22 lines
697 B
Perl
Executable File
22 lines
697 B
Perl
Executable File
#!/usr/bin/env perl
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use warnings;
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use strict;
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if (scalar(@ARGV) != 1) {
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die("Usage: annotate_single_maf.pl <maf>\n");
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}
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my ($maf) = @ARGV;
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# TODO: Have a common checkout of https://svn/CancerGenomeAnalysis
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# or a compiled version of this matlab program like Firehose uses.
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my $cmd = "matlab <<STOP\n" .
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"addpath /humgen/gsa-hphome1/kshakir/src/cga_matlab_r7169/mike" . "\n" .
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"addpath /humgen/gsa-hphome1/kshakir/src/cga_matlab_r7169/seq" . "\n" .
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"addpath /humgen/gsa-hphome1/kshakir/src/cga_matlab_r7169" . "\n" .
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"annotate_maflite('$maf', '$maf.annotated')" . "\n" .
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"quit" . "\n" .
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"STOP" . "\n";
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system($cmd) == 0 or die();
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