated into your SEED data store.
2403 :	olson	1.155
2404 :			We store this information in FIG/Data/Global/Peers/<peer-id>.
2405 :
2406 :	parrello	1.287	=over 4
2407 :
2408 :			=item peer_id
2409 :
2410 :			Universally Unique ID for the desired peer.
2411 :
2412 :			=item RETURN
2413 :
2414 :			Returns the date/time stamp for the last peer-to-peer updated performed
2415 :			with the identified SEED instance.
2416 :
2417 :			=back
2418 :
2419 :	olson	1.155	=cut
2420 :	parrello	1.213	#: Return Type $;
2421 :	parrello	1.287	sub get_peer_last_update {
2422 :	olson	1.155	my($self, $peer_id) = @_;
2423 :
2424 :			my $dir = "$FIG_Config::data/Global/Peers";
2425 :			&verify_dir($dir);
2426 :			$dir .= "/$peer_id";
2427 :			&verify_dir($dir);
2428 :
2429 :			my $update_file = "$dir/last_update";
2430 :	parrello	1.287	if (-f $update_file) {
2431 :			my $time = file_head($update_file, 1);
2432 :			chomp $time;
2433 :			return $time;
2434 :			} else {
2435 :			return undef;
2436 :	olson	1.155	}
2437 :			}
2438 :
2439 :	parrello	1.287	=head3 set_peer_last_update
2440 :	parrello	1.213
2441 :	parrello	1.287	C<< $fig->set_peer_last_update($peer_id, $time); >>
2442 :	parrello	1.213
2443 :	parrello	1.287	Manually set the update timestamp for a specified peer. This informs
2444 :			the SEED that you have all of the assignments and updates from a
2445 :			particular SEED instance as of a certain date.
2446 :	parrello	1.213
2447 :			=cut
2448 :			#: Return Type ;
2449 :
2450 :	parrello	1.287	sub set_peer_last_update {
2451 :	olson	1.155	my($self, $peer_id, $time) = @_;
2452 :
2453 :			my $dir = "$FIG_Config::data/Global/Peers";
2454 :			&verify_dir($dir);
2455 :			$dir .= "/$peer_id";
2456 :			&verify_dir($dir);
2457 :
2458 :			my $update_file = "$dir/last_update";
2459 :			open(F, ">$update_file");
2460 :			print F "$time\n";
2461 :			close(F);
2462 :			}
2463 :
2464 :	redwards	1.302	=head3 clean_spaces
2465 :
2466 :	parrello	1.320	Remove any extra spaces from input fields. This will (currently) remove ^\s, \s$, and concatenate multiple spaces into one.
2467 :	redwards	1.302
2468 :			my $input=$fig->clean_spaces($cgi->param('input'));
2469 :
2470 :			=cut
2471 :
2472 :			sub clean_spaces
2473 :			{
2474 :			my ($self, $s)=@_;
2475 :			# note at the moment I do not use \s because that recognizes \t and \n too. This should only remove multiple spaces.
2476 :	parrello	1.320	$s =~ s/^ +//;
2477 :	redwards	1.302	$s =~ s/ +$//;
2478 :			$s =~ s/ +/ /g;
2479 :			return $s;
2480 :			}
2481 :
2482 :
2483 :
2484 :	parrello	1.213	=head3 cgi_url
2485 :
2486 :	parrello	1.287	C<< my $url = FIG::$fig->cgi_url(); >>
2487 :
2488 :			Return the URL for the CGI script directory.
2489 :	parrello	1.213
2490 :			=cut
2491 :			#: Return Type $;
2492 :	efrank	1.1	sub cgi_url {
2493 :	overbeek	1.377	# return &plug_url($FIG_Config::cgi_url);
2494 :
2495 :			#
2496 :			# In order to globally make relative references work properly, return ".".
2497 :			# This might break some stuff in p2p, but this will get us most of the way there.
2498 :			# The things that break we can repair by inspecting the value of $ENV{SCRIPT_NAME}
2499 :			#
2500 :			return ".";
2501 :	efrank	1.1	}
2502 :	parrello	1.200
2503 :	overbeek	1.382	=head3 top_link
2504 :
2505 :			C<< my $url = FIG::top_link(); >>
2506 :
2507 :			Return the relative URL for the top of the CGI script directory.
2508 :
2509 :			We determine this based on the SCRIPT_NAME environment variable, falling
2510 :			back to FIG_Config::cgi_base if necessary.
2511 :
2512 :			=cut
2513 :
2514 :			sub top_link
2515 :			{
2516 :	parrello	1.518
2517 :	overbeek	1.382	#
2518 :			# Determine if this is a toplevel cgi or one in one of the subdirs (currently
2519 :			# just /p2p).
2520 :			#
2521 :
2522 :			my @parts = split(/\//, $ENV{SCRIPT_NAME});
2523 :			my $top;
2524 :			if ($parts[-2] eq 'FIG')
2525 :			{
2526 :	parrello	1.485	$top = '.';
2527 :			# warn "toplevel @parts\n";
2528 :	overbeek	1.382	}
2529 :			elsif ($parts[-3] eq 'FIG')
2530 :			{
2531 :	parrello	1.485	$top = '..';
2532 :			# warn "subdir @parts\n";
2533 :	overbeek	1.382	}
2534 :			else
2535 :			{
2536 :	parrello	1.485	$top = $FIG_Config::cgi_base;
2537 :			# warn "other @parts\n";
2538 :	overbeek	1.382	}
2539 :
2540 :			return $top;
2541 :			}
2542 :
2543 :	parrello	1.213	=head3 temp_url
2544 :
2545 :	parrello	1.287	C<< my $url = FIG::temp_url(); >>
2546 :
2547 :			Return the URL of the temporary file directory.
2548 :	parrello	1.213
2549 :			=cut
2550 :			#: Return Type $;
2551 :	efrank	1.1	sub temp_url {
2552 :	overbeek	1.377	# return &plug_url($FIG_Config::temp_url);
2553 :
2554 :			#
2555 :			# Similarly, make this relative.
2556 :			#
2557 :			return "../FIG-Tmp";
2558 :	efrank	1.1	}
2559 :	parrello	1.200
2560 :	parrello	1.213	=head3 plug_url
2561 :
2562 :	parrello	1.287	C<< my $url2 = $fig->plug_url($url); >>
2563 :
2564 :			or
2565 :
2566 :			C<< my $url2 = $fig->plug_url($url); >>
2567 :
2568 :			Change the domain portion of a URL to point to the current domain. This essentially
2569 :			relocates URLs into the current environment.
2570 :
2571 :			=over 4
2572 :
2573 :			=item url
2574 :
2575 :			URL to relocate.
2576 :
2577 :			=item RETURN
2578 :
2579 :			Returns a new URL with the base portion converted to the current operating host.
2580 :			If the URL does not begin with C<http://>, the URL will be returned unmodified.
2581 :
2582 :			=back
2583 :	parrello	1.213
2584 :			=cut
2585 :			#: Return Type $;
2586 :	efrank	1.1	sub plug_url {
2587 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
2588 :	efrank	1.1	my($url) = @_;
2589 :
2590 :	golsen	1.44	my $name;
2591 :
2592 :			# Revised by GJO
2593 :			# First try to get url from the current http request
2594 :
2595 :			if ( defined( $ENV{ 'HTTP_HOST' } ) # This is where $cgi->url gets its value
2596 :			&& ( $name = $ENV{ 'HTTP_HOST' } )
2597 :			&& ( $url =~ s~^http://[^/]*~http://$name~ ) # ~ is delimiter
2598 :			) {}
2599 :
2600 :			# Otherwise resort to alternative sources
2601 :
2602 :			elsif ( ( $name = &get_local_hostname )
2603 :			&& ( $url =~ s~^http://[^/]*~http://$name~ ) # ~ is delimiter
2604 :			) {}
2605 :
2606 :	efrank	1.1	return $url;
2607 :			}
2608 :
2609 :	parrello	1.213	=head3 file_read
2610 :
2611 :	parrello	1.287	C<< my $text = $fig->file_read($fileName); >>
2612 :
2613 :			or
2614 :
2615 :			C<< my @lines = $fig->file_read($fileName); >>
2616 :
2617 :			or
2618 :
2619 :			C<< my $text = FIG::file_read($fileName); >>
2620 :
2621 :			or
2622 :
2623 :			C<< my @lines = FIG::file_read($fileName); >>
2624 :
2625 :			Read an entire file into memory. In a scalar context, the file is returned
2626 :			as a single text string with line delimiters included. In a list context, the
2627 :			file is returned as a list of lines, each line terminated by a line
2628 :			delimiter. (For a method that automatically strips the line delimiters,
2629 :			use C<Tracer::GetFile>.)
2630 :
2631 :			=over 4
2632 :
2633 :			=item fileName
2634 :
2635 :			Fully-qualified name of the file to read.
2636 :
2637 :			=item RETURN
2638 :
2639 :			In a list context, returns a list of the file lines. In a scalar context, returns
2640 :			a string containing all the lines of the file with delimiters included.
