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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 pgSnp file to snp table (Webb format?)
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5
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6 #snp table format:
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7 #1. chr
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8 #2. position (0 based)
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9 #3. ref allele
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10 #4. second allele
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11 #5. overall quality
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12 #foreach individual (6-9, 10-13, ...)
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13 #a. count of allele in 3
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14 #b. count of allele in 4
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15 #c. genotype call (-1, or count of ref allele)
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16 #d. quality of genotype call (quality of non-ref allele from masterVar)
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17
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18 if (!@ARGV) {
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19 print "usage: pgSnp2gd_snp.pl file.pgSnp[.gz|.bz2] [-tab=snpTable.txt -addColsOnly -build=hg19 -name=na -ref=#1based -chr=#1based ] > newSnpTable.txt\n";
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20 exit;
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21 }
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22
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23 my $in = shift @ARGV;
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24 my $tab;
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25 my $tabOnly;
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26 my $build;
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27 my $name;
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28 my $ref;
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29 my $binChr = 1; #position of chrom column, indicates if bin is added
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30 foreach (@ARGV) {
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31 if (/-tab=(.*)/) { $tab = $1; }
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32 elsif (/-addColsOnly/) { $tabOnly = 1; }
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33 elsif (/-build=(.*)/) { $build = $1; }
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34 elsif (/-name=(.*)/) { $name = $1; }
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35 elsif (/-ref=(\d+)/) { $ref = $1 - 1; } #go to index
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36 elsif (/-chr=(\d+)/) { $binChr = $1; }
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37 }
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38
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39 if ($binChr == 2 && $ref) { $ref--; } #shift over by 1, we will delete bin
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40 if ((!$tab or !$tabOnly) && !$ref) {
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41 print "Error the reference allele must be in a column in the file if not just adding to a previous SNP table.\n";
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42 exit;
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43 }
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44
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45 #WARNING loads snp table in memory, this could take > 1G ram
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46 my %old;
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47 my $colcnt = 0;
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48 my @head;
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49 if ($tab) {
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50 open(FH, $tab) or die "Couldn't open $tab, $!\n";
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51 while (<FH>) {
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52 chomp;
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53 if (/^#/) { push(@head, $_); next; }
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54 my @f = split(/\t/);
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55 $old{"$f[0]:$f[1]"} = join("\t", @f);
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56 $colcnt = scalar @f;
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57 }
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58 close FH or die "Couldn't close $tab, $!\n";
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59 }
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60
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61 if ($in =~ /.gz$/) {
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62 open(FH, "zcat $in |") or die "Couldn't open $in, $!\n";
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63 }elsif ($in =~ /.bz2$/) {
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64 open(FH, "bzcat $in |") or die "Couldn't open $in, $!\n";
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65 }else {
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66 open(FH, $in) or die "Couldn't open $in, $!\n";
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67 }
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68 prepHeader();
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69 if (@head) { #keep old header, add new?
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70 print join("\n", @head), "\n";
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71 }
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72 while (<FH>) {
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73 chomp;
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74 if (/^#/) { next; }
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75 if (/^\s*$/) { next; }
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76 my @f = split(/\t/);
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77 if ($binChr == 2) { #must have a bin column prepended on the beginning
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78 shift @f; #delete it
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79 }
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80 if (!$f[3]) { next; } #WHAT? most likely still zipped?
