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1 #!/usr/bin/perl -w
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2 use strict;
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3
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4 #convert from master variant file to snp table (Webb format?)
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5 #new format for version 2.0, also different format for cancer normal pairs
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6 #set columns for 2.0 version Cancer format
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7 my $aCnt1 = 21;
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8 my $aCnt2 = 22;
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9
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10 #snp table format:
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11 #1. chr
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12 #2. position (0 based)
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13 #3. ref allele
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14 #4. second allele
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15 #5. overall quality
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16 #foreach individual (6-9, 10-13, ...)
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17 #a. count of allele in 3
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18 #b. count of allele in 4
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19 #c. genotype call (-1, or count of ref allele)
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20 #d. quality of genotype call (quality of non-ref allele from masterVar)
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21
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22 if (!@ARGV) {
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23 print "usage: master2gd_snp.pl masterVar.txt[.gz|.bz2] [-tab=snpTable.txt -addColsOnly -build=hg19 -name=na ] > newSnpTable.txt\n";
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24 exit;
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25 }
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26
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27 my $in = shift @ARGV;
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28 my $tab;
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29 my $tabOnly;
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30 my $build;
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31 my $name;
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32 foreach (@ARGV) {
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33 if (/-tab=(.*)/) { $tab = $1; }
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34 elsif (/-addColsOnly/) { $tabOnly = 1; }
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35 elsif (/-build=(.*)/) { $build = $1; }
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36 elsif (/-name=(.*)/) { $name = $1; }
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37 }
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38
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39 #WARNING loads snp table in memory, this could take > 1G ram
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40 my %old;
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41 my $colcnt = 0;
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42 my @head;
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43 if ($tab) {
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44 open(FH, $tab) or die "Couldn't open $tab, $!\n";
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45 while (<FH>) {
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46 chomp;
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47 if (/^#/) { push(@head, $_); next; }
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48 my @f = split(/\t/);
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49 $old{"$f[0]:$f[1]"} = join("\t", @f);
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50 $colcnt = scalar @f;
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51 }
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52 close FH or die "Couldn't close $tab, $!\n";
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53 }
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54
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55 if ($in =~ /.gz$/) {
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56 open(FH, "zcat $in |") or die "Couldn't open $in, $!\n";
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57 }elsif ($in =~ /.bz2$/) {
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58 open(FH, "bzcat $in |") or die "Couldn't open $in, $!\n";
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59 }else {
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60 open(FH, $in) or die "Couldn't open $in, $!\n";
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61 }
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62 prepHeader();
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63 if (@head) { #keep old header, add new?
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64 print join("\n", @head), "\n";
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65 }
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66 while (<FH>) {
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67 chomp;
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68 #FORMAT_VERSION 2.0
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69 if (/^#FORMAT_VERSION\s+1\./) {
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70 $aCnt1 = 16;
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71 $aCnt2 = 17;
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72 }
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73 if (/^#/) { next; }
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74 if (/^>/) { next; } #headers
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75 if (/^\s*$/) { next; }
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76 my @f = split(/\t/);
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77 if (!$f[6]) { next; } #WHAT? most likely still zipped?
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78 if ($f[6] ne 'snp') { next; } #table only has substitutions
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79 if ($f[5] eq 'het-alt') { next; } #skip heterozygous with no ref match
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80 if ($f[5] =~ /(hom|het)/) { #zygosity #haploid chrX and chrY?
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81 my $a = $f[7]; #reference allele
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82 my $a2;
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83 my $freq;
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84 my $freq2;
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85 my $sc = -1;
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86 my $alt;
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87 my $g = 1; #genotype == ref allele count
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88 if ($f[8] eq $f[9]) { #should be homozygous?
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89 $a2 = $f[8];
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90 $g = 0;
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91 if ($f[10] && $f[10] ne '') { $sc = $f[10]; }#is this the best one to use? or smallest?
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92 }else {
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93 if ($a ne $f[8]) { $a2 = $f[8]; $alt = 8; }
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94 elsif ($a ne $f[9]) { $a2 = $f[9]; $alt = 9; }
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95 }
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96 if (defined $f[10] && defined $f[11] && $alt) { #VAF score in 2.0 format
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97 if ($f[$alt+2] && $f[$alt+2] ne '') { $sc = $f[$alt+2]; }
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98 }
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99 #version 1.12 columns 16 & 17, version 2.0 Cancer columns 21 & 22
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100 if (defined $f[$aCnt1] && defined $f[$aCnt2] && $alt) {
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101 if ($alt == 8) {
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102 $freq = $f[$aCnt2];
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103 $freq2 = $f[$aCnt1];
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104 }elsif ($alt == 9) {
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105 $freq = $f[$aCnt1];
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106 $freq2 = $f[$aCnt2];
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107 }
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108 }elsif (defined $f[$aCnt1]) {
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109 $freq = 0;
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110 $freq2 = $f[$aCnt1];
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111 }
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112 #if starting a new table or new SNP in old table
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113 #add option to only build on current table?
