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1 #!/usr/bin/perl
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2
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3 # Wrapper script written by: Roger Ngo, Sam Min and Todd H. Oakley, UCSB
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4
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5 use warnings;
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6 use strict;
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7 use Cwd;
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8
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9 my $dir = getcwd();
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10
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11 my $iAssemblerBinPath = '/home/galaxy/pkgs/iAssembler';
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12 my $iAssemblerToolPath = '/home/galaxy/galaxy-dist/tools/iAssembler';
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13
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14 #iAssembler_wrapper.pl -i $input -e $maxlength -h $minoverlap -p $minpercent ...example
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15
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16 my $input=$ARGV[1];
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17 my $maxlength=$ARGV[3];
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18 my $minoverlap=$ARGV[5];
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19 my $minpercent=$ARGV[7];
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20
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21 open my $file, '<', $iAssemblerToolPath."\/increment.txt";
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22 my $increment = <$file>;
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23 $increment = int($increment);
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24 close $file;
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25
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26 my $temp = $increment;
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27
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28 open(UPDATE, '>'.$iAssemblerToolPath."\/increment.txt");
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29 $increment = $increment + 1;
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30 print UPDATE $increment;
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31 close(UPDATE);
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32
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33 qx/cp $input $iAssemblerBinPath\/input.$temp.fasta/;
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34
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35 chdir($iAssemblerBinPath);
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36
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37 qx/$iAssemblerBinPath\/iAssembler.pl -i input.$temp.fasta -e $maxlength -h $minoverlap -p $minpercent 2>$dir\/log/;
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38
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39 chdir("$dir");
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40
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41 qx/cp $iAssemblerBinPath\/input.$temp.fasta_output\/unigene_seq.fasta unigene_seq.fasta/;
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42
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43 qx/rm -rf $iAssemblerBinPath\/input.$temp.*/;
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