-
Notifications
You must be signed in to change notification settings - Fork 7
/
extractFromGenomeByGFF.pl
executable file
·572 lines (473 loc) · 19.4 KB
/
extractFromGenomeByGFF.pl
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
#!/usr/bin/perl
#
# INGLÊS/ENGLISH
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
# http://www.gnu.org/copyleft/gpl.html
#
#
# PORTUGUÊS/PORTUGUESE
# Este programa é distribuído na expectativa de ser útil aos seus
# usuários, porém NÃO TEM NENHUMA GARANTIA, EXPLÍCITAS OU IMPLÍCITAS,
# COMERCIAIS OU DE ATENDIMENTO A UMA DETERMINADA FINALIDADE. Consulte
# a Licença Pública Geral GNU para maiores detalhes.
# http://www.gnu.org/copyleft/gpl.html
#
# Copyright (C) 2012 Universidade de São Paulo
#
# Universidade de São Paulo
# Laboratório de Biologia do Desenvolvimento de Abelhas
# Núcleo de Bioinformática (LBDA-BioInfo)
#
# Daniel Guariz Pinheiro
# dgpinheiro@gmail.com
# http://zulu.fmrp.usp.br/bioinfo
#
# $Id$
=head1 NAME
extractFromGenomeByGFF.pl
=head1 SYNOPSIS
perl extractFromGenomeByGFF.pl -g /data/files/Amel_4.5/BeeBase/ -f amel_OGSv3.1_with_UTR.gff3 -o ./output \
-p OGS_
=head1 ABSTRACT
Extract sequences of 5' UTR, 3' UTR and CDS of mRNA sequences from chromosome files in FASTA format using
GFF coordinates. The global statistics are displayed in STDERR output.
=head1 DESCRIPTION
Arguments:
-h/--help Help
-l/--level Log level [Default: FATAL]
OFF
FATAL
ERROR
WARN
INFO
DEBUG
TRACE
ALL
-g/--genome Genome directory
-f/--gff GFF file
-o/--outdir Output directory
-p/--outprefix Output filenames' prefix
=head1 AUTHOR
Daniel Guariz Pinheiro E<lt>dgpinheiro@gmail.comE<gt>
Copyright (c) 2012 Universidade de São Paulo
=head1 LICENSE
GNU General Public License
http://www.gnu.org/copyleft/gpl.html
=cut
use strict;
use warnings;
use Readonly;
use Getopt::Long;
#use Bio::Factory::SeqAnalysisParserFactory;
use Bio::Tools::GFF;
use Bio::SeqIO;
use Bio::Seq;
use vars qw/$LOGGER/;
INIT {
use Log::Log4perl qw/:easy/;
Log::Log4perl->easy_init($FATAL);
$LOGGER = Log::Log4perl->get_logger($0);
}
my ($level, $gfffile, $genomedir, $outdir, $outprefix, $genomefile, $statsfile, $threepminsize);
Usage("Too few arguments") if $#ARGV < 0;
GetOptions( "h|?|help" => sub { &Usage(); },
"l|level=s"=> \$level,
"d|genomedir=s"=>\$genomedir,
"g|genomefile=s"=>\$genomefile,
"s|statsfile=s"=>\$statsfile,
"f|gff=s"=>\$gfffile,
"o|outdir=s"=>\$outdir,
"p|outprefix=s"=>\$outprefix,
"m|threepminsize=i"=>\$threepminsize
) or &Usage();
$threepminsize||=0;
if ($level) {
my %LEVEL = (
'OFF' =>$OFF,
'FATAL' =>$FATAL,
'ERROR' =>$ERROR,
'WARN' =>$WARN,
'INFO' =>$INFO,
'DEBUG' =>$DEBUG,
'TRACE' =>$TRACE,
'ALL' =>$ALL);
$LOGGER->logdie("Wrong log level ($level). Choose one of: ".join(', ', keys %LEVEL)) unless (exists $LEVEL{$level});
Log::Log4perl->easy_init($LEVEL{$level});
}
use File::Temp qw/ tempfile tempdir /;
$LOGGER->logdie('Missing genome directory or genome file') if ((!$genomedir)&&(!$genomefile));
if ($genomefile) {
$LOGGER->logdie('Wrong genome file ('.$genomefile.')') unless (-e $genomefile);
my $in = Bio::SeqIO->new(
-file => $genomefile,
