Mercurial > repos > rogerngo > iassembler

comparison iAssembler_wrapper.pl @ 4:00edccfa662b draft

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iAssembler perl wrapper
author rogerngo
date Wed, 16 May 2012 00:24:20 -0400
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3:cfe16849421e 4:00edccfa662b
1 #!/usr/bin/perl
2
3 # Wrapper script written by: Roger Ngo, Sam Min and Todd H. Oakley, UCSB
4
5 use warnings;
6 use strict;
7 use Cwd;
8
9 my $dir = getcwd();
10
11 my $iAssemblerBinPath = '/labdata/nfs/galaxy/pkgs/iAssembler';
12 my $iAssemblerToolPath = '/labdata/nfs/galaxy/galaxy-dist/tools/iAssembler';
13
14 #iAssembler_wrapper.pl -i $input -e $maxlength -h $minoverlap -p $minpercent ...example
15
16 my $input=$ARGV[1];
17 my $maxlength=$ARGV[3];
18 my $minoverlap=$ARGV[5];
19 my $minpercent=$ARGV[7];
20
21 open my $file, '<', $iAssemblerToolPath."\/increment.txt";
22 my $increment = <$file>;
23 $increment = int($increment);
24 close $file;
25
26 my $temp = $increment;
27
28 open(UPDATE, '>'.$iAssemblerToolPath."\/increment.txt");
29 $increment = $increment + 1;
30 print UPDATE $increment;
31 close(UPDATE);
32
33 qx/cp $input $iAssemblerBinPath\/input.$temp.fasta/;
34
35 chdir($iAssemblerBinPath);
36
37 qx/$iAssemblerBinPath\/iAssembler.pl -i input.$temp.fasta -e $maxlength -h $minoverlap -p $minpercent/;
38
39 chdir("$dir");
40
41 qx/cp $iAssemblerBinPath\/input.$temp.fasta_output\/unigene_seq.fasta unigene_seq.fasta/;
42
43 qx/rm -rf $iAssemblerBinPath\/input.$temp.*/;