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114 if (!$tab) {
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115 print "$f[2]\t$f[3]\t$a\t$a2\t-1";
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116 }elsif (!$tabOnly && !exists $old{"$f[2]:$f[3]"}) {
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117 print "$f[2]\t$f[3]\t$a\t$a2\t-1";
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118 }elsif (exists $old{"$f[2]:$f[3]"}) {
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119 print $old{"$f[2]:$f[3]"};
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120 $old{"$f[2]:$f[3]"} = ''; #unset so we know it is printed
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121 }elsif ($tabOnly && !exists $old{"$f[2]:$f[3]"}) {
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122 next; #skip this one entirely
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123 }
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124 if ($colcnt && !exists $old{"$f[2]:$f[3]"}) {
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125 #new SNP pad for missing individuals
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126 my $i = 5;
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127 while ($i < $colcnt) {
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128 print "\t-1\t-1\t-1\t-1";
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129 $i += 4;
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130 }
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131 }
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132 #add columns for individual
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133 print "\t$freq\t$freq2\t$g\t$sc\n";
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134 }elsif ($f[5] eq 'hap') {
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135 my $g = 0;
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136 my $freq = 0;
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137 my $freq2 = 0;
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138 if (defined $f[10]) { $freq2 = $f[10]; }
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139 my $sc = -1;
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140 if (defined $f[$aCnt1] && $f[$aCnt1] ne '') { $sc = $f[$aCnt1]; }
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141 if ($f[8]) {
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142 if (!$tab) {
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143 print "$f[2]\t$f[3]\t$f[7]\t$f[8]\t-1";
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144 }elsif (!$tabOnly && !exists $old{"$f[2]:$f[3]"}) {
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145 print "$f[2]\t$f[3]\t$f[7]\t$f[8]\t-1";
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146 }elsif (exists $old{"$f[2]:$f[3]"}) {
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147 print $old{"$f[2]:$f[3]"};
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148 $old{"$f[2]:$f[3]"} = ''; #unset so we know it is printed
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149 }elsif ($tabOnly && !exists $old{"$f[2]:$f[3]"}) {
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150 next; #skip this one entirely
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151 }
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152 if ($colcnt && !exists $old{"$f[2]:$f[3]"}) {
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153 #new SNP pad for missing individuals
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154 my $i = 5;
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155 while ($i < $colcnt) {
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156 print "\t-1\t-1\t-1\t-1";
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157 $i += 4;
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158 }
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159 }
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160 #add columns for individual
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161 print "\t$freq\t$freq2\t$g\t$sc\n";
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162 }
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163 }
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164 }
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165 close FH or die "Couldn't close $in, $!\n";
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166
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167 #if adding to a snp table, now we need to finish those not in the latest set
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168 foreach my $k (keys %old) {
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169 if ($old{$k} ne '') { #not printed yet
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170 print $old{$k}, "\t-1\t-1\t-1\t-1\n"; #plus blank for this one
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171 }
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172 }
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173
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174 exit;
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175
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176 #parse old header and add or create new
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177 sub prepHeader {
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178 if (!$build) { $build = 'hg19'; } #set default
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179 my @cnames;
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180 my @ind;
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181 my $n;
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182 if (@head) { #parse previous header
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183 my $h = join("", @head); #may split between lines
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184 if ($h =~ /"column_names":\[(.*?)\]/) {
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185 my @t = split(/,/, $1);
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186 foreach (@t) { s/"//g; }
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187 @cnames = @t;
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188 $n = $cnames[$#cnames];
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189 $n =~ s/Q//;
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190 $n++;
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191 }
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192 if ($h =~ /"dbkey":"(.*?)"/) { $build = $1; }
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193 if ($h =~ /"individuals":\[(.*)\]/) {
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194 my $t = $1;
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195 $t =~ s/\]\].*/]/; #remove if there is more categories
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196 @ind = split(/,/, $t);
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197 }
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198 }else { #start new header
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199 @cnames = ("chr", "pos", "A", "B", "Q");
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200 $n = 1;
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201 }
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202 #add current
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203 if (!$name) { $name= 'na'; }
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204 my $stcol = $colcnt + 1;
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205 if ($stcol == 1) { $stcol = 6; } #move past initial columns
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206 push(@ind, "[\"$name\",$stcol]");
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207 push(@cnames, "${n}A", "${n}B", "${n}G", "${n}Q");
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208 #reassign head
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209 undef @head;
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210 foreach (@cnames) { $_ = "\"$_\""; } #quote name
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211 $head[0] = "#{\"column_names\":[" . join(",", @cnames) . "],";
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212 $head[1] = "#\"individuals\":[" . join(",", @ind) . "],";
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213 $head[2] = "#\"dbkey\":\"$build\",\"pos\":2,\"rPos\":2,\"ref\":1,\"scaffold\":1,\"species\":\"$build\"}";
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214 }
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215 ####End
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216
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217 ##example header
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218 #{"column_names":["chr","pos","A","B","Q","1A","1B","1G","1Q","2A","2B","2G","2Q","3A","3B","3G","3Q","4A","4B","4G","4Q","5A","5B","5G","5Q","6A","6B","6G","6Q","7A","7B","7G","7Q","8A","8B","8G",
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219 #"8Q","9A","9B","9G","9Q","10A","10B","10G","10Q"],"dbkey":"hg19","individuals":[["Boh_15M",6],["Boh_19M",10],["Paya_27F",14],["Paya_2F",18],["Paya_32F",22],["Ruil_2M",26],["Ruil_36M",30],["Ruil_3M",
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220 #34],["Ruil_40",38],["Ruil_47F",42]],"pos":2,"rPos":2,"ref":1,"scaffold":1,"species":"hg19"}
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221 #chr1 10290 C T 46.4 0 2 0 7 1 2 0 4 3 2 1 22 0 0 -1 0 1 0 1 4 0 2 0 7 0 0 -1 0 2 3 1 14 0 1 0 4 1 1 1 6
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