-format => 'fasta'
);
if ($genomedir) {
unless (-e $genomedir) {
mkdir($genomedir);
$LOGGER->logdie('Cannot create genome directory ('.$genomedir.')') unless (-d $genomedir);
}
}
else {
$genomedir = tempdir( CLEANUP => 1 );
}
my @f = glob("$genomedir/*.fa");
if ( scalar(@f) < 1) {
while ( my $seq = $in->next_seq() ) {
my $out = Bio::SeqIO->new(
-file => '>'.$genomedir.'/'.$seq->display_id().'.fa',
-format => 'fasta'
);
$out->write_seq($seq);
}
}
}
else {
if ($genomedir) {
$LOGGER->logdie('Wrong genome directory ('.$genomedir.')') unless (-d $genomedir);
}
}
$LOGGER->logdie('Missing gff file') unless ($gfffile);
$LOGGER->logdie('Wrong gff file ('.$gfffile.')') unless (-e $gfffile);
if ($outdir) {
$LOGGER->logdie('Wrong output directory ('.$outdir.')') unless (-d $outdir);
}
else {
$outdir='.';
}
$outprefix||='out_';
my %feature;
my %parent;
my $gffio = Bio::Tools::GFF->new(-file =>$gfffile, -gff_version => 3);
my $feat;
# loop over the input stream
my $c = 0;
my %chromosome;
my $idcounter = 0;
my %allgene;
while ($feat = $gffio->next_feature()) {
$c++;
die "Not found ".$feat->seq_id()." on $genomedir" unless (-e "$genomedir/".$feat->seq_id().'.fa');
my ($id,$parent);
if ($feat->has_tag('ID')) {
($id) = $feat->get_tag_values('ID');
}
else {
($id) = 'UNK'.$idcounter++;
}
unless (exists $feature{$id}) {
$feature{$id} = { 'primary_tag' => $feat->primary_tag(),
'child' => undef };
push(@{$chromosome{ $feat->seq_id() }}, $id);
}
if ($feat->has_tag('Parent')) {
($parent) = $feat->get_tag_values('Parent');
if ($id) {
$parent{$id} = $parent unless (exists $parent{$id});
}
push(@{$feature{$parent}->{'child'}->{ $feat->primary_tag() }}, $feat);
}
else {
$allgene{ $feat->seq_id() }->{$id} = $feat;
}
}
my %out;
my %count = (
'scaffold' => 0,
'gene' => 0,
'mRNA' => 0,
'5pCDS3pmRNA' => 0,
'5pCDSmRNA' => 0,
'CDS3pmRNA' => 0,
'CDSmRNA' => 0,
'ncRNA' => 0,
'byGroup' => {}
);
foreach my $chr ( keys %allgene ) {
my ($group) = $chr=~/^(Group(?:\d+|Un\d*)|MT)/i;
@{ $count{'byGroup'}->{$group} }{ 'scaffold', 'gene', 'mRNA', '5pCDS3pmRNA', '5pCDSmRNA', 'CDS3pmRNA', 'CDSmRNA', 'ncRNA' } = (0, 0, 0, 0, 0, 0, 0, 0) unless (exists $count{'byGroup'}->{$group});
$count{'scaffold'}++;
$count{'byGroup'}->{$group}->{'scaffold'}++;
my $in = Bio::SeqIO->new(
-file => "$genomedir/" . $chr . '.fa',
-format => 'fasta'
);
my $seq = $in->next_seq();
foreach my $id ( keys %{$allgene{ $chr } } ) {
# gene
if (!exists $parent{$id}) {
# print $id,"\t",$feature{$id}->{'primary_tag'},"\n";
$count{'gene'}++;
$count{'byGroup'}->{$group}->{'gene'}++;
# print STDERR "GENE: $id","\n";
foreach my $mRNAfeat (@{ $feature{$id}->{'child'}->{ 'mRNA' } } ) {
my ($mRNAid) = $mRNAfeat->get_tag_values('ID');
# print STDERR "\t",$mRNAid,"\n";
my $strseq='';
{
my @fe;
if ($mRNAfeat->strand() == -1) {
@fe = sort { $b->start() <=> $a->start() } @{ $feature{$mRNAid}->{'child'}->{'exon'} };
}
elsif ($mRNAfeat->strand() == 1) {
@fe = sort { $a->start() <=> $b->start() } @{ $feature{$mRNAid}->{'child'}->{'exon'} };
}
else {
$LOGGER->logdie("Cannot found strand for $mRNAid");
}
foreach my $f ( @fe ) {
#print "\t",$f->primary_tag(),"\n";