2641 :	parrello	1.213
2642 :	parrello	1.287	=back
2643 :	parrello	1.213
2644 :			=cut
2645 :			#: Return Type $;
2646 :			#: Return Type @;
2647 :	parrello	1.287	sub file_read {
2648 :
2649 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
2650 :	parrello	1.287	my($fileName) = @_;
2651 :			return file_head($fileName, '*');
2652 :	olson	1.90
2653 :			}
2654 :
2655 :
2656 :	parrello	1.213	=head3 file_head
2657 :
2658 :	parrello	1.287	C<< my $text = $fig->file_head($fileName, $count); >>
2659 :
2660 :			or
2661 :
2662 :			C<< my @lines = $fig->file_head($fileName, $count); >>
2663 :	parrello	1.213
2664 :	parrello	1.287	or
2665 :	parrello	1.213
2666 :	parrello	1.287	C<< my $text = FIG::file_head($fileName, $count); >>
2667 :	olson	1.90
2668 :	parrello	1.287	or
2669 :	olson	1.90
2670 :	parrello	1.287	C<< my @lines = FIG::file_head($fileName, $count); >>
2671 :	olson	1.90
2672 :	parrello	1.287	Read a portion of a file into memory. In a scalar context, the file portion is
2673 :			returned as a single text string with line delimiters included. In a list
2674 :			context, the file portion is returned as a list of lines, each line terminated
2675 :			by a line delimiter.
2676 :	olson	1.155
2677 :	parrello	1.287	=over 4
2678 :	olson	1.90
2679 :	parrello	1.287	=item fileName
2680 :	olson	1.90
2681 :	parrello	1.287	Fully-qualified name of the file to read.
2682 :	efrank	1.1
2683 :	parrello	1.287	=item count (optional)
2684 :	efrank	1.1
2685 :	parrello	1.287	Number of lines to read from the file. If omitted, C<1> is assumed. If the
2686 :			non-numeric string C<*> is specified, the entire file will be read.
2687 :	efrank	1.1
2688 :	parrello	1.287	=item RETURN
2689 :	efrank	1.1
2690 :	parrello	1.287	In a list context, returns a list of the desired file lines. In a scalar context, returns
2691 :			a string containing the desired lines of the file with delimiters included.
2692 :	efrank	1.1
2693 :	parrello	1.287	=back
2694 :	efrank	1.1
2695 :			=cut
2696 :	parrello	1.287	#: Return Type $;
2697 :			#: Return Type @;
2698 :			sub file_head {
2699 :	efrank	1.1
2700 :	parrello	1.287	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
2701 :			my($file, $count) = @_;
2702 :	efrank	1.1
2703 :	parrello	1.287	my ($n, $allFlag);
2704 :			if ($count eq '*') {
2705 :	olson	1.304	Trace("Full file read for \"$file\".") if T(3);
2706 :	parrello	1.287	$allFlag = 1;
2707 :			$n = 0;
2708 :			} else {
2709 :			$allFlag = 0;
2710 :			$n = (!$count ? 1 : $count);
2711 :	olson	1.304	Trace("Reading $n record(s) from \"$file\".") if T(3);
2712 :	parrello	1.287	}
2713 :	efrank	1.1
2714 :	parrello	1.287	if (open(my $fh, "<$file")) {
2715 :	parrello	1.298	my(@ret, $i);
2716 :	parrello	1.287	$i = 0;
2717 :			while (<$fh>) {
2718 :			push(@ret, $_);
2719 :			$i++;
2720 :			last if !$allFlag && $i >= $n;
2721 :			}
2722 :			close($fh);
2723 :			if (wantarray) {
2724 :			return @ret;
2725 :			} else {
2726 :			return join("", @ret);
2727 :			}
2728 :	efrank	1.1	}
2729 :			}
2730 :
2731 :			################ Basic Routines [ existed since WIT ] ##########################
2732 :
2733 :	parrello	1.287	=head3 min
2734 :
2735 :			C<< my $min = FIG::min(@x); >>
2736 :
2737 :			or
2738 :
2739 :			C<< my $min = $fig->min(@x); >>
2740 :
2741 :			Return the minimum numeric value from a list.
2742 :
2743 :			=over 4
2744 :
2745 :			=item x1, x2, ... xN
2746 :	efrank	1.1
2747 :	parrello	1.287	List of numbers to process.
2748 :	efrank	1.1
2749 :	parrello	1.287	=item RETURN
2750 :	efrank	1.1
2751 :	parrello	1.287	Returns the numeric value of the list entry possessing the lowest value. Returns
2752 :			C<undef> if the list is empty.
2753 :	efrank	1.1
2754 :	parrello	1.287	=back
2755 :	efrank	1.1
2756 :			=cut
2757 :	parrello	1.213	#: Return Type $;
2758 :	efrank	1.1	sub min {
2759 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
2760 :	efrank	1.1	my(@x) = @_;
2761 :			my($min,$i);
2762 :
2763 :			(@x > 0) \|\| return undef;
2764 :			$min = $x[0];
2765 :	parrello	1.287	for ($i=1; ($i < @x); $i++) {
2766 :			$min = ($min > $x[$i]) ? $x[$i] : $min;
2767 :	efrank	1.1	}
2768 :			return $min;
2769 :			}
2770 :
2771 :	parrello	1.287	=head3 max
2772 :
2773 :			C<< my $max = FIG::max(@x); >>
2774 :
2775 :			or
2776 :
2777 :			C<< my $max = $fig->max(@x); >>
2778 :	efrank	1.1
2779 :	parrello	1.287	Return the maximum numeric value from a list.
2780 :	efrank	1.1
2781 :	parrello	1.287	=over 4
2782 :
2783 :			=item x1, x2, ... xN
2784 :
2785 :			List of numbers to process.
2786 :
2787 :			=item RETURN
2788 :
2789 :			Returns the numeric value of t/he list entry possessing the highest value. Returns
2790 :			C<undef> if the list is empty.
2791 :	efrank	1.1
2792 :	parrello	1.287	=back
2793 :	efrank	1.1
2794 :			=cut
2795 :	parrello	1.213	#: Return Type $;
2796 :	efrank	1.1	sub max {
2797 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
2798 :	efrank	1.1	my(@x) = @_;
2799 :			my($max,$i);
2800 :
2801 :			(@x > 0) \|\| return undef;
2802 :			$max = $x[0];
2803 :	parrello	1.287	for ($i=1; ($i < @x); $i++) {
2804 :			$max = ($max < $x[$i]) ? $x[$i] : $max;
2805 :	efrank	1.1	}
2806 :			return $max;
2807 :			}
2808 :
2809 :	parrello	1.287	=head3 between
2810 :	efrank	1.1
2811 :	parrello	1.287	C<< my $flag = FIG::between($x, $y, $z); >>
2812 :	efrank	1.1
2813 :	parrello	1.287	or
2814 :
2815 :			C<< my $flag = $fig->between($x, $y, $z); >>
2816 :
2817 :			Determine whether or not $y is between $x and $z.
2818 :
2819 :			=over 4
2820 :
2821 :			=item x
2822 :
2823 :			First edge number.
2824 :
2825 :			=item y
2826 :	efrank	1.1
2827 :	parrello	1.287	Number to examine.
2828 :
2829 :			=item z
2830 :
2831 :			Second edge number.
2832 :
2833 :			=item RETURN
2834 :
2835 :			Return TRUE if the number I<$y> is between the numbers I<$x> and I<$z>. The check
2836 :			is inclusive (that is, if I<$y> is equal to I<$x> or I<$z> the function returns
2837 :			TRUE), and the order of I<$x> and I<$z> does not matter. If I<$x> is lower than
2838 :			I<$z>, then the return is TRUE if I<$x> <= I<$y> <= I<$z>. If I<$z> is lower,
2839 :			then the return is TRUE if I<$x> >= I$<$y> >= I<$z>.
2840 :
2841 :			=back
2842 :	efrank	1.1
2843 :			=cut
2844 :	parrello	1.213	#: Return Type $;
2845 :	efrank	1.1	sub between {
2846 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
2847 :	efrank	1.1	my($x,$y,$z) = @_;
2848 :
2849 :	parrello	1.287	if ($x < $z) {
2850 :			return (($x <= $y) && ($y <= $z));
2851 :			} else {
2852 :			return (($x >= $y) && ($y >= $z));
2853 :	efrank	1.1	}
2854 :			}
2855 :
2856 :	parrello	1.287	=head3 standard_genetic_code
2857 :	efrank	1.1
2858 :	parrello	1.287	C<< my $code = FIG::standard_genetic_code(); >>
2859 :	efrank	1.1
2860 :	parrello	1.287	Return a hash containing the standard translation of nucleotide triples to proteins.
2861 :			Methods such as L</translate> can take a translation scheme as a parameter. This method
2862 :			returns the default translation scheme. The scheme is implemented as a reference to a
2863 :			hash that contains nucleotide triplets as keys and has protein letters as values.
