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comparison Snmf.pl @ 1:395c7ab476a6 draft

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Uploaded
author dereeper
date Tue, 21 Jun 2016 19:38:29 -0400
parents 9a1729b89405
children 84becfc8c803
comparison
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0:9a1729b89405 1:395c7ab476a6
33 if ( !$input || !$output || !$kmin || !$kmax || !$directory || !$threshold); 33 if ( !$input || !$output || !$kmin || !$kmax || !$directory || !$threshold);
34 34
35 35
36 my $PLINK_EXE = "plink"; 36 my $PLINK_EXE = "plink";
37 37
38 system("$PLINK_EXE --vcf $input --allow-extra-chr --recode-vcf --out $directory/input >>$directory/plink.log 2>&1"); 38 system("$PLINK_EXE --vcf $input --allow-extra-chr --recode vcf-fid --out $directory/input >>$directory/logs 2>&1");
39 39
40 system("vcf2geno $directory/input.vcf $directory/polymorphisms.geno >>$directory/vcf2geno.log 2>&1"); 40 system("vcf2geno $directory/input.vcf $directory/polymorphisms.geno >>$directory/logs 2>&1");
41 41
42 42
43 my $ind_cmd = `grep '#CHROM' $input`; 43 my $ind_cmd = `grep '#CHROM' $input`;
44 chomp($ind_cmd); 44 chomp($ind_cmd);
45 my @individuals = split(/\t/,$ind_cmd);shift @individuals;shift @individuals;shift @individuals;shift @individuals;shift @individuals;shift @individuals;shift @individuals;shift @individuals; 45 my @individuals = split(/\t/,$ind_cmd);shift @individuals;shift @individuals;shift @individuals;shift @individuals;shift @individuals;shift @individuals;shift @individuals;shift @individuals;