Mercurial > repos > yusuf > generate_genomeid
diff generateID.pl @ 0:7e4eb6957b8a default tip
initial commit for genomeid tool
author | Yusuf Ali <ali@yusuf.email> |
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date | Thu, 12 Mar 2015 09:49:46 -0600 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/generateID.pl Thu Mar 12 09:49:46 2015 -0600 @@ -0,0 +1,46 @@ +#!/usr/bin/perl + +use strict; +use warnings; +use Getopt::Long; + +use Bio::Seq::GenomeID qw(generate_id); + +my ($outFile, $inFile, $type, $index, $hg); +my ($noise, $baq, $sex, $ucn, $ref, $name); + +GetOptions("o=s"=> \$outFile, + "n=f"=>\$noise, + "hg=s"=> \$hg, + "b=i"=> \$baq, + "s=s"=> \$sex, + "u=s"=> \$ucn, + "r=s"=> \$ref, + "type=s"=> \$type, + "file=s"=> \$inFile, + "sN=s"=> \$name, +); +$ucn = ($ucn eq "true")? 1:0; $sex = ($sex eq "true")?1:0; $ref = ($ref eq "true")?1:0; + +my %obj; +$obj{'type'} = $type; $obj{'file'} = $inFile; +$obj{'ucn'} = $ucn; $obj{'sex'} = $sex; $obj{'ref'} = $ref; +$obj{'noise'} = $noise; $obj{'baq'} = $baq; + +if($type eq "tbi"){ + `tabix -p vcf $inFile`; +} + + +if($hg ne "none"){ + $obj{'hg'} = $hg; +} + +if( defined $name ){ + $obj{'sampleName'} = $name; +} + +my $genomeID = generate_id(%obj); +open(my $fh, '>', $outFile); +print $fh $genomeID; +close $fh;