2864 :	efrank	1.1
2865 :			=cut
2866 :	overbeek	1.583
2867 :			sub genetic_code {
2868 :			my ($ncbi_genetic_code_num) = @_;
2869 :	overbeek	1.585	my $code = &standard_genetic_code();
2870 :	overbeek	1.583
2871 :	overbeek	1.584	if ($ncbi_genetic_code_num == 11) {
2872 :			#...Do nothing
2873 :			}
2874 :			elsif ($ncbi_genetic_code_num == 4) {
2875 :	overbeek	1.583	$code->{TGA} = 'W';
2876 :			}
2877 :	overbeek	1.584	else {
2878 :			die "Sorry, only genetic codes 11 and 4 are currently supported";
2879 :			}
2880 :	overbeek	1.583
2881 :			return $code;
2882 :			}
2883 :
2884 :	parrello	1.213	#: Return Type $;
2885 :	efrank	1.1	sub standard_genetic_code {
2886 :	parrello	1.200
2887 :	efrank	1.1	my $code = {};
2888 :
2889 :			$code->{"AAA"} = "K";
2890 :			$code->{"AAC"} = "N";
2891 :			$code->{"AAG"} = "K";
2892 :			$code->{"AAT"} = "N";
2893 :			$code->{"ACA"} = "T";
2894 :			$code->{"ACC"} = "T";
2895 :			$code->{"ACG"} = "T";
2896 :			$code->{"ACT"} = "T";
2897 :			$code->{"AGA"} = "R";
2898 :			$code->{"AGC"} = "S";
2899 :			$code->{"AGG"} = "R";
2900 :			$code->{"AGT"} = "S";
2901 :			$code->{"ATA"} = "I";
2902 :			$code->{"ATC"} = "I";
2903 :			$code->{"ATG"} = "M";
2904 :			$code->{"ATT"} = "I";
2905 :			$code->{"CAA"} = "Q";
2906 :			$code->{"CAC"} = "H";
2907 :			$code->{"CAG"} = "Q";
2908 :			$code->{"CAT"} = "H";
2909 :			$code->{"CCA"} = "P";
2910 :			$code->{"CCC"} = "P";
2911 :			$code->{"CCG"} = "P";
2912 :			$code->{"CCT"} = "P";
2913 :			$code->{"CGA"} = "R";
2914 :			$code->{"CGC"} = "R";
2915 :			$code->{"CGG"} = "R";
2916 :			$code->{"CGT"} = "R";
2917 :			$code->{"CTA"} = "L";
2918 :			$code->{"CTC"} = "L";
2919 :			$code->{"CTG"} = "L";
2920 :			$code->{"CTT"} = "L";
2921 :			$code->{"GAA"} = "E";
2922 :			$code->{"GAC"} = "D";
2923 :			$code->{"GAG"} = "E";
2924 :			$code->{"GAT"} = "D";
2925 :			$code->{"GCA"} = "A";
2926 :			$code->{"GCC"} = "A";
2927 :			$code->{"GCG"} = "A";
2928 :			$code->{"GCT"} = "A";
2929 :			$code->{"GGA"} = "G";
2930 :			$code->{"GGC"} = "G";
2931 :			$code->{"GGG"} = "G";
2932 :			$code->{"GGT"} = "G";
2933 :			$code->{"GTA"} = "V";
2934 :			$code->{"GTC"} = "V";
2935 :			$code->{"GTG"} = "V";
2936 :			$code->{"GTT"} = "V";
2937 :			$code->{"TAA"} = "*";
2938 :			$code->{"TAC"} = "Y";
2939 :			$code->{"TAG"} = "*";
2940 :			$code->{"TAT"} = "Y";
2941 :			$code->{"TCA"} = "S";
2942 :			$code->{"TCC"} = "S";
2943 :			$code->{"TCG"} = "S";
2944 :			$code->{"TCT"} = "S";
2945 :			$code->{"TGA"} = "*";
2946 :			$code->{"TGC"} = "C";
2947 :			$code->{"TGG"} = "W";
2948 :			$code->{"TGT"} = "C";
2949 :			$code->{"TTA"} = "L";
2950 :			$code->{"TTC"} = "F";
2951 :			$code->{"TTG"} = "L";
2952 :			$code->{"TTT"} = "F";
2953 :	parrello	1.200
2954 :	efrank	1.1	return $code;
2955 :			}
2956 :
2957 :	hwang	1.547
2958 :			sub fr_to_go {
2959 :	overbeek	1.548	my($self,$role) = @_;
2960 :	hwang	1.547
2961 :	overbeek	1.549	my $roleQ = quotemeta $role;
2962 :	overbeek	1.548	my $rdbH = $self->db_handle;
2963 :	overbeek	1.549	my $relational_db_response = $rdbH->SQL("SELECT go_id FROM fr2go WHERE role = '$roleQ'");
2964 :	overbeek	1.548	return map { $_->[0] } @{$relational_db_response};
2965 :	hwang	1.547	}
2966 :
2967 :	parrello	1.287	=head3 translate
2968 :
2969 :			C<< my $aa_seq = &FIG::translate($dna_seq, $code, $fix_start); >>
2970 :
2971 :			Translate a DNA sequence to a protein sequence using the specified genetic code.
2972 :			If I<$fix_start> is TRUE, will translate an initial C<TTG> or C<GTG> code to
2973 :			C<M>. (In the standard genetic code, these two combinations normally translate
2974 :			to C<V> and C<L>, respectively.)
2975 :
2976 :			=over 4
2977 :	efrank	1.1
2978 :	parrello	1.287	=item dna_seq
2979 :	efrank	1.1
2980 :	parrello	1.287	DNA sequence to translate. Note that the DNA sequence can only contain
2981 :			known nucleotides.
2982 :	efrank	1.1
2983 :	parrello	1.287	=item code
2984 :	efrank	1.1
2985 :	parrello	1.287	Reference to a hash specifying the translation code. The hash is keyed by
2986 :			nucleotide triples, and the value for each key is the corresponding protein
2987 :			letter. If this parameter is omitted, the L</standard_genetic_code> will be
2988 :			used.
2989 :	efrank	1.1
2990 :	parrello	1.287	=item fix_start
2991 :
2992 :			TRUE if the first triple is to get special treatment, else FALSE. If TRUE,
2993 :			then a value of C<TTG> or C<GTG> in the first position will be translated to
2994 :			C<M> instead of the value specified in the translation code.
2995 :
2996 :			=item RETURN
2997 :
2998 :			Returns a string resulting from translating each nucleotide triple into a
2999 :			protein letter.
3000 :
3001 :			=back
3002 :
3003 :			=cut
3004 :			#: Return Type $;
3005 :			sub translate {
3006 :			shift if UNIVERSAL::isa($_[0],__PACKAGE__);
3007 :
3008 :			my( $dna,$code,$start ) = @_;
3009 :			my( $i,$j,$ln );
3010 :			my( $x,$y );
3011 :			my( $prot );
3012 :
3013 :			if (! defined($code)) {
3014 :			$code = &FIG::standard_genetic_code;
3015 :	efrank	1.1	}
3016 :			$ln = length($dna);
3017 :			$prot = "X" x ($ln/3);
3018 :			$dna =~ tr/a-z/A-Z/;
3019 :
3020 :	parrello	1.287	for ($i=0,$j=0; ($i < ($ln-2)); $i += 3,$j++) {
3021 :			$x = substr($dna,$i,3);
3022 :			if ($y = $code->{$x}) {
3023 :			substr($prot,$j,1) = $y;
3024 :	efrank	1.1	}
3025 :			}
3026 :	parrello	1.200
3027 :	parrello	1.287	if (($start) && ($ln >= 3) && (substr($dna,0,3) =~ /^[GT]TG$/)) {
3028 :			substr($prot,0,1) = 'M';
3029 :	efrank	1.1	}
3030 :			return $prot;
3031 :			}
3032 :
3033 :	parrello	1.287	=head3 reverse_comp
3034 :
3035 :			C<< my $dnaR = FIG::reverse_comp($dna); >>
3036 :
3037 :			or
3038 :
3039 :			C<< my $dnaR = $fig->reverse_comp($dna); >>
3040 :
3041 :			Return the reverse complement os the specified DNA sequence.
3042 :	efrank	1.1
3043 :	parrello	1.287	NOTE: for extremely long DNA strings, use L</rev_comp>, which allows you to
3044 :			pass the strings around in the form of pointers.
3045 :	efrank	1.1
3046 :	parrello	1.287	=over 4
3047 :
3048 :			=item dna
3049 :	efrank	1.1
3050 :	parrello	1.287	DNA sequence whose reverse complement is desired.
3051 :
3052 :			=item RETURN
3053 :
3054 :			Returns the reverse complement of the incoming DNA sequence.
3055 :
3056 :			=back
3057 :	efrank	1.1
3058 :			=cut
3059 :	parrello	1.213	#: Return Type $;
3060 :	efrank	1.1	sub reverse_comp {
3061 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
3062 :	efrank	1.1	my($seq) = @_;
3063 :
3064 :			return ${&rev_comp(\$seq)};
3065 :			}
3066 :
3067 :	parrello	1.287	=head3 rev_comp
3068 :
3069 :			C<< my $dnaRP = FIG::rev_comp(\$dna); >>
3070 :
3071 :			or
3072 :
3073 :			C<< my $dnaRP = $fig->rev_comp(\$dna); >>
3074 :
3075 :			Return the reverse complement of the specified DNA sequence. The DNA sequence
3076 :			is passed in as a string reference rather than a raw string for performance
3077 :			reasons. If this is unnecessary, use L</reverse_comp>, which processes strings
3078 :			instead of references to strings.
3079 :
3080 :			=over 4
3081 :
3082 :			=item dna
3083 :
3084 :			Reference to the DNA sequence whose reverse complement is desired.
3085 :
3086 :			=item RETURN
3087 :
3088 :			Returns a reference to the reverse complement of the incoming DNA sequence.
3089 :
3090 :			=back
3091 :	parrello	1.213
3092 :			=cut
3093 :			#: Return Type $;
3094 :	efrank	1.1	sub rev_comp {
3095 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
3096 :	efrank	1.1	my( $seqP ) = @_;
3097 :			my( $rev );
3098 :
3099 :			$rev = reverse( $$seqP );
3100 :	overbeek	1.317	$rev =~ tr/A-Z/a-z/;
3101 :			$rev =~ tr/acgtumrwsykbdhv/tgcaakywsrmvhdb/;
3102 :	efrank	1.1	return \$rev;
3103 :			}
3104 :
3105 :	overbeek	1.572	# This routine was written by Gary to definitively handle the "scratch" subdirectory issue.
