Mercurial > repos > ucsb-phylogenetics > osiris_phylogenetics

annotate phyloconversion/remove_gbs_dupes.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
parents
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 use strict;
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3
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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4 my $datafile = $ARGV[0];
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5 my $keepfile = $ARGV[1];
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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6 my $delfile = $ARGV[2];
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7 my $subsp = $ARGV[3];
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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8 my $var = $ARGV[4];
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9
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10 open (FILE,"<$datafile") or die "Cannot open file input file\n";
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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11 open (KFILE,">$keepfile") or die "Cannot open file $keepfile\n";
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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12 open (DFILE,">$delfile") or die "Cannot open file delfile\n";
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13
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14 my $keep = 1;
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15
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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16 while (<FILE>)
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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17 {
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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18 if($_ =~ m/_\d/){
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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19 $keep=0;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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20 }else{
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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21 if($subsp==1){
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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22 if($_ =~ m/subsp/){
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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23 $keep=0;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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24 }
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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25 }
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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26 if($var==1){
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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27 if($_ =~ m/_var_/){
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28 $keep=0;
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29 }
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30 }
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31 }
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32
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33 if($keep == 0){
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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34 print DFILE $_;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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35 }else{
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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36 print KFILE $_;
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37 }
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38 $keep=1; #reset variable. Default is keep
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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39 }
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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40 close FILE;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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41 close KFILE;
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42 close DFILE;
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43