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