3106 :			# It takes as parameters key-value pairs. The relevant ones are
3107 :			#
3108 :			# tmpdir => NameOfTmpDirectoryToBeUsed [can be ommitted]
3109 :			# tmp => TheNameOfTheTmpDirectoryToContainTheSubdirectory [can be ommitted]
3110 :			#
3111 :			# if tmpdir exists, save_tmp is set to "true". You need to test this at the end
3112 :			# of your script and blow away the directory unless save_tmp is true.
3113 :			# if tmpdir does not exist, it will be created if possible.
3114 :			#
3115 :			# tmp is where to put tmpdir, if it is not specified. if tmp is omitted, it
3116 :			# will all be ok.
3117 :			#
3118 :			#- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
3119 :			# ( $tmp_dir, $save_tmp ) = temporary_directory( \%options )
3120 :			#- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
3121 :			sub temporary_directory
3122 :			{
3123 :			my $options = shift;
3124 :
3125 :			my $tmp_dir = $options->{ tmpdir };
3126 :			my $save_tmp = $options->{ savetmp } \|\| '';
3127 :
3128 :			if ( $tmp_dir )
3129 :			{
3130 :			if ( -d $tmp_dir ) { $options->{ savetmp } = $save_tmp = 1 }
3131 :			}
3132 :			else
3133 :			{
3134 :			my $tmp = $options->{ tmp } && -d $options->{ tmp } ? $options->{ tmp }
3135 :			: $FIG_Config::temp && -d $FIG_Config::temp ? $FIG_Config::temp
3136 :			: -d '/tmp' ? '/tmp'
3137 :			: '.';
3138 :			$tmp_dir = sprintf( "$tmp/fig_tmp_dir.%05d.%09d", $$, int(1000000000*rand) );
3139 :			}
3140 :
3141 :			if ( $tmp_dir && ! -d $tmp_dir )
3142 :			{
3143 :			mkdir $tmp_dir;
3144 :			if ( ! -d $tmp_dir )
3145 :			{
3146 :	overbeek	1.586	print STDERR "FIG::temporary_directory could not create '$tmp_dir: $!'\n";
3147 :	overbeek	1.572	$options->{ tmpdir } = $tmp_dir = undef;
3148 :			}
3149 :			}
3150 :
3151 :			return ( $tmp_dir, $save_tmp );
3152 :			}
3153 :
3154 :	overbeek	1.454	sub verify_external_tool {
3155 :			my(@progs) = @_;
3156 :
3157 :			my $prog;
3158 :			foreach $prog (@progs)
3159 :			{
3160 :			my @tmp = `which $prog`;
3161 :			if ($tmp[0] =~ /^no $prog/)
3162 :			{
3163 :			print STDERR $tmp[0];
3164 :			exit(1);
3165 :			}
3166 :			}
3167 :			}
3168 :
3169 :	parrello	1.287	=head3 verify_dir
3170 :
3171 :			C<< FIG::verify_dir($dir); >>
3172 :	efrank	1.1
3173 :	parrello	1.287	or
3174 :	efrank	1.1
3175 :	parrello	1.287	C<< $fig->verify_dir($dir); >>
3176 :	efrank	1.1
3177 :	parrello	1.287	Insure that the specified directory exists. If it must be created, the permissions will
3178 :			be set to C<0777>.
3179 :	efrank	1.1
3180 :			=cut
3181 :
3182 :			sub verify_dir {
3183 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
3184 :	efrank	1.1	my($dir) = @_;
3185 :
3186 :	olson	1.416	if (!defined($dir))
3187 :			{
3188 :	parrello	1.485	Confess("FIG::verify_dir: missing \$dir argument\n");
3189 :	olson	1.416	}
3190 :			if ($dir eq "")
3191 :			{
3192 :	parrello	1.485	confess("FIG::verify_dir: refusing to create a directory named ''\n");
3193 :	olson	1.416	}
3194 :
3195 :	parrello	1.287	if (-d $dir) {
3196 :			return
3197 :			}
3198 :	olson	1.416	if ($dir =~ /^(.*)\/[^\/]+$/ and $1 ne '') {
3199 :	parrello	1.287	&verify_dir($1);
3200 :	efrank	1.1	}
3201 :	overbeek	1.522	mkdir($dir,0777) \|\| confess "Could not make directory $dir: $!";
3202 :	efrank	1.1	}
3203 :
3204 :	parrello	1.287	=head3 run
3205 :	efrank	1.1
3206 :	parrello	1.287	C<< FIG::run($cmd); >>
3207 :	overbeek	1.283
3208 :	parrello	1.287	or
3209 :
3210 :			C<< $fig->run($cmd); >>
3211 :	overbeek	1.283
3212 :	parrello	1.287	Run a command. If the command fails, the error will be traced.
3213 :	overbeek	1.283
3214 :			=cut
3215 :
3216 :	parrello	1.287	sub run {
3217 :			shift if UNIVERSAL::isa($_[0],__PACKAGE__);
3218 :			my($cmd) = @_;
3219 :
3220 :	overbeek	1.363	if ($ENV{FIG_VERBOSE}) {
3221 :	parrello	1.287	my @tmp = `date`;
3222 :			chomp @tmp;
3223 :			print STDERR "$tmp[0]: running $cmd\n";
3224 :			}
3225 :			Trace("Running command: $cmd") if T(3);
3226 :			(system($cmd) == 0) \|\| Confess("FAILED: $cmd");
3227 :			}
3228 :
3229 :	olson	1.388	=head3 run_gathering_output
3230 :
3231 :			C<< FIG::run_gathering_output($cmd, @args); >>
3232 :
3233 :			or
3234 :
3235 :			C<< $fig->run_gathering_output($cmd, @args); >>
3236 :
3237 :			Run a command, gathering the output. This is similar to the backtick
3238 :			operator, but it does not invoke the shell. Note that the argument list
3239 :	parrello	1.518	must be explicitly passed one command line argument per argument to
3240 :	olson	1.388	run_gathering_output.
3241 :
3242 :			If the command fails, the error will be traced.
3243 :
3244 :			=cut
3245 :
3246 :			sub run_gathering_output {
3247 :			shift if UNIVERSAL::isa($_[0],__PACKAGE__);
3248 :			my($cmd, @args) = @_;
3249 :
3250 :			#
3251 :			# Run the command in a safe fork-with-pipe/exec.
3252 :			#
3253 :
3254 :			my $pid = open(PROC_READ, "-\|");
3255 :
3256 :			if ($pid == 0)
3257 :			{
3258 :	parrello	1.485	exec { $cmd } $cmd, @args;
3259 :			die "could not execute $cmd @args: $!\n";
3260 :	olson	1.388	}
3261 :
3262 :			if (wantarray)
3263 :			{
3264 :	parrello	1.485	my @out;
3265 :			while (<PROC_READ>)
3266 :			{
3267 :			push(@out, $_);
3268 :			}
3269 :			if (!close(PROC_READ))
3270 :			{
3271 :			Confess("FAILED: $cmd @args with error return $?");
3272 :			}
3273 :			return @out;
3274 :	olson	1.388	}
3275 :			else
3276 :			{
3277 :	parrello	1.485	my $out = '';
3278 :	parrello	1.518
3279 :	parrello	1.485	while (<PROC_READ>)
3280 :			{
3281 :			$out .= $_;
3282 :			}
3283 :			if (!close(PROC_READ))
3284 :			{
3285 :			Confess("FAILED: $cmd @args with error return $?");
3286 :			}
3287 :			return $out;
3288 :	olson	1.388	}
3289 :			}
3290 :
3291 :	parrello	1.287	=head3 augment_path
3292 :
3293 :			C<< FIG::augment_path($dirName); >>
3294 :	overbeek	1.283
3295 :	parrello	1.287	Add a directory to the system path.
3296 :	overbeek	1.283
3297 :	parrello	1.287	This method adds a new directory to the front of the system path. It looks in the
3298 :			configuration file to determine whether this is Windows or Unix, and uses the
3299 :			appropriate separator.
3300 :	efrank	1.1
3301 :	parrello	1.287	=over 4
3302 :	efrank	1.1
3303 :	parrello	1.287	=item dirName
3304 :
3305 :			Name of the directory to add to the path.
3306 :
3307 :			=back
3308 :	efrank	1.1
3309 :			=cut
3310 :
3311 :	parrello	1.287	sub augment_path {
3312 :			my ($dirName) = @_;
3313 :			if ($FIG_Config::win_mode) {
3314 :			$ENV{PATH} = "$dirName;$ENV{PATH}";
3315 :			} else {
3316 :			$ENV{PATH} = "$dirName:$ENV{PATH}";
3317 :	overbeek	1.278	}
3318 :	efrank	1.1	}
3319 :
3320 :	parrello	1.287	=head3 read_fasta_record
3321 :	gdpusch	1.45
3322 :	parrello	1.287	C<< my ($seq_id, $seq_pointer, $comment) = FIG::read_fasta_record(\*FILEHANDLE); >>
3323 :	gdpusch	1.45
3324 :	parrello	1.287	or
3325 :	gdpusch	1.45
3326 :	parrello	1.287	C<< my ($seq_id, $seq_pointer, $comment) = $fig->read_fasta_record(\*FILEHANDLE); >>
3327 :	gdpusch	1.45
3328 :	parrello	1.287	Read and parse the next logical record of a FASTA file. A FASTA logical record
3329 :			consists of multiple lines of text. The first line begins with a C<< > >> symbol
3330 :			and contains the sequence ID followed by an optional comment. (NOTE: comments
3331 :			are currently deprecated, because not all tools handle them properly.) The
3332 :			remaining lines contain the sequence data.
