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comparison Admixture.pl @ 6:3f66f32dc5d9 draft

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planemo upload
author dereeper
date Wed, 13 Apr 2016 07:53:25 -0400
parents 97c9c8daa3c3
children c3ebf600f975
comparison
equal deleted inserted replaced
5:97c9c8daa3c3 6:3f66f32dc5d9
65 # launch admixture for different K 65 # launch admixture for different K
66 ################################### 66 ###################################
67 my %errors; 67 my %errors;
68 for (my $k = $kmin; $k <= $kmax; $k++) 68 for (my $k = $kmin; $k <= $kmax; $k++)
69 { 69 {
70 system("/apps/www/sniplay.cirad.fr/tools/admixture/admixture_linux-1.23/admixture --cv $input.bed $k >>$directory/log.$k 2>&1"); 70 system("admixture --cv $input.bed $k >>$directory/log.$k 2>&1");
71 my $cv_error_line = `grep -h CV $directory/log.$k`; 71 my $cv_error_line = `grep -h CV $directory/log.$k`;
72 if ($cv_error_line =~/: (\d+\.*\d*)$/) 72 if ($cv_error_line =~/: (\d+\.*\d*)$/)
73 { 73 {
74 $errors{$1} = $k; 74 $errors{$1} = $k;
75 } 75 }