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annotate alignment/jmodeltest.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
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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1 #!/usr/bin/perl
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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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4 use warnings;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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5 use Cwd;
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6
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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7 my $jmodeltest_path = '/home/galaxy/pkgs/jmodeltest';
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8 my $jmodeltest_tool = '/home/galaxy/galaxy-dist/tools/jmodeltest';
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9
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10 my $galaxyPath = getcwd();
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11
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12 my $input = $ARGV[0];
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13 my $likelihoodStyle = $ARGV[1];
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14 my $likelihood = $ARGV[2];
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15 my $criterion = $ARGV[3];
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16 my $extension = $ARGV[4];
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17
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18 # open increment file
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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19 open my $file, '<', $jmodeltest_tool."\/increment.txt";
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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20 my $increment = <$file>;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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21 $increment = int($increment);
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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22 close $file;
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23
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24 # get the current increment
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25 my $temp = $increment;
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26
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27 # update the increment
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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28 open(UPDATE, '>'.$jmodeltest_tool."\/increment.txt");
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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29 $increment = $increment + 1;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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30 print UPDATE $increment;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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31 close(UPDATE);
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32
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33 chdir("$jmodeltest_path");
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34
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35 if($likelihoodStyle eq "-t") {
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36 #only need to copy input file
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37 qx/cp $input input.$temp.$extension/;
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38
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39 #print qx/ls/;
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40
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41 qx/java -jar jModelTest.jar -d input.$temp.$extension $likelihoodStyle $likelihood -$criterion > $galaxyPath\/output.txt 2> $galaxyPath\/err_log.txt/;
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42 qx/rm input.$temp.*/;
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43 }
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44 elsif($likelihoodStyle eq "-u") {
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45 #copy input file
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46 qx/cp $input input.$temp.$extension/;
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47 #copy likelihood tree
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48 qx/cp $likelihood likelihood.$temp.tre/;
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49 qx/java -jar jModelTest.jar -d input.$temp.$extension $likelihoodStyle likelihood.$temp.tre -$criterion > $galaxyPath\/output.txt 2> $galaxyPath\/err_log.txt/;
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50
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51 # clean up
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52 qx/rm input.$temp.*/;
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53 qx/rm likelihood.$temp.tre/;
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54
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55 }
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56
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57 chdir("$galaxyPath");