Mercurial > repos > dereeper > sniplay
annotate hapmap2mlmm/HapmapToMLMMFiles.pl @ 11:15b23cdde685 draft
planemo upload commit 305985afd3b7c3d47f531149c2f1a279af2d12aa-dirty
| author | dereeper |
|---|---|
| date | Fri, 20 Apr 2018 09:04:25 -0400 |
| parents | c6640c49fd01 |
| children |
| rev | line source |
|---|---|
| 9 | 1 #!/usr/bin/perl |
| 2 | |
| 3 use strict; | |
| 4 | |
| 5 use Getopt::Long; | |
| 6 | |
| 7 my $usage = qq~Usage:$0 <args> [<opts>] | |
| 8 where <args> are: | |
| 9 -h, --hapmap <Hapmap input file> | |
| 10 -m, --map <Map output file> | |
| 11 -g, --geno <Genotype output file> | |
| 12 -p, --path <Path for transpose executable> | |
| 13 ~; | |
| 14 $usage .= "\n"; | |
| 15 | |
| 16 my ($hapmap,$map,$geno,$path); | |
| 17 | |
| 18 | |
| 19 GetOptions( | |
| 20 "geno=s" => \$geno, | |
| 21 "map=s" => \$map, | |
| 22 "hapmap=s" => \$hapmap, | |
| 23 "path=s" => \$path, | |
| 24 ); | |
| 25 | |
| 26 | |
| 27 die $usage | |
| 28 if ( !$geno || !$map || !$hapmap || !$path); | |
| 29 | |
| 30 my $TRANSPOSE_EXE = "$path/transpose.awk"; | |
| 31 | |
| 32 my @snps; | |
| 33 my %chrom_pos; | |
| 34 my $num_line = 0; | |
| 35 open(my $O,">geno_transposed"); | |
| 36 open(my $H,$hapmap); | |
| 37 while(<$H>) | |
| 38 { | |
| 39 $num_line++; | |
| 40 my $line = $_; | |
| 41 chomp($line); | |
| 42 $line =~s/\r//g; | |
| 43 $line =~s/\n//g; | |
| 44 my @infos = split(/\t/,$line); | |
| 45 if ($num_line == 1) | |
| 46 { | |
| 47 print $O "Ind_id"; | |
| 48 for (my $i = 11; $i <= $#infos; $i++) | |
| 49 { | |
| 50 my $individual = $infos[$i]; | |
| 51 print $O " " . $individual; | |
| 52 } | |
| 53 print $O "\n"; | |
| 54 } | |
| 55 elsif ($num_line > 1) | |
| 56 { | |
| 57 my $snp = $infos[0]; | |
| 58 my $variation = $infos[1]; | |
| 59 my %scores; | |
| 60 if ($variation =~/(\w)\/(\w)/) | |
| 61 { | |
| 62 my $allele1 = $1; | |
| 63 my $allele2 = $2; | |
| 64 $scores{$allele1} = 0; | |
| 65 $scores{$allele2} = 1; | |
| 66 } | |
| 67 my $chrom = $infos[2]; | |
| 68 my $pos = $infos[3]; | |
| 69 $chrom_pos{$snp}{"chrom"} = $chrom; | |
| 70 $chrom_pos{$snp}{"pos"} = $pos; | |
| 71 push(@snps,$snp); | |
| 72 print $O "$snp"; | |
| 73 for (my $i = 11; $i <= $#infos; $i++) | |
| 74 { | |
| 75 my $genotype = $infos[$i]; | |
| 76 my @alleles = split("",$genotype); | |
| 77 if ($genotype ne "NN") | |
| 78 { | |
| 79 my $score = $scores{$alleles[0]} + $scores{$alleles[1]}; | |
| 80 print $O " $score"; | |
| 81 } | |
| 82 else | |
| 83 { | |
| 84 print $O " NA"; | |
| 85 } | |
| 86 } | |
| 87 print $O "\n"; | |
| 88 } | |
| 89 } | |
| 90 close($H); | |
| 91 close($O); | |
| 92 | |
| 93 open(my $M,">$map"); | |
| 94 print $M "SNP Chr Pos\n"; | |
| 95 foreach my $snp(@snps) | |
| 96 { | |
| 97 print $M "$snp " . $chrom_pos{$snp}{"chrom"} . " ". $chrom_pos{$snp}{"pos"} . "\n"; | |
| 98 } | |
| 99 close($M); | |
| 100 | |
|
10
c6640c49fd01
planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents:
9
diff
changeset
|
101 system("gawk -E $TRANSPOSE_EXE geno_transposed >geno_transposed2"); |
| 9 | 102 |
| 103 open(my $F,">$geno"); | |
| 104 open(my $G,"geno_transposed2"); | |
| 105 while(<$G>) | |
| 106 { | |
| 107 my $line = $_; | |
| 108 $line =~s/ /\t/g; | |
| 109 print $F $line; | |
| 110 } | |
| 111 close($G); | |
| 112 close($F); | |
| 113 | |
| 114 unlink("geno_transposed"); | |
| 115 unlink("geno_transposed2"); | |
| 116 | |
| 117 |