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comparison admixture/Admixture.pl @ 4:fb274c4ae95a draft

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author dereeper
date Fri, 20 Feb 2015 10:11:57 -0500
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3:d953daae86f6 4:fb274c4ae95a
1 #!/usr/bin/perl
2
3 use strict;
4 use Switch;
5 use Getopt::Long;
6 use Bio::SeqIO;
7
8 my $usage = qq~Usage:$0 <args> [<opts>]
9 where <args> are:
10 -i, --input <input HAPMAP>
11 -o, --output <output>
12 -k, --kmin <K min. int>
13 -m, --maxK <K max. int>
14 -d, --directory <temporary directory>
15 -p, --path <path to executables>
16 ~;
17 $usage .= "\n";
18
19 my ($input,$output,$kmin,$kmax,$directory,$path);
20
21
22 GetOptions(
23 "input=s" => \$input,
24 "output=s" => \$output,
25 "kmin=s" => \$kmin,
26 "maxK=s" => \$kmax,
27 "directory=s" => \$directory,
28 "path=s" => \$path
29 );
30
31
32 die $usage
33 if ( !$input || !$output || !$kmin || !$kmax || !$directory || !$path);
34
35 if ($kmin =~/^(\d+)\s*$/){
36 $kmin = $1;
37 }
38 else{
39 die "Error: kmin must be an integer\n";
40 }
41 if ($kmax =~/^(\d+)\s*$/){
42 $kmax = $1;
43 }
44 else{
45 die "Error: kmax must be an integer\n";
46 }
47
48
49 ######################
50 # create map file
51 ######################
52 open(my $M,">$directory/input.map");
53 open(my $H,$input);
54 <$H>;
55 while(<$H>)
56 {
57 my @infos = split(/\t/,$_);
58 print $M $infos[2] . "\t" . $infos[0] . "\t" . "0" . "\t" . $infos[3] . "\n";
59 }
60 close($H);
61 close($M);
62
63 ######################
64 # create ped file
65 ######################
66 system("$path/transpose.awk $input >$directory/input.ped.2");
67
68 open(my $P,">$directory/input.ped");
69 open(my $P2,"$directory/input.ped.2");
70 my $n = 0;
71 my $ind_num = 0;
72 my @individus;
73 while(<$P2>)
74 {
75 $n++;
76 if ($n > 11)
77 {
78 my $line = $_;
79 $line =~s/N/0/g;
80 if (/^([^\s]+)\s+(.*)$/)
81 {
82 $ind_num++;
83 my $ind = $1;
84 push(@individus,$ind);
85 my $genoyping_line = $2;
86 print $P "$ind $ind_num 0 0 1 2";
87 my @genotypes = split(/\s/,$genoyping_line);
88 foreach my $genotype(@genotypes)
89 {
90 $genotype =~s/N/0/g;
91 my @alleles = split("",$genotype);
92 print $P " " . join(" ",@alleles);
93 }
94
95 print $P "\n";
96 }
97 }
98 }
99 close($P2);
100 close($P);
101
102 unlink("$directory/input.ped.2");
103
104 system("plink --file $directory/input --out $directory/out --make-bed --noweb >>$directory/plink.log 2>&1");
105
106
107 ###################################
108 # launch admixture for different K
109 ###################################
110 my %errors;
111 for (my $k = $kmin; $k <= $kmax; $k++)
112 {
113 system("admixture --cv $directory/out.bed $k >>$directory/log.$k 2>&1");
114 my $cv_error_line = `grep -h CV $directory/log.$k`;
115 if ($cv_error_line =~/: (\d+\.*\d*)$/)
116 {
117 $errors{$1} = $k;
118 }
119 system("cat $directory/log.$k >>$directory/logs");
120 system("echo '\n\n====================================\n\n' >>$directory/logs");
121 system("cat out.$k.Q >>$directory/outputs.Q");
122 system("echo '\n\n====================================\n\n' >>$directory/outputs.Q");
123 system("cat out.$k.P >>$directory/outputs.P");
124 system("echo '\n\n====================================\n\n' >>$directory/outputs.P");
125 }
126
127 my @sorted_errors = sort {$a<=>$b} keys(%errors);
128 my $best_K = $errors{@sorted_errors[0]};
129
130
131 #system("cp -rf out.$best_K.Q $directory/output");
132
133 open(BEST1,"out.$best_K.Q");
134 open(BEST2,">$directory/output");
135 print BEST2 "<Covariate>\n";
136 print BEST2 "<Trait>";
137 for (my $j=1;$j<=$best_K;$j++)
138 {
139 print BEST2 " Q" . $j;
140 }
141 print BEST2 "\n";
142 my $i = 0;
143 while(<BEST1>)
144 {
145 my $line = $_;
146 $line =~s/ /\t/g;
147 my $ind = $individus[$i];
148 print BEST2 "$ind ";
149 print BEST2 $line;
150 $i++;
151 }
152 close(BEST1);
153 close(BEST2);
154
155 system("cp -rf $directory/log.$best_K $directory/log");
156
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