Mercurial > repos > ucsb-phylogenetics > osiris_phylogenetics

annotate phyloconversion/raxify_fasta.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:
rev   line source
0
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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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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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3
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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4 my $infile = $ARGV[0];
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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5 my $outfile = $ARGV[1];
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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6
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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7 open(IN, "$infile") or exit;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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8 open(OUT, ">$outfile") or exit;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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9
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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10 while (<IN>) {
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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11 my $line = $_;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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12 if($line =~ m/\>/ ){
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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13 $line=raxify($line);
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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14 }
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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15 if($line =~ m/\n/){
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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16 print OUT $line;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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17 }else{
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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18 print OUT $line."\n";
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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19 }
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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 close(IN);
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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22 close(OUT);
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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 sub raxify
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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 my $raxline = shift;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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27 $raxline = substr($raxline,0,51);
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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28 $raxline =~ s/\./_/g;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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29 $raxline =~ s/\|/_/g;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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30 $raxline =~ s/ /_/g;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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31 return $raxline;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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32 }