Mercurial > repos > miller-lab > snp_analysis_conversion

annotate master2pg.pl @ 2:35c20b109be5

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Retrying upload with "bare" tarball (i.e. one without a top containing directory).
author cathy
date Tue, 28 May 2013 17:54:02 -0400
parents
children
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2
35c20b109be5 Retrying upload with "bare" tarball (i.e. one without a top containing directory).
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1 #!/usr/bin/perl -w
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2 use strict;
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3
35c20b109be5 Retrying upload with "bare" tarball (i.e. one without a top containing directory).
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4 #convert from master variant file to pgSnp
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5 my $snpsOnly = 1; #flag for if doing SNPs or indels
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6 my $addRef = 0; #flag whether to append ref allele
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7 if (@ARGV && $ARGV[0] eq 'indel') { shift @ARGV; $snpsOnly = 0; }
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8 if (@ARGV && $ARGV[0] eq 'addRef') { shift @ARGV; $addRef = 1; }
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9 if (!@ARGV) {
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10 print STDERR "usage: master2pg.pl [indel addRef] infile.masterVar > outfile.pgSnp\n";
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11 exit;
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12 }
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13 my $in = shift @ARGV;
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14 open(FH, $in) or die "Couldn't open input file $in, $!\n";
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15
35c20b109be5 Retrying upload with "bare" tarball (i.e. one without a top containing directory).
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16 while (<FH>) {
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17 chomp;
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18 if (/^#/) { next; }
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19 if (/^>/) { next; } #headers
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20 if (/^\s*$/) { next; }
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21 my @f = split(/\t/);
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22 if (!$f[5]) { next; } #WHAT? most likely still zipped?
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23 if ($f[5] =~ /(hom|het)/) { #zygosity #haploid chrX and chrY?
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24 #only get snps for now
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25 if ($snpsOnly && $f[6] eq 'snp') { #varType
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26 my $a;
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27 my $c = 2;
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28 my $freq = 0; #set defaults
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29 my $sc = 0;
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30 if ($f[8] eq $f[9]) { #should be homozygous?
35c20b109be5 Retrying upload with "bare" tarball (i.e. one without a top containing directory).
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31 $a = $f[8];
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32 $c = 1;
35c20b109be5 Retrying upload with "bare" tarball (i.e. one without a top containing directory).
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33 }else {
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34 $a = "$f[8]/$f[9]";
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35 $sc = "0,0"; #set defaults in case not included
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36 $freq = '0,0';
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37 }
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38 if (defined $f[10] && $f[10] eq '') { $f[10] = 0; }
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39 if (defined $f[11] && $f[11] eq '') { $f[11] = 0; }
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40 if (defined $f[10] && $c == 1) {
35c20b109be5 Retrying upload with "bare" tarball (i.e. one without a top containing directory).
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41 $sc = $f[10];
35c20b109be5 Retrying upload with "bare" tarball (i.e. one without a top containing directory).
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42 }elsif (defined $f[10] && defined $f[11] && $c == 2) {
35c20b109be5 Retrying upload with "bare" tarball (i.e. one without a top containing directory).
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43 $sc = "$f[10],$f[11]";
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44 }
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45 if (defined $f[16] && $f[16] eq '') { $f[16] = 0; }
35c20b109be5 Retrying upload with "bare" tarball (i.e. one without a top containing directory).
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46 if (defined $f[17] && $f[17] eq '') { $f[17] = 0; }
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47 if (defined $f[16] && $c == 1) {
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48 $freq = $f[16];
35c20b109be5 Retrying upload with "bare" tarball (i.e. one without a top containing directory).
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49 }elsif (defined $f[16] && defined $f[17] && $c == 2) {
35c20b109be5 Retrying upload with "bare" tarball (i.e. one without a top containing directory).
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50 $freq = "$f[16],$f[17]";
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51 }
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52 print "$f[2]\t$f[3]\t$f[4]\t$a\t$c\t$freq\t$sc";
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53 if ($addRef) { print "\t$f[7]\n"; }
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54 else { print "\n"; }
35c20b109be5 Retrying upload with "bare" tarball (i.e. one without a top containing directory).
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55 }elsif (!$snpsOnly) {
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56 if ($f[8] =~ /^\s*$/) { undef $f[8]; }
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57 if ($f[9] =~ /^\s*$/) { undef $f[9]; }
35c20b109be5 Retrying upload with "bare" tarball (i.e. one without a top containing directory).
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58 my $a;
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59 my $c = 2;
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60 #do indels
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61 if ($f[6] eq "ins") {
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62 if (defined $f[8] && defined $f[9] && $f[8] eq $f[9]) { $a = $f[8]; $c = 1; }
35c20b109be5 Retrying upload with "bare" tarball (i.e. one without a top containing directory).
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63 elsif (defined $f[8] && defined $f[9] && $f[8] ne '?' && $f[9] ne '?') {
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64 $a = "$f[8]/$f[9]";
35c20b109be5 Retrying upload with "bare" tarball (i.e. one without a top containing directory).