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81 if ($f[4] > 2) { next; } #can only do cases of 2 alleles
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82 if ($f[2] == $f[1] or $f[2] - $f[1] != 1) { next; } #no indels
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83 if ($f[3] =~ /-/) { next; } #no indels
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84 #if creating a new table need the reference allele in a column
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85 if (%old && $old{"$f[0]:$f[1]"}) {
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86 my @o = split(/\t/, $old{"$f[0]:$f[1]"});
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87 my $freq = 0;
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88 my $freq2 = 0;
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89 my $sc;
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90 my $g = 1; #genotype == ref allele count
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91 if ($f[4] == 1) { #should be homozygous
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92 if ($f[3] eq $o[2]) { $g = 2; $freq = $f[5]; }
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93 elsif ($f[3] eq $o[3]) { $g = 0; $freq2 = $f[5]; }
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94 else { next; } #doesn't match either allele, skip
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95 $sc = $f[6];
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96 }else {
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97 my $a = 0; #index of a alleles, freq, scores
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98 my $b = 1; #same for b
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99 my @all = split(/\//, $f[3]);
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100 if ($o[2] ne $all[0] && $o[2] ne $all[1]) { next; } #must match one
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101 if ($o[3] ne $all[0] && $o[3] ne $all[1]) { next; }
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102 if ($o[2] eq $all[1]) { #switch indexes
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103 $a = 1;
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104 $b = 0;
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105 }
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106 my @fr = split(/,/, $f[5]);
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107 $freq = $fr[$a];
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108 $freq2 = $fr[$b];
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109 my @s = split(/,/, $f[6]);
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110 $sc = $s[$b];
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111 }
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112 #print old
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113 print $old{"$f[0]:$f[1]"};
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114 #add new columns
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115 print "\t$freq\t$freq2\t$g\t$sc\n";
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116 $old{"$f[0]:$f[1]"} = '';
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117 }elsif (!$tabOnly) { #new table, or don't have this SNP
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118 #need reference allele
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119 if ($f[3] !~ /$f[$ref]/ && $f[4] == 2) { next; } #no reference allele
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120 my $freq = 0;
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121 my $freq2 = 0;
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122 my $sc;
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123 my $g = 1; #genotype == ref allele count
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124 my $alt;
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125 if ($f[4] == 1) { #should be homozygous
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126 if ($f[3] eq $f[$ref]) { $g = 2; $freq = $f[5]; $alt = 'N'; }
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127 else { $g = 0; $freq2 = $f[5]; $alt = $f[3]; } #matches alternate
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128 $sc = $f[6];
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129 }else {
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130 my $a = 0; #index of a alleles, freq, scores
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131 my $b = 1; #same for b
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132 my @all = split(/\//, $f[3]);
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133 if ($f[$ref] ne $all[0] && $f[$ref] ne $all[1]) { next; } #must match one
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134 if ($f[$ref] eq $all[1]) { #switch indexes
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135 $a = 1;
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136 $b = 0;
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137 }
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138 my @fr = split(/,/, $f[5]);
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139 $freq = $fr[$a];
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140 $freq2 = $fr[$b];
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141 my @s = split(/,/, $f[6]);
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142 $sc = $s[$b];
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143 $alt = $all[$b];
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144 }
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145 #print initial columns
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146 print "$f[0]\t$f[1]\t$f[$ref]\t$alt\t-1";
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147 #pad for other individuals if needed
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148 my $i = 5;
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149 while ($i < $colcnt) {
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150 print "\t-1\t-1\t-1\t-1";
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151 $i += 4;
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152 }
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153 #add new columns
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154 print "\t$freq\t$freq2\t$g\t$sc\n";
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155 }
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156 }
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157 close FH or die "Couldn't close $in, $!\n";
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158
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159 #if adding to a snp table, now we need to finish those not in the latest set
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160 foreach my $k (keys %old) {
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161 if ($old{$k} ne '') { #not printed yet
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162 print $old{$k}, "\t-1\t-1\t-1\t-1\n"; #plus blank for this one
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163 }
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164 }
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165
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166 exit;
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167
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168 #parse old header and add or create new
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169 sub prepHeader {
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170 if (!$build) { $build = 'hg19'; } #set default
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171 my @cnames;
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172 my @ind;
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173 my $n;
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174 if (@head) { #parse previous header
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175 my $h = join("", @head); #may split between lines
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176 if ($h =~ /"column_names":\[(.*?)\]/) {
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177 my @t = split(/,/, $1);
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178 foreach (@t) { s/"//g; }
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179 @cnames = @t;
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180 $n = $cnames[$#cnames];
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181 $n =~ s/Q//;
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182 $n++;
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183 }
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184 if ($h =~ /"dbkey":"(.*?)"/) { $build = $1; }
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185 if ($h =~ /"individuals":\[(.*)\]/) {
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186 my $t = $1;
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187 $t =~ s/\]\].*/]/; #remove if there is more categories
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188 @ind = split(/,/, $t);
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189 }
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190 }else { #start new header
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191 @cnames = ("chr", "pos", "A", "B", "Q");
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192 $n = 1;
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193 }
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194 #add current
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195 if (!$name) { $name= 'na'; }
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196 my $stcol = $colcnt + 1;
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197 if ($stcol == 1) { $stcol = 6; } #move past initial columns
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198 push(@ind, "[\"$name\",$stcol]");
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199 push(@cnames, "${n}A", "${n}B", "${n}G", "${n}Q");
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200 #reassign head
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201 undef @head;
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202 foreach (@cnames) { $_ = "\"$_\""; } #quote name
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203 $head[0] = "#{\"column_names\":[" . join(",", @cnames) . "],";
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204 $head[1] = "#\"individuals\":[" . join(",", @ind) . "],";
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205 $head[2] = "#\"dbkey\":\"$build\",\"pos\":2,\"rPos\":2,\"ref\":1,\"scaffold\":1,\"species\":\"$build\"}";
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206 }
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207 ####End
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208
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