#print "\t",$seq->subseq($f->location()),"\n";
$strseq.=$seq->subseq($f->location());
}
}
my $extseq='';
if ($threepminsize>0) {
my ($ts, $te) = ($mRNAfeat->start(), $mRNAfeat->end());
if ($mRNAfeat->strand() == -1) {
if ($ts > $threepminsize) {
$extseq = $seq->trunc($ts-1-($threepminsize-1), $ts-1)->revcom()->seq();
}
else {
if ($ts>1) {
$extseq = $seq->trunc(1, $ts-1)->revcom()->seq();
}
}
}
elsif ($mRNAfeat->strand() == 1) {
if ( ($te+1+$threepminsize) <= $seq->length() ) {
$extseq = $seq->trunc($te+1, $te+1+($threepminsize-1))->seq();
}
else {
if ( $te < $seq->length() ) {
$extseq = $seq->trunc($te+1, $seq->length())->seq();
}
}
}
else {
$LOGGER->logdie("Cannot found strand for $mRNAid");
}
}
my $smallest3plen = $threepminsize;
if (exists $feature{$mRNAid}->{'child'}->{'CDS'}) {
my %eachCDS;
{
my @allcds = @{ $feature{$mRNAid}->{'child'}->{'CDS'} };
foreach my $cf (@allcds) {
my ($CDSid);
if ($cf->has_tag('ID')) {
($CDSid) = $cf->get_tag_values('ID');
$CDSid=~s/-\d+$//;
}
else {
# OGS (each mRNA has only one CDS)
($CDSid) = $cf->get_tag_values('Parent');
$CDSid=~s/-R([ABC])/-P$1/;
}
my ($CDSgroup) = $CDSid=~/^([^#]+)/;
push(@{$eachCDS{ $CDSgroup }}, $cf);
}
}
foreach my $CDSgroup (keys %eachCDS) {
my @fc;
if ($mRNAfeat->strand() == -1) {
@fc = sort { $b->start() <=> $a->start() } @{ $eachCDS{ $CDSgroup } };
}
elsif ($mRNAfeat->strand() == 1) {
@fc = sort { $a->start() <=> $b->start() } @{ $eachCDS{ $CDSgroup } };
}
else {
$LOGGER->logdie("Cannot found strand for $mRNAid");
}
my $cdsseq='';
foreach my $f ( @fc ) {
$cdsseq.=$seq->subseq($f->location());
}
{
my $seqobj = Bio::Seq->new(
-seq => $cdsseq,
-display_id => 'CDSmRNA'.'|'.$CDSgroup.'|'.$mRNAid.'|'.$chr,
-description => ''
);
unless (exists $out{'CDSmRNA'}) {
$out{'CDSmRNA'} = Bio::SeqIO->new(
-file => ">$outdir/$outprefix".'CDSmRNA'.'.fa',
-format => 'fasta'
);
}
$out{'CDSmRNA'}->write_seq($seqobj);
}
if ($strseq=~/(.*)$cdsseq(.*)/) {
my ($fivep,$threep) = ($1,$2);
if ($fivep) {
my $seqobj = Bio::Seq->new(
-seq => $fivep,
-display_id => 'UTR5p'.'|'.$CDSgroup.'|'.$mRNAid.'|'.$chr,
-description => ''
);
unless (exists $out{'UTR5p'}) {
$out{'UTR5p'} = Bio::SeqIO->new(
-file => ">$outdir/$outprefix".'UTR5p'.'.fa',
-format => 'fasta'
);
}
$out{'UTR5p'}->write_seq($seqobj);
}
$smallest3plen = length($threep);
my $ext = 0;
if (length($extseq)>0) {
my $lenthreep = (($threep) ? length($threep) : 0);
if (length($extseq)>$lenthreep) {
$ext = length($extseq)-$lenthreep;
}
$threep.=substr($extseq,0, $ext);
}
if ($threep) {
my $seqobj = Bio::Seq->new(
-seq => $threep,
-display_id => 'UTR3p'.(($ext) ? '-'.$ext : '').'|'.$CDSgroup.'|'.$mRNAid.'|'.$chr,
-description => ''
);
unless (exists $out{'UTR3p'}) {
$out{'UTR3p'} = Bio::SeqIO->new(
-file => ">$outdir/$outprefix".'UTR3p'.'.fa',
-format => 'fasta'
);
}
$out{'UTR3p'}->write_seq($seqobj);
}
if ($fivep) {
if ($threep) {
$count{'5pCDS3pmRNA'}++;
$count{'byGroup'}->{$group}->{'5pCDS3pmRNA'}++;
}
else {
$count{'5pCDSmRNA'}++;
$count{'byGroup'}->{$group}->{'5pCDSmRNA'}++;
}
}
elsif ($threep) {
if ($fivep) {
$count{'5pCDS3pmRNA'}++;
