Mercurial > repos > ucsb-phylogenetics > osiris_phylogenetics
comparison phyloconversion/gb2phytab.pl @ 0:5b9a38ec4a39 draft default tip
First commit of old repositories
| author | osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> |
|---|---|
| date | Tue, 11 Mar 2014 12:19:13 -0700 |
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| children |
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| -1:000000000000 | 0:5b9a38ec4a39 |
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| 1 #!/usr/bin/perl -w | |
| 2 use strict; | |
| 3 | |
| 4 use Bio::SeqIO; | |
| 5 | |
| 6 | |
| 7 my $datafile = $ARGV[0]; | |
| 8 my $outfile = $ARGV[1]; | |
| 9 | |
| 10 open FILE, ">$outfile" or die "Cannot Write File\n"; | |
| 11 | |
| 12 my $seqio_object = Bio::SeqIO->new(-file => $datafile,'-format' => 'genbank'); | |
| 13 | |
| 14 while(my $seq_object = $seqio_object->next_seq){ | |
| 15 my $organism = $seq_object->species->binomial(); | |
| 16 $organism =~ s/ /_/g; | |
| 17 my $accession = $seq_object->id; | |
| 18 for my $feat_object ($seq_object->get_SeqFeatures) { | |
| 19 if ($feat_object->primary_tag eq "CDS") { | |
| 20 my $sequence = $feat_object->spliced_seq->seq; | |
| 21 if ($feat_object->has_tag('gene')) { | |
| 22 for my $name ($feat_object->get_tag_values('product')){ | |
| 23 $name =~ s/ /_/g; | |
| 24 print FILE $organism."\t".$name."\t".$accession."\t".$sequence."\n"; | |
| 25 } | |
| 26 } | |
| 27 }elsif ($feat_object->primary_tag eq "misc_RNA") { | |
| 28 my $sequence = $feat_object->spliced_seq->seq; | |
| 29 if ($feat_object->has_tag('product')) { | |
| 30 for my $name ($feat_object->get_tag_values('product')){ | |
| 31 $name =~ s/ /_/g; | |
| 32 print FILE $organism."\t".$name."\t".$accession."\t".$sequence."\n"; | |
| 33 } | |
| 34 } | |
| 35 } | |
| 36 | |
| 37 } | |
| 38 } | |
| 39 close FILE; | |
| 40 | |
| 41 |