3333 :
3334 :			This method uses a trick to smooth its operation: the line terminator character
3335 :			is temporarily changed to C<< \n> >> so that a single read operation brings in
3336 :			the entire logical record.
3337 :	gdpusch	1.45
3338 :	parrello	1.287	=over 4
3339 :	gdpusch	1.45
3340 :	parrello	1.287	=item FILEHANDLE
3341 :	gdpusch	1.45
3342 :	parrello	1.287	Open handle of the FASTA file. If not specified, C<STDIN> is assumed.
3343 :
3344 :			=item RETURN
3345 :
3346 :			If we are at the end of the file, returns C<undef>. Otherwise, returns a
3347 :			three-element list. The first element is the sequence ID, the second is
3348 :			a pointer to the sequence data (that is, a string reference as opposed to
3349 :			as string), and the third is the comment.
3350 :
3351 :			=back
3352 :	gdpusch	1.45
3353 :			=cut
3354 :	parrello	1.213	#: Return Type @;
3355 :	parrello	1.287	sub read_fasta_record {
3356 :
3357 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
3358 :	gdpusch	1.45	my ($file_handle) = @_;
3359 :	parrello	1.287	my ($old_end_of_record, $fasta_record, @lines, $head, $sequence, $seq_id, $comment, @parsed_fasta_record);
3360 :	parrello	1.200
3361 :	gdpusch	1.45	if (not defined($file_handle)) { $file_handle = \*STDIN; }
3362 :	parrello	1.200
3363 :	gdpusch	1.45	$old_end_of_record = $/;
3364 :			$/ = "\n>";
3365 :	parrello	1.200
3366 :	parrello	1.287	if (defined($fasta_record = <$file_handle>)) {
3367 :			chomp $fasta_record;
3368 :			@lines = split( /\n/, $fasta_record );
3369 :			$head = shift @lines;
3370 :			$head =~ s/^>?//;
3371 :			$head =~ m/^(\S+)/;
3372 :			$seq_id = $1;
3373 :			if ($head =~ m/^\S+\s+(.*)$/) { $comment = $1; } else { $comment = ""; }
3374 :			$sequence = join( "", @lines );
3375 :			@parsed_fasta_record = ( $seq_id, \$sequence, $comment );
3376 :			} else {
3377 :			@parsed_fasta_record = ();
3378 :	gdpusch	1.45	}
3379 :	parrello	1.200
3380 :	gdpusch	1.45	$/ = $old_end_of_record;
3381 :	parrello	1.200
3382 :	gdpusch	1.45	return @parsed_fasta_record;
3383 :			}
3384 :
3385 :	parrello	1.287	=head3 display_id_and_seq
3386 :
3387 :			C<< FIG::display_id_and_seq($id_and_comment, $seqP, $fh); >>
3388 :
3389 :			or
3390 :
3391 :	parrello	1.355	C<< $fig->display_id_and_seq($id_and_comment, \$seqP, $fh); >>
3392 :	parrello	1.287
3393 :			Display a fasta ID and sequence to the specified open file. This method is designed
3394 :			to work well with L</read_fasta_sequence> and L</rev_comp>, because it takes as
3395 :			input a string pointer rather than a string. If the file handle is omitted it
3396 :			defaults to STDOUT.
3397 :
3398 :			The output is formatted into a FASTA record. The first line of the output is
3399 :			preceded by a C<< > >> symbol, and the sequence is split into 60-character
3400 :			chunks displayed one per line. Thus, this method can be used to produce
3401 :			FASTA files from data gathered by the rest of the system.
3402 :
3403 :			=over 4
3404 :
3405 :			=item id_and_comment
3406 :
3407 :			The sequence ID and (optionally) the comment from the sequence's FASTA record.
3408 :			The ID
3409 :	gdpusch	1.45
3410 :	parrello	1.287	=item seqP
3411 :	efrank	1.1
3412 :	parrello	1.287	Reference to a string containing the sequence. The sequence is automatically
3413 :			formatted into 60-character chunks displayed one per line.
3414 :	efrank	1.1
3415 :	parrello	1.287	=item fh
3416 :	efrank	1.1
3417 :	parrello	1.287	Open file handle to which the ID and sequence should be output. If omitted,
3418 :	parrello	1.355	C<\*STDOUT> is assumed.
3419 :	parrello	1.287
3420 :			=back
3421 :	efrank	1.1
3422 :			=cut
3423 :
3424 :	parrello	1.287	sub display_id_and_seq {
3425 :	mkubal	1.53
3426 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
3427 :	parrello	1.287
3428 :	overbeek	1.326	my( $id, $seqP, $fh ) = @_;
3429 :	parrello	1.200
3430 :	efrank	1.1	if (! defined($fh) ) { $fh = \*STDOUT; }
3431 :	parrello	1.200
3432 :	efrank	1.1	print $fh ">$id\n";
3433 :	overbeek	1.326	&display_seq($seqP, $fh);
3434 :	efrank	1.1	}
3435 :
3436 :	parrello	1.355	=head3 display_seq
3437 :	parrello	1.287
3438 :	parrello	1.355	C<< FIG::display_seq(\$seqP, $fh); >>
3439 :	parrello	1.287
3440 :			or
3441 :
3442 :	parrello	1.355	C<< $fig->display_seq(\$seqP, $fh); >>
3443 :	parrello	1.287
3444 :			Display a fasta sequence to the specified open file. This method is designed
3445 :			to work well with L</read_fasta_sequence> and L</rev_comp>, because it takes as
3446 :			input a string pointer rather than a string. If the file handle is omitted it
3447 :			defaults to STDOUT.
3448 :
3449 :			The sequence is split into 60-character chunks displayed one per line for
3450 :			readability.
3451 :
3452 :			=over 4
3453 :
3454 :			=item seqP
3455 :
3456 :			Reference to a string containing the sequence.
3457 :
3458 :			=item fh
3459 :
3460 :			Open file handle to which the sequence should be output. If omitted,
3461 :			C<STDOUT> is assumed.
3462 :
3463 :			=back
3464 :
3465 :			=cut
3466 :
3467 :	efrank	1.1	sub display_seq {
3468 :	parrello	1.287
3469 :	olson	1.111	shift if UNIVERSAL::isa($_[0],__PACKAGE__);
3470 :	parrello	1.287
3471 :	overbeek	1.326	my ( $seqP, $fh ) = @_;
3472 :	efrank	1.1	my ( $i, $n, $ln );
3473 :	parrello	1.200
3474 :	efrank	1.1	if (! defined($fh) ) { $fh = \*STDOUT; }
3475 :
3476 :	overbeek	1.326	$n = length($$seqP);
3477 :	efrank	1.1	# confess "zero-length sequence ???" if ( (! defined($n)) \|\| ($n == 0) );
3478 :	parrello	1.287	for ($i=0; ($i < $n); $i += 60) {
3479 :			if (($i + 60) <= $n) {
3480 :	overbeek	1.326	$ln = substr($$seqP,$i,60);
3481 :	parrello	1.287	} else {
3482 :	overbeek	1.326	$ln = substr($$seqP,$i,($n-$i));
3483 :	parrello	1.287	}
3484 :			print $fh "$ln\n";
3485 :	efrank	1.1	}
3486 :			}
3487 :
3488 :	overbeek	1.529
3489 :			=head3 flatten_dumper
3490 :
3491 :			C<< FIG::flatten_dumper( $perl_ref_or_object_1, ... ); >>
3492 :
3493 :			C<< $fig->flatten_dumper( $perl_ref_or_object_1, ... ); >>
3494 :
3495 :			Takes a list of perl references or objects, and "flattens" their Data::Dumper() output
3496 :			so that it can be printed on a single line.
3497 :
3498 :			=cut
3499 :
3500 :			sub flatten_dumper {
3501 :			my @x = @_;
3502 :			my $x;
3503 :
3504 :			foreach $x (@x)
3505 :			{
3506 :			$x = Dumper($x);
3507 :
3508 :			$x =~ s/\$VAR\d+\s+\=\s+//o;
3509 :			$x =~ s/\n//gso;
3510 :			$x =~ s/\s+/ /go;
3511 :			$x =~ s/\'//go;
3512 :			# $x =~ s/^[^\(\[\{]+//o;
3513 :			# $x =~ s/[^\)\]\}]+$//o;
3514 :			}
3515 :
3516 :			return @x;
3517 :			}
3518 :
3519 :
3520 :	efrank	1.1	########## I commented the pods on the following routines out, since they should not
3521 :			########## be part of the SOAP/WSTL interface
3522 :			#=pod
3523 :			#
3524 :	parrello	1.287	#=head3 file2N
3525 :	efrank	1.1	#
3526 :			#usage: $n = $fig->file2N($file)
3527 :			#
3528 :			#In some of the databases I need to store filenames, which can waste a lot of
3529 :			#space. Hence, I maintain a database for converting filenames to/from integers.
3530 :			#
3531 :			#=cut
3532 :			#
3533 :	parrello	1.328	sub file2N :Scalar {
3534 :	efrank	1.1	my($self,$file) = @_;
3535 :			my($relational_db_response);
3536 :
3537 :			my $rdbH = $self->db_handle;
3538 :
3539 :	olson	1.403	#
3540 :			# Strip the figdisk path from the file. N2file replaces it if the path
3541 :			# in the database is relative.