$count{'byGroup'}->{$group}->{'5pCDS3pmRNA'}++;
}
else {
$count{'CDS3pmRNA'}++;
$count{'byGroup'}->{$group}->{'CDS3pmRNA'}++;
}
}
else {
$count{'CDSmRNA'}++;
$count{'byGroup'}->{$group}->{'CDSmRNA'}++;
}
#print $CDSgroup."\t".$fivep."\n";
#print $CDSgroup."\t".$threep."\n";
}
else {
$LOGGER->logdie("Something wrong! Not match CDS ($CDSgroup) into mRNA ($mRNAid)");
}
}
{
my $ext = 0;
my $threepcomp = '';
if (length($extseq)>0) {
my $lenthreep = $smallest3plen;
if (length($extseq)>$lenthreep) {
$ext = length($extseq)-$lenthreep;
}
$threepcomp.=substr($extseq,0, $ext);
}
$count{'mRNA'}++;
$count{'byGroup'}->{$group}->{'mRNA'}++;
my $seqobj = Bio::Seq->new(
-seq => $strseq.$threepcomp,
-display_id => 'mRNA'.(($ext) ? '-'.$ext : '').'|'.$mRNAid.'|'.$parent{$mRNAid}.'|'.$chr,
-description => ''
);
unless (exists $out{'mRNA'}) {
$out{'mRNA'} = Bio::SeqIO->new(
-file => ">$outdir/$outprefix".'mRNA'.'.fa',
-format => 'fasta'
);
}
$out{'mRNA'}->write_seq($seqobj);
}
}
else {
$count{'ncRNA'}++;
$count{'byGroup'}->{$group}->{'ncRNA'}++;
my $seqobj = Bio::Seq->new(
-seq => $strseq,
-display_id => 'ncRNA'.'|'.$mRNAid.'|'.$parent{$mRNAid}.'|'.$chr,
-description => ''
);
unless (exists $out{'ncRNA'}) {
$out{'ncRNA'} = Bio::SeqIO->new(
-file => ">$outdir/$outprefix".'ncRNA'.'.fa',
-format => 'fasta'
);
}
$out{'ncRNA'}->write_seq($seqobj);
}
}
}
}
}
if ($statsfile) {
open(STATS, ">", $statsfile) or $LOGGER->logdie("$!");
print STATS "
*** GENERAL REPORT ***
Nº of scaffolds scanned.: $count{'scaffold'}
Nº of genes found.......: $count{'gene'}
Nº of mRNAs found.......: $count{'mRNA'}
5p CDS 3p...........: $count{'5pCDS3pmRNA'}
5p CDS..............: $count{'5pCDSmRNA'}
CDS 3p..............: $count{'CDS3pmRNA'}
CDS.................: $count{'CDSmRNA'}
Nº of ncRNAs found......: $count{'ncRNA'}
";
print STATS "
*** REPORT BY GROUP ***
";
foreach my $group (sort {$a cmp $b} keys %{$count{'byGroup'}} ) {
print STATS "
* $group
Nº of scaffolds scanned.: $count{'byGroup'}->{$group}->{'scaffold'}
Nº of genes found.......: $count{'byGroup'}->{$group}->{'gene'}
Nº of mRNAs found.......: $count{'byGroup'}->{$group}->{'mRNA'}
5p CDS 3p...........: $count{'byGroup'}->{$group}->{'5pCDS3pmRNA'}
5p CDS..............: $count{'byGroup'}->{$group}->{'5pCDSmRNA'}
CDS 3p..............: $count{'byGroup'}->{$group}->{'CDS3pmRNA'}
CDS.................: $count{'byGroup'}->{$group}->{'CDSmRNA'}
Nº of ncRNAs found......: $count{'byGroup'}->{$group}->{'ncRNA'}
";
}
close(STATS);
}
# Subroutines
sub Usage {
my ($msg) = @_;
Readonly my $USAGE => <<"END_USAGE";
Daniel Guariz Pinheiro (dgpinheiro\@gmail.com)
(c)2012 Universidade de São Paulo
Usage
$0 [-h/--help] [-l/--level <LEVEL>]
Argument(s)
-h --help Help
-l --level Log level [Default: FATAL]
-g --genomefile Genome file
-d --genomedir Genome directory
-f --gff GFF file
-o --outdir Output directory
-p --outprefix Output filenames' prefix
-s --statsfile Output Statistics file
-m --threepminsize 3' minimum size (extends if possible) [Default: 0]
END_USAGE
print STDERR "\nERR: $msg\n\n" if $msg;
print STDERR qq[$0 ] . q[$Revision$] . qq[\n];
print STDERR $USAGE;
exit(1);
}