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65 }elsif (!defined $f[8] && defined $f[9]) {
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66 $a = "$f[9]/-";
35c20b109be5 Retrying upload with "bare" tarball (i.e. one without a top containing directory).
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67 }elsif (defined $f[8] && !defined $f[9]) {
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68 $a = "$f[8]/-";
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69 }
35c20b109be5 Retrying upload with "bare" tarball (i.e. one without a top containing directory).
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70 }elsif ($f[6] eq "del") {
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71 if (!defined $f[8] && !defined $f[9]) {
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72 $a = '-'; #homozygous deletion
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73 $c = 1;
35c20b109be5 Retrying upload with "bare" tarball (i.e. one without a top containing directory).
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74 }elsif (!defined $f[8] && defined $f[9]) {
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75 $a = "$f[9]/-";
35c20b109be5 Retrying upload with "bare" tarball (i.e. one without a top containing directory).
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76 }elsif (defined $f[8] && !defined $f[9]) {
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77 $a = "$f[8]/-";
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78 }
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79 }elsif ($f[6] eq "sub") { #multiple nt substitutions
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80 if ($f[8] eq $f[9]) {
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81 $a = $f[8];
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82 $c = 1;
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83 }else {
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84 $a = "$f[8]/$f[9]";
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85 }
35c20b109be5 Retrying upload with "bare" tarball (i.e. one without a top containing directory).
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86 }elsif ($f[6] eq "complex") { #treat same as multi-nt sub
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87 if ($f[5] =~ /het-alt/ && !defined $f[8]) { $f[8] = '-'; }
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88 if ($f[5] =~ /het-alt/ && !defined $f[9]) { $f[9] = '-'; }
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89 if (defined $f[8] && defined $f[9] && $f[8] eq $f[9]) {
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90 $c = 1;
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91 $a = $f[8];
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92 }elsif (defined $f[8] && defined $f[9]) {
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93 $a = "$f[8]/$f[9]";
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94 }
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95 }
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96 my $sc = '0';
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97 my $freq = '0';
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98 if ($c == 2) { $sc = '0,0'; $freq = '0,0'; }
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99 if (defined $f[10] && $f[10] eq '') { $f[10] = 0; }
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100 if (defined $f[11] && $f[11] eq '') { $f[11] = 0; }
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101 if (defined $f[10] && $c == 1) {
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102 $sc = $f[10];
35c20b109be5 Retrying upload with "bare" tarball (i.e. one without a top containing directory).
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103 }elsif (defined $f[10] && defined $f[11] && $c == 2) {
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104 $sc = "$f[10],$f[11]";
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105 }
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106 if (defined $f[16] && $f[16] eq '') { $f[16] = 0; }
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107 if (defined $f[17] && $f[17] eq '') { $f[17] = 0; }
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108 if (defined $f[16] && $c == 1) {
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109 if ($f[16] eq '') { $f[16] = 0; }
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110 $freq = $f[16];
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111 }elsif (defined $f[16] && defined $f[17] && $c == 2) {
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112 $freq = "$f[16],$f[17]";
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113 }
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114 if ($a) {
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115 print "$f[2]\t$f[3]\t$f[4]\t$a\t$c\t$freq\t$sc";
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116 if ($addRef) { print "\t$f[7]\n"; }
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117 else { print "\n"; }
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118 }
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119 }
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120 }elsif ($f[5] eq 'hap' && $f[6] eq 'snp' && $snpsOnly) {
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121 my $c = 1;
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122 my $freq = '0';
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123 if (defined $f[10] && $f[10] ne '') { $freq = $f[10]; }
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124 my $sc = '0';
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125 if (defined $f[16] && $f[16] ne '') { $sc = $f[16]; }
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126 if ($f[8]) {
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127 print "$f[2]\t$f[3]\t$f[4]\t$f[8]\t$c\t$freq\t$sc";
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128 if ($addRef) { print "\t$f[7]\n"; }
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129 else { print "\n"; }
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130 }
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131 }elsif ($f[5] eq 'hap' && !$snpsOnly && $f[6] =~ /(del|ins|sub)/) {
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132 if ($f[8] =~ /^\s*$/) { undef $f[8]; }
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133 my $a;
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134 my $c = 1;
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135 #do indels
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136 if ($f[6] eq "ins") {
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137 $a = $f[8];
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138 }elsif ($f[6] eq "del") {
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139 $a = '-'; #deletion
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140 }elsif ($f[6] eq "sub") { #multiple nt substitutions
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141 $a = $f[8];
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142 }
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143 my $sc = '0';
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144 my $freq = '0';
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145 if (defined $f[10] && $f[10] ne '') { $sc = $f[10]; }
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146 if (defined $f[16] && $f[16] ne '') { $freq = $f[16]; }
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147 if ($a) {
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148 print "$f[2]\t$f[3]\t$f[4]\t$a\t$c\t$freq\t$sc";
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149 if ($addRef) { print "\t$f[7]\n"; }
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150 else { print "\n"; }
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151 }
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152 }
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153 }
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154
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155 close FH or die "Couldn't close $in, $!\n";
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156
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157 exit;