3542 :			#
3543 :			$file =~ s,^$FIG_Config::fig_disk/,,;
3544 :
3545 :	efrank	1.1	if (($relational_db_response = $rdbH->SQL("SELECT fileno FROM file_table WHERE ( file = \'$file\')")) &&
3546 :	parrello	1.298	(@$relational_db_response == 1)) {
3547 :	parrello	1.287	return $relational_db_response->[0]->[0];
3548 :			} elsif (($relational_db_response = $rdbH->SQL("SELECT MAX(fileno) FROM file_table ")) && (@$relational_db_response == 1) && ($relational_db_response->[0]->[0])) {
3549 :			my $fileno = $relational_db_response->[0]->[0] + 1;
3550 :			if ($rdbH->SQL("INSERT INTO file_table ( file, fileno ) VALUES ( \'$file\', $fileno )")) {
3551 :			return $fileno;
3552 :			}
3553 :			} elsif ($rdbH->SQL("INSERT INTO file_table ( file, fileno ) VALUES ( \'$file\', 1 )")) {
3554 :			return 1;
3555 :	efrank	1.1	}
3556 :			return undef;
3557 :			}
3558 :
3559 :			#=pod
3560 :			#
3561 :	parrello	1.287	#=head3 N2file
3562 :	efrank	1.1	#
3563 :			#usage: $filename = $fig->N2file($n)
3564 :			#
3565 :			#In some of the databases I need to store filenames, which can waste a lot of
3566 :			#space. Hence, I maintain a database for converting filenames to/from integers.
3567 :			#
3568 :			#=cut
3569 :			#
3570 :	overbeek	1.364	sub N2file :Scalar
3571 :			{
3572 :	efrank	1.1	my($self,$fileno) = @_;
3573 :	overbeek	1.364
3574 :			#
3575 :			# Cache outputs. This results in a huge savings of time when files are
3576 :			# accessed multiple times (as in when a bunch of sims are requested).
3577 :			#
3578 :
3579 :			my $fcache = $self->cached("_n2file");
3580 :	parrello	1.379
3581 :	overbeek	1.364	my $fname;
3582 :			if (defined($fname = $fcache->{$fileno}))
3583 :			{
3584 :	parrello	1.365	return $fname;
3585 :	overbeek	1.364	}
3586 :	efrank	1.1
3587 :			my $rdbH = $self->db_handle;
3588 :	parrello	1.379
3589 :	overbeek	1.364	my $relational_db_response = $rdbH->SQL("SELECT file FROM file_table WHERE ( fileno = $fileno )");
3590 :	efrank	1.1
3591 :	overbeek	1.364	if ($relational_db_response and @$relational_db_response == 1)
3592 :			{
3593 :	parrello	1.365	$fname = $relational_db_response->[0]->[0];
3594 :	olson	1.403
3595 :	parrello	1.420	#
3596 :			# If $fname is relative, prepend the base of the fig_disk.
3597 :			# (Updated to use PERL's system-independent filename utilities.
3598 :			#
3599 :	parrello	1.518
3600 :	parrello	1.420	$fname = File::Spec->rel2abs($fname, $FIG_Config::fig_disk);
3601 :	parrello	1.518
3602 :	parrello	1.365	$fcache->{$fileno} = $fname;
3603 :			return $fname;
3604 :	efrank	1.1	}
3605 :			return undef;
3606 :			}
3607 :
3608 :
3609 :			#=pod
3610 :			#
3611 :	parrello	1.287	#=head3 openF
3612 :	efrank	1.1	#
3613 :			#usage: $fig->openF($filename)
3614 :			#
3615 :			#Parts of the system rely on accessing numerous different files. The most obvious case is
3616 :			#the situation with similarities. It is important that the system be able to run in cases in
3617 :			#which an arbitrary number of files cannot be open simultaneously. This routine (with closeF) is
3618 :			#a hack to handle this. I should probably just pitch them and insist that the OS handle several
3619 :			#hundred open filehandles.
3620 :			#
3621 :			#=cut
3622 :			#
3623 :			sub openF {
3624 :			my($self,$file) = @_;
3625 :			my($fxs,$x,@fxs,$fh);
3626 :
3627 :			$fxs = $self->cached('_openF');
3628 :	parrello	1.287	if ($x = $fxs->{$file}) {
3629 :			$x->[1] = time();
3630 :			return $x->[0];
3631 :	efrank	1.1	}
3632 :	parrello	1.200
3633 :	efrank	1.1	@fxs = keys(%$fxs);
3634 :	parrello	1.287	if (defined($fh = new FileHandle "<$file")) {
3635 :			if (@fxs >= 50) {
3636 :			@fxs = sort { $fxs->{$a}->[1] <=> $fxs->{$b}->[1] } @fxs;
3637 :			$x = $fxs->{$fxs[0]};
3638 :			undef $x->[0];
3639 :			delete $fxs->{$fxs[0]};
3640 :			}
3641 :			$fxs->{$file} = [$fh,time()];
3642 :			return $fh;
3643 :	efrank	1.1	}
3644 :			return undef;
3645 :			}
3646 :
3647 :			#=pod
3648 :			#
3649 :	parrello	1.287	#=head3 closeF
3650 :	efrank	1.1	#
3651 :			#usage: $fig->closeF($filename)
3652 :			#
3653 :			#Parts of the system rely on accessing numerous different files. The most obvious case is
3654 :			#the situation with similarities. It is important that the system be able to run in cases in
3655 :			#which an arbitrary number of files cannot be open simultaneously. This routine (with openF) is
3656 :			#a hack to handle this. I should probably just pitch them and insist that the OS handle several
3657 :			#hundred open filehandles.
3658 :			#
3659 :			#=cut
3660 :			#
3661 :			sub closeF {
3662 :			my($self,$file) = @_;
3663 :			my($fxs,$x);
3664 :
3665 :	parrello	1.287	if (($fxs = $self->{_openF}) && ($x = $fxs->{$file})) {
3666 :			undef $x->[0];
3667 :			delete $fxs->{$file};
3668 :	efrank	1.1	}
3669 :			}
3670 :
3671 :	parrello	1.287	=head3 ec_name
3672 :
3673 :			C<< my $enzymatic_function = $fig->ec_name($ec); >>
3674 :	efrank	1.1
3675 :	parrello	1.287	Returns the enzymatic name corresponding to the specified enzyme code.
3676 :	efrank	1.1
3677 :	parrello	1.287	=over 4
3678 :
3679 :			=item ec
3680 :	efrank	1.1
3681 :	parrello	1.287	Code number for the enzyme whose name is desired. The code number is actually
3682 :			a string of digits and periods (e.g. C<1.2.50.6>).
3683 :
3684 :			=item RETURN
3685 :
3686 :			Returns the name of the enzyme specified by the indicated code, or a null string
3687 :			if the code is not found in the database.
3688 :
3689 :			=back
3690 :	efrank	1.1
3691 :			=cut
3692 :
3693 :			sub ec_name {
3694 :			my($self,$ec) = @_;
3695 :
3696 :			($ec =~ /^\d+\.\d+\.\d+\.\d+$/) \|\| return "";
3697 :			my $rdbH = $self->db_handle;
3698 :			my $relational_db_response = $rdbH->SQL("SELECT name FROM ec_names WHERE ( ec = \'$ec\' )");
3699 :
3700 :			return (@$relational_db_response == 1) ? $relational_db_response->[0]->[0] : "";
3701 :			return "";
3702 :			}
3703 :
3704 :	parrello	1.287	=head3 all_roles
3705 :	efrank	1.1
3706 :	parrello	1.287	C<< my @roles = $fig->all_roles; >>
3707 :	efrank	1.1
3708 :	parrello	1.287	Return a list of the known roles. Currently, this is a list of the enzyme codes and names.
3709 :	efrank	1.1
3710 :	parrello	1.287	The return value is a list of list references. Each element of the big list contains an
3711 :			enzyme code (EC) followed by the enzymatic name.
3712 :	efrank	1.1
3713 :			=cut
3714 :
3715 :			sub all_roles {
3716 :			my($self) = @_;
3717 :
3718 :			my $rdbH = $self->db_handle;
3719 :			my $relational_db_response = $rdbH->SQL("SELECT ec,name FROM ec_names");
3720 :
3721 :			return @$relational_db_response;
3722 :			}
3723 :
3724 :	parrello	1.287	=head3 expand_ec
3725 :	efrank	1.1
3726 :	parrello	1.287	C<< my $expanded_ec = $fig->expand_ec($ec); >>
3727 :	efrank	1.1
3728 :			Expands "1.1.1.1" to "1.1.1.1 - alcohol dehydrogenase" or something like that.
3729 :
3730 :			=cut
3731 :
3732 :			sub expand_ec {
3733 :			my($self,$ec) = @_;
3734 :			my($name);
3735 :
3736 :			return ($name = $self->ec_name($ec)) ? "$ec - $name" : $ec;
3737 :			}
3738 :
3739 :	parrello	1.287	=head3 clean_tmp
3740 :	efrank	1.1
3741 :	parrello	1.287	C<< FIG::clean_tmp(); >>
3742 :	efrank	1.1
3743 :	parrello	1.287	Delete temporary files more than two days old.
3744 :	efrank	1.1
3745 :			We store temporary files in $FIG_Config::temp. There are specific classes of files
3746 :			that are created and should be saved for at least a few days. This routine can be
3747 :			invoked to clean out those that are over two days old.
