Mercurial > repos > ucsb-phylogenetics > osiris_phylogenetics

annotate alignment/fasconcat.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
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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
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5 my $fasconcatPath = '/home/galaxy/galaxy_dist/tools/fasconcat/FASconCAT_v1.0.pl';
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6
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7 my $outputFormat = $ARGV[0];
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8 my $limit = $ARGV[1];
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9 my $outFormat;
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10 my @inputFiles;
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11
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12 for(my $i = 2; $i <= $limit; $i++) {
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13 $inputFiles[$i] = " -f ";
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14 $inputFiles[$i] = $inputFiles[$i].$ARGV[$i];
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15 }
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16
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17 if($outputFormat == "0") {
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18 $outFormat = "";
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19 }
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20 elsif($outputFormat == "1") {
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21 $outFormat = " -p -p";
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22 }
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23 else {
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24 $outFormat = " -n -n";
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25 }
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27 my $run = qx/$fasconcatPath -s -i "@inputfiles" $outFormat /;
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28
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29 if($outputFormat == "0") {
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30 qx/cp FcC_smatrix.fas output/;
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31 }
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32 elsif($outputFormat == "1") {
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33 qx/cp FcC_smatrix.phy output/;
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34 }
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35 else {
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36 qx/cp FcC_smatrix.nex output/;
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37 }