Mercurial > repos > miller-lab > snp_analysis_conversion
comparison snp_analysis_conversion/pgSnp2gd_snp.pl @ 0:3871157bc013
Initial upload to toolshed.g2 via UI.
| author | cathy |
|---|---|
| date | Tue, 28 May 2013 17:01:14 -0400 |
| parents | |
| children |
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| -1:000000000000 | 0:3871157bc013 |
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| 1 #!/usr/bin/perl -w | |
| 2 use strict; | |
| 3 | |
| 4 #convert from pgSnp file to snp table (Webb format?) | |
| 5 | |
| 6 #snp table format: | |
| 7 #1. chr | |
| 8 #2. position (0 based) | |
| 9 #3. ref allele | |
| 10 #4. second allele | |
| 11 #5. overall quality | |
| 12 #foreach individual (6-9, 10-13, ...) | |
| 13 #a. count of allele in 3 | |
| 14 #b. count of allele in 4 | |
| 15 #c. genotype call (-1, or count of ref allele) | |
| 16 #d. quality of genotype call (quality of non-ref allele from masterVar) | |
| 17 | |
| 18 if (!@ARGV) { | |
| 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"; | |
| 20 exit; | |
| 21 } | |
| 22 | |
| 23 my $in = shift @ARGV; | |
| 24 my $tab; | |
| 25 my $tabOnly; | |
| 26 my $build; | |
| 27 my $name; | |
| 28 my $ref; | |
| 29 my $binChr = 1; #position of chrom column, indicates if bin is added | |
| 30 foreach (@ARGV) { | |
| 31 if (/-tab=(.*)/) { $tab = $1; } | |
| 32 elsif (/-addColsOnly/) { $tabOnly = 1; } | |
| 33 elsif (/-build=(.*)/) { $build = $1; } | |
| 34 elsif (/-name=(.*)/) { $name = $1; } | |
| 35 elsif (/-ref=(\d+)/) { $ref = $1 - 1; } #go to index | |
| 36 elsif (/-chr=(\d+)/) { $binChr = $1; } | |
| 37 } | |
| 38 | |
| 39 if ($binChr == 2 && $ref) { $ref--; } #shift over by 1, we will delete bin | |
| 40 if ((!$tab or !$tabOnly) && !$ref) { | |
| 41 print "Error the reference allele must be in a column in the file if not just adding to a previous SNP table.\n"; | |
| 42 exit; | |
| 43 } | |
| 44 | |
| 45 #WARNING loads snp table in memory, this could take > 1G ram | |
| 46 my %old; | |
| 47 my $colcnt = 0; | |
| 48 my @head; | |
| 49 if ($tab) { | |
| 50 open(FH, $tab) or die "Couldn't open $tab, $!\n"; | |
| 51 while (<FH>) { | |
| 52 chomp; | |
| 53 if (/^#/) { push(@head, $_); next; } | |
| 54 my @f = split(/\t/); | |
| 55 $old{"$f[0]:$f[1]"} = join("\t", @f); | |
| 56 $colcnt = scalar @f; | |
| 57 } | |
| 58 close FH or die "Couldn't close $tab, $!\n"; | |
| 59 } | |
| 60 | |
| 61 if ($in =~ /.gz$/) { | |
| 62 open(FH, "zcat $in |") or die "Couldn't open $in, $!\n"; | |
| 63 }elsif ($in =~ /.bz2$/) { | |
| 64 open(FH, "bzcat $in |") or die "Couldn't open $in, $!\n"; | |
| 65 }else { | |
| 66 open(FH, $in) or die "Couldn't open $in, $!\n"; | |
| 67 } | |
| 68 prepHeader(); | |
| 69 if (@head) { #keep old header, add new? | |
| 70 print join("\n", @head), "\n"; | |
| 71 } | |
| 72 while (<FH>) { | |
| 73 chomp; | |
| 74 if (/^#/) { next; } | |
| 75 if (/^\s*$/) { next; } | |
| 76 my @f = split(/\t/); | |
| 77 if ($binChr == 2) { #must have a bin column prepended on the beginning | |
| 78 shift @f; #delete it | |
| 79 } | |
| 80 if (!$f[3]) { next; } #WHAT? most likely still zipped? | |
| 81 if ($f[4] > 2) { next; } #can only do cases of 2 alleles | |
| 82 if ($f[2] == $f[1] or $f[2] - $f[1] != 1) { next; } #no indels | |
| 83 if ($f[3] =~ /-/) { next; } #no indels | |
| 84 #if creating a new table need the reference allele in a column | |
| 85 if (%old && $old{"$f[0]:$f[1]"}) { | |
| 86 my @o = split(/\t/, $old{"$f[0]:$f[1]"}); | |
| 87 my $freq = 0; | |
| 88 my $freq2 = 0; | |
| 89 my $sc; | |
| 90 my $g = 1; #genotype == ref allele count | |
| 91 if ($f[4] == 1) { #should be homozygous | |
| 92 if ($f[3] eq $o[2]) { $g = 2; $freq = $f[5]; } | |
| 93 elsif ($f[3] eq $o[3]) { $g = 0; $freq2 = $f[5]; } | |
| 94 else { next; } #doesn't match either allele, skip | |
| 95 $sc = $f[6]; | |
| 96 }else { | |
| 97 my $a = 0; #index of a alleles, freq, scores | |
| 98 my $b = 1; #same for b | |
| 99 my @all = split(/\//, $f[3]); | |
| 100 if ($o[2] ne $all[0] && $o[2] ne $all[1]) { next; } #must match one | |
| 101 if ($o[3] ne $all[0] && $o[3] ne $all[1]) { next; } | |
| 102 if ($o[2] eq $all[1]) { #switch indexes | |
| 103 $a = 1; | |
| 104 $b = 0; | |
| 105 } | |
| 106 my @fr = split(/,/, $f[5]); | |
| 107 $freq = $fr[$a]; | |
| 108 $freq2 = $fr[$b]; | |
| 109 my @s = split(/,/, $f[6]); | |
| 110 $sc = $s[$b]; | |
| 111 } | |
| 112 #print old | |
| 113 print $old{"$f[0]:$f[1]"}; | |
| 114 #add new columns | |
| 115 print "\t$freq\t$freq2\t$g\t$sc\n"; | |
| 116 $old{"$f[0]:$f[1]"} = ''; | |
| 117 }elsif (!$tabOnly) { #new table, or don't have this SNP | |
| 118 #need reference allele | |
| 119 if ($f[3] !~ /$f[$ref]/ && $f[4] == 2) { next; } #no reference allele | |
| 120 my $freq = 0; | |
| 121 my $freq2 = 0; | |
| 122 my $sc; | |
| 123 my $g = 1; #genotype == ref allele count | |
| 124