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annotate phyloconversion/fasta2phytab.pl @ 0:5b9a38ec4a39 draft default tip

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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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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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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
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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3 use strict;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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4
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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5 use FindBin;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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6 use lib "$FindBin::Bin/lib";
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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7 use Bio::DB::Fasta;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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8 use Bio::SeqIO;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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9 use Bio::Seq;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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10
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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11 #inputs
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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12 my $infile=shift(@ARGV);
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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13 my $species=shift(@ARGV);
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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14 my $partition=shift(@ARGV);
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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15 my $delpipes=shift(@ARGV);
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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16 my $fromfasta;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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17 #for debugging xml input
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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18 #print "$infile $species $partition $delpipes\n";
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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19 #exit;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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20
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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21 if($species eq "from fasta"){
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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22 $fromfasta=1;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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23 }
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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24 my $seqid;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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25 # open infile fasta file
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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26 my $in_obj = Bio::SeqIO->new(-file => $infile, '-format' =>'fasta');
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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27
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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28 #no warnings 'uninitialized'; #Was getting error on one fasta for uninitialized sequences. Never could track down why and used this as a workaround
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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29 while (my $seq = $in_obj->next_seq() ) {
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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30 my $sequence = $seq->seq;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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31 $seqid = $seq->id;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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32 if($delpipes eq 'yes'){
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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33 $seqid =~ s/\|/_/g;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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34 }
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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35 if($fromfasta){
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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36 $species = $seqid;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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37 }
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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38 $sequence =~ s/\n//g;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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39 print $species."\t".$partition."\t".$seqid."\t".$sequence."\n";
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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40 }