3748 :
3749 :			=cut
3750 :
3751 :			sub clean_tmp {
3752 :
3753 :			my($file);
3754 :	parrello	1.287	if (opendir(TMP,"$FIG_Config::temp")) {
3755 :			# change the pattern to pick up other files that need to be cleaned up
3756 :			my @temp = grep { $_ =~ /^(Geno\|tmp)/ } readdir(TMP);
3757 :			foreach $file (@temp) {
3758 :			if (-M "$FIG_Config::temp/$file" > 2) {
3759 :			unlink("$FIG_Config::temp/$file");
3760 :			}
3761 :			}
3762 :	efrank	1.1	}
3763 :			}
3764 :
3765 :			################ Routines to process genomes and genome IDs ##########################
3766 :
3767 :
3768 :	parrello	1.287	=head3 genomes
3769 :	efrank	1.1
3770 :	parrello	1.287	C<< my @genome_ids = $fig->genomes($complete, $restrictions, $domain); >>
3771 :	efrank	1.1
3772 :	parrello	1.287	Return a list of genome IDs. If called with no parameters, all genome IDs
3773 :			in the database will be returned.
3774 :	efrank	1.1
3775 :			Genomes are assigned ids of the form X.Y where X is the taxonomic id maintained by
3776 :			NCBI for the species (not the specific strain), and Y is a sequence digit assigned to
3777 :			this particular genome (as one of a set with the same genus/species). Genomes also
3778 :			have versions, but that is a separate issue.
3779 :
3780 :	parrello	1.287	=over 4
3781 :
3782 :			=item complete
3783 :
3784 :			TRUE if only complete genomes should be returned, else FALSE.
3785 :
3786 :			=item restrictions
3787 :
3788 :			TRUE if only restriction genomes should be returned, else FALSE.
3789 :
3790 :			=item domain
3791 :
3792 :			Name of the domain from which the genomes should be returned. Possible values are
3793 :			C<Bacteria>, C<Virus>, C<Eukaryota>, C<unknown>, C<Archaea>, and
3794 :			C<Environmental Sample>. If no domain is specified, all domains will be
3795 :			eligible.
3796 :
3797 :			=item RETURN
3798 :
3799 :			Returns a list of all the genome IDs with the specified characteristics.
3800 :
3801 :			=back
3802 :
3803 :	efrank	1.1	=cut
3804 :	parrello	1.320	#: Return Type @;
3805 :	parrello	1.328	sub genomes :Remote :List {
3806 :	golsen	1.150	my( $self, $complete, $restrictions, $domain ) = @_;
3807 :	overbeek	1.13
3808 :			my $rdbH = $self->db_handle;
3809 :
3810 :			my @where = ();
3811 :	parrello	1.287	if ($complete) {
3812 :			push(@where, "( complete = \'1\' )")
3813 :	overbeek	1.13	}
3814 :
3815 :	parrello	1.287	if ($restrictions) {
3816 :			push(@where, "( restrictions = \'1\' )")
3817 :	overbeek	1.13	}
3818 :	golsen	1.150
3819 :	parrello	1.287	if ($domain) {
3820 :			push( @where, "( maindomain = '$domain' )" )
3821 :	golsen	1.150	}
3822 :
3823 :	overbeek	1.13	my $relational_db_response;
3824 :	parrello	1.287	if (@where > 0) {
3825 :			my $where = join(" AND ",@where);
3826 :			$relational_db_response = $rdbH->SQL("SELECT genome FROM genome where $where");
3827 :			} else {
3828 :			$relational_db_response = $rdbH->SQL("SELECT genome FROM genome");
3829 :	overbeek	1.13	}
3830 :			my @genomes = sort { $a <=> $b } map { $_->[0] } @$relational_db_response;
3831 :	efrank	1.1	return @genomes;
3832 :			}
3833 :
3834 :	paczian	1.599	sub genome_list {
3835 :			my( $self ) = @_;
3836 :
3837 :			my $rdbH = $self->db_handle;
3838 :			my $relational_db_response = $rdbH->SQL("SELECT genome, gname, maindomain FROM genome where complete=1");
3839 :
3840 :			return $relational_db_response;
3841 :			}
3842 :
3843 :	parrello	1.287	=head3 is_complete
3844 :
3845 :			C<< my $flag = $fig->is_complete($genome); >>
3846 :
3847 :			Return TRUE if the genome with the specified ID is complete, else FALSE.
3848 :
3849 :			=over 4
3850 :
3851 :			=item genome
3852 :
3853 :			ID of the relevant genome.
3854 :
3855 :			=item RETURN
3856 :
3857 :			Returns TRUE if there is a complete genome in the database with the specified ID,
3858 :			else FALSE.
3859 :
3860 :			=back
3861 :
3862 :			=cut
3863 :
3864 :	overbeek	1.180	sub is_complete {
3865 :			my($self,$genome) = @_;
3866 :
3867 :			my $rdbH = $self->db_handle;
3868 :			my $relational_db_response = $rdbH->SQL("SELECT genome FROM genome where (genome = '$genome') AND (complete = '1')");
3869 :			return (@$relational_db_response == 1)
3870 :	parrello	1.287	}
3871 :
3872 :	parrello	1.490	=head3 is_genome
3873 :
3874 :			C<< my $flag = $fig->is_genome($genome); >>
3875 :
3876 :			Return TRUE if the specified genome exists, else FALSE.
3877 :
3878 :			=over 4
3879 :
3880 :			=item genome
3881 :
3882 :			ID of the genome to test.
3883 :
3884 :			=item RETURN
3885 :
3886 :			Returns TRUE if a genome with the specified ID exists in the data store, else FALSE.
3887 :
3888 :			=back
3889 :
3890 :			=cut
3891 :
3892 :	overbeek	1.421	sub is_genome {
3893 :			my($self,$genome) = @_;
3894 :	olson	1.613	my($y);
3895 :	overbeek	1.421
3896 :	olson	1.613	my $is_genome = $self->cached("_is_genome");
3897 :
3898 :			if (defined($y = $is_genome->{$genome}))
3899 :	overbeek	1.421	{
3900 :	olson	1.613	return $y;
3901 :	overbeek	1.421	}
3902 :
3903 :			my $rdbH = $self->db_handle;
3904 :			my $relational_db_response = $rdbH->SQL("SELECT genome FROM genome where (genome = '$genome')");
3905 :			$y = (@$relational_db_response == 1);
3906 :	olson	1.613	$is_genome->{$genome} = $y;
3907 :	overbeek	1.421	return $y;
3908 :			}
3909 :
3910 :	olson	1.613	=head3 assert_genomes
3911 :
3912 :			C<< $fig->assert_genomes(gid, gid, ...)>>
3913 :
3914 :			Assert that the given list of genomes does exist, and allow is_genome() to succeed for them.
3915 :
3916 :			This is used in FIG-based computations in the context of the RAST genome-import code, so that
3917 :			genomes that currently exist only in RAST are treated as present for the purposes of FIG.pm-based
3918 :			code.
3919 :
3920 :			=cut
3921 :
3922 :			sub assert_genomes
3923 :			{
3924 :			my($self, @genomes) = @_;
3925 :
3926 :			my $assert = $self->cached("_is_genome");
3927 :			map { $assert->{$_} = 1 } @genomes;
3928 :			}
3929 :
3930 :	parrello	1.287	=head3 genome_counts
3931 :
3932 :			C<< my ($arch, $bact, $euk, $vir, $env, $unk) = $fig->genome_counts($complete); >>
3933 :
3934 :			Count the number of genomes in each domain. If I<$complete> is TRUE, only complete
3935 :			genomes will be included in the counts.
3936 :
3937 :			=over 4
3938 :
3939 :			=item complete
3940 :
3941 :			TRUE if only complete genomes are to be counted, FALSE if all genomes are to be
3942 :			counted
3943 :
3944 :			=item RETURN
3945 :
3946 :			A six-element list containing the number of genomes in each of six categories--
3947 :			Archaea, Bacteria, Eukaryota, Viral, Environmental, and Unknown, respectively.
3948 :
3949 :			=back
3950 :
3951 :			=cut
3952 :	golsen	1.150
3953 :	efrank	1.2	sub genome_counts {
3954 :	overbeek	1.13	my($self,$complete) = @_;
3955 :			my($x,$relational_db_response);
3956 :	efrank	1.2
3957 :	overbeek	1.13	my $rdbH = $self->db_handle;
3958 :
3959 :	parrello	1.287	if ($complete) {
3960 :			$relational_db_response = $rdbH->SQL("SELECT genome, maindomain FROM genome where complete = '1'");
3961 :			} else {
3962 :			$relational_db_response = $rdbH->SQL("SELECT genome,maindomain FROM genome");
3963 :	overbeek	1.13	}
3964 :
3965 :	gdpusch	1.107	my ($arch, $bact, $euk, $vir, $env, $unk) = (0, 0, 0, 0, 0, 0);
3966 :	parrello	1.287	if (@$relational_db_response > 0) {
3967 :			foreach $x (@$relational_db_response) {
3968 :			if ($x->[1] =~ /^archaea/i) { ++$arch }
3969 :			elsif ($x->[1] =~ /^bacter/i) { ++$bact }
3970 :			elsif ($x->[1] =~ /^eukar/i) { ++$euk }
3971 :			elsif ($x->[1] =~ /^vir/i) { ++$vir }
3972 :			elsif ($x->[1] =~ /^env/i) { ++$env }
3973 :			else { ++$unk }
3974 :	parrello	1.298	}
3975 :	efrank	1.2	}
3976 :	parrello	1.200
3977 :	gdpusch	1.107	return ($arch, $bact, $euk, $vir, $env, $unk);
3978 :			}
3979 :
3980 :
3981 :	parrello	1.287	=head3 genome_domain
3982 :
3983 :			C<< my $domain = $fig->genome_domain($genome_id); >>
3984 :
3985 :			Find the domain of a genome.
