Mercurial > repos > ucsb-phylogenetics > osiris_phylogenetics
annotate alignment/fasconcat.pl @ 0:5b9a38ec4a39 draft default tip
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author | osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> |
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date | Tue, 11 Mar 2014 12:19:13 -0700 |
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1 #!/usr/bin/perl |
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2 |
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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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26 |
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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 } |