Mercurial > repos > ucsb-phylogenetics > osiris_phylogenetics

annotate phyloconversion/uniprotfasta2phytab.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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children
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 $partition=shift(@ARGV);
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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14 #my $delpipes=shift(@ARGV);
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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15 my $species;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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16
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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17 my $seqid;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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18 # open infile fasta file
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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19 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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20
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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21 while (my $seq = $in_obj->next_seq() ) {
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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22 my $sequence = $seq->seq;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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23 my @rawid = split(/\|/, $seq->id);
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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24 $seqid = $rawid[1];
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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25 # $seqid = $seq->id;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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26
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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27 $sequence =~ s/\n//g;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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28 $species = $seq->desc;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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29 #species Name is after OS=
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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30 $species =~ s/.+OS\=//;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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31 $species =~ s/.+OS\=//;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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32 #species Name is before GN= sometimes PE=
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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33 $species =~ s/ GN\=.+//;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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34 $species =~ s/ PE\=.+//;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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35 $species =~ s/ /_/g;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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36
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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37 print $species."\t".$partition."\t".$seqid."\t".$sequence."\n";
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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38 }