3986 :	gdpusch	1.107
3987 :	parrello	1.287	=over 4
3988 :
3989 :			=item genome_id
3990 :	gdpusch	1.107
3991 :	parrello	1.287	ID of the genome whose domain is desired.
3992 :	gdpusch	1.107
3993 :	parrello	1.287	=item RETURN
3994 :
3995 :			Returns the name of the genome's domain (archaea, bacteria, etc.), or C<undef> if
3996 :			the genome is not in the database.
3997 :	gdpusch	1.107
3998 :	parrello	1.292	=back
3999 :
4000 :	gdpusch	1.107	=cut
4001 :
4002 :			sub genome_domain {
4003 :			my($self,$genome) = @_;
4004 :			my $relational_db_response;
4005 :			my $rdbH = $self->db_handle;
4006 :	parrello	1.200
4007 :	parrello	1.287	if ($genome) {
4008 :			if (($relational_db_response = $rdbH->SQL("SELECT genome,maindomain FROM genome WHERE ( genome = \'$genome\' )"))
4009 :			&& (@$relational_db_response == 1)) {
4010 :			# die Dumper($relational_db_response);
4011 :			return $relational_db_response->[0]->[1];
4012 :			}
4013 :	gdpusch	1.107	}
4014 :			return undef;
4015 :	efrank	1.2	}
4016 :
4017 :	gdpusch	1.92
4018 :	parrello	1.287	=head3 genome_pegs
4019 :	gdpusch	1.92
4020 :	parrello	1.287	C<< my $num_pegs = $fig->genome_pegs($genome_id); >>
4021 :	gdpusch	1.92
4022 :	parrello	1.287	Return the number of protein-encoding genes (PEGs) for a specified
4023 :			genome.
4024 :	gdpusch	1.92
4025 :	parrello	1.287	=over 4
4026 :
4027 :			=item genome_id
4028 :
4029 :			ID of the genome whose PEG count is desired.
4030 :
4031 :			=item RETURN
4032 :
4033 :			Returns the number of PEGs for the specified genome, or C<undef> if the genome
4034 :			is not indexed in the database.
4035 :
4036 :			=back
4037 :	gdpusch	1.92
4038 :			=cut
4039 :
4040 :			sub genome_pegs {
4041 :			my($self,$genome) = @_;
4042 :			my $relational_db_response;
4043 :			my $rdbH = $self->db_handle;
4044 :	parrello	1.200
4045 :	parrello	1.287	if ($genome) {
4046 :			if (($relational_db_response = $rdbH->SQL("SELECT pegs FROM genome WHERE ( genome = \'$genome\' )"))
4047 :			&& (@$relational_db_response == 1)) {
4048 :			return $relational_db_response->[0]->[0];
4049 :			}
4050 :	gdpusch	1.92	}
4051 :			return undef;
4052 :			}
4053 :
4054 :
4055 :	parrello	1.287	=head3 genome_rnas
4056 :
4057 :			C<< my $num_rnas = $fig->genome_rnas($genome_id); >>
4058 :
4059 :			Return the number of RNA-encoding genes for a genome.
4060 :			"$genome_id" is indexed in the "genome" database, and 'undef' otherwise.
4061 :	efrank	1.1
4062 :	parrello	1.287	=over 4
4063 :
4064 :			=item genome_id
4065 :
4066 :			ID of the genome whose RNA count is desired.
4067 :
4068 :			=item RETURN
4069 :	gdpusch	1.92
4070 :	parrello	1.287	Returns the number of RNAs for the specified genome, or C<undef> if the genome
4071 :			is not indexed in the database.
4072 :	gdpusch	1.92
4073 :	parrello	1.287	=back
4074 :	gdpusch	1.92
4075 :			=cut
4076 :
4077 :			sub genome_rnas {
4078 :			my($self,$genome) = @_;
4079 :			my $relational_db_response;
4080 :			my $rdbH = $self->db_handle;
4081 :	parrello	1.200
4082 :	parrello	1.287	if ($genome) {
4083 :			if (($relational_db_response = $rdbH->SQL("SELECT rnas FROM genome WHERE ( genome = \'$genome\' )"))
4084 :			&& (@$relational_db_response == 1)) {
4085 :			return $relational_db_response->[0]->[0];
4086 :			}
4087 :	gdpusch	1.92	}
4088 :			return undef;
4089 :			}
4090 :
4091 :
4092 :	parrello	1.287	=head3 genome_szdna
4093 :
4094 :	parrello	1.580	C<< my $szdna = $fig->genome_szdna($genome_id); >>
4095 :	parrello	1.287
4096 :			Return the number of DNA base-pairs in a genome's contigs.
4097 :
4098 :			=over 4
4099 :
4100 :			=item genome_id
4101 :
4102 :			ID of the genome whose base-pair count is desired.
4103 :	gdpusch	1.92
4104 :	parrello	1.287	=item RETURN
4105 :	efrank	1.1
4106 :	parrello	1.287	Returns the number of base pairs in the specified genome's contigs, or C<undef>
4107 :			if the genome is not indexed in the database.
4108 :	gdpusch	1.91
4109 :	parrello	1.287	=back
4110 :	gdpusch	1.91
4111 :			=cut
4112 :
4113 :	gdpusch	1.92	sub genome_szdna {
4114 :	gdpusch	1.91	my($self,$genome) = @_;
4115 :			my $relational_db_response;
4116 :			my $rdbH = $self->db_handle;
4117 :	parrello	1.200
4118 :	parrello	1.287	if ($genome) {
4119 :			if (($relational_db_response =
4120 :			$rdbH->SQL("SELECT szdna FROM genome WHERE ( genome = \'$genome\' )"))
4121 :			&& (@$relational_db_response == 1)) {
4122 :
4123 :			return $relational_db_response->[0]->[0];
4124 :
4125 :			}
4126 :	gdpusch	1.91	}
4127 :			return undef;
4128 :			}
4129 :
4130 :	parrello	1.287	=head3 genome_version
4131 :	gdpusch	1.91
4132 :	parrello	1.287	C<< my $version = $fig->genome_version($genome_id); >>
4133 :	gdpusch	1.91
4134 :	parrello	1.287	Return the version number of the specified genome.
4135 :	efrank	1.1
4136 :			Versions are incremented for major updates. They are put in as major
4137 :			updates of the form 1.0, 2.0, ...
4138 :
4139 :			Users may do local "editing" of the DNA for a genome, but when they do,
4140 :			they increment the digits to the right of the decimal. Two genomes remain
4141 :	parrello	1.200	comparable only if the versions match identically. Hence, minor updating should be
4142 :	efrank	1.1	committed only by the person/group responsible for updating that genome.
4143 :
4144 :			We can, of course, identify which genes are identical between any two genomes (by matching
4145 :			the DNA or amino acid sequences). However, the basic intent of the system is to
4146 :			support editing by the main group issuing periodic major updates.
4147 :
4148 :	parrello	1.287	=over 4
4149 :
4150 :			=item genome_id
4151 :
4152 :			ID of the genome whose version is desired.
4153 :
4154 :			=item RETURN
4155 :
4156 :			Returns the version number of the specified genome, or C<undef> if the genome is not in
4157 :			the data store or no version number has been assigned.
4158 :
4159 :			=back
4160 :
4161 :	efrank	1.1	=cut
4162 :
4163 :	parrello	1.328	sub genome_version :Scalar {
4164 :	efrank	1.1	my($self,$genome) = @_;
4165 :
4166 :			my(@tmp);
4167 :			if ((-s "$FIG_Config::organisms/$genome/VERSION") &&
4168 :	parrello	1.298	(@tmp = `cat $FIG_Config::organisms/$genome/VERSION`) &&
4169 :			($tmp[0] =~ /^(\S+)$/)) {
4170 :			return $1;
4171 :	efrank	1.1	}
4172 :			return undef;
4173 :			}
4174 :
4175 :	parrello	1.287	=head3 genome_md5sum
4176 :	olson	1.236
4177 :	parrello	1.287	C<< my $md5sum = $fig->genome_md5sum($genome_id); >>
4178 :	olson	1.236
4179 :	parrello	1.287	Returns the MD5 checksum of the specified genome.
4180 :	olson	1.236
4181 :			The checksum of a genome is defined as the checksum of its signature file. The signature
4182 :			file consists of tab-separated lines, one for each contig, ordered by the contig id.
4183 :	parrello	1.287	Each line contains the contig ID, the length of the contig in nucleotides, and the
4184 :	olson	1.236	MD5 checksum of the nucleotide data, with uppercase letters forced to lower case.
4185 :
4186 :	parrello	1.287	The checksum is indexed in the database. If you know a genome's checksum, you can use
4187 :			the L</genome_with_md5sum> method to find its ID in the database.
4188 :
4189 :			=over 4
4190 :
4191 :			=item genome
4192 :
4193 :			ID of the genome whose checksum is desired.
4194 :
4195 :			=item RETURN
4196 :
4197 :			Returns the specified genome's checksum, or C<undef> if the genome is not in the
4198 :			database.
4199 :
4200 :			=back
4201 :	olson	1.236
4202 :			=cut
4203 :
4204 :	parrello	1.328	sub genome_md5sum :Scalar {
4205 :	olson	1.236	my($self,$genome) = @_;
4206 :			my $relational_db_response;
4207 :			my $rdbH = $self->db_handle;
4208 :
4209 :	parrello	1.287	if ($genome) {
4210 :			if (($relational_db_response =
4211 :			$rdbH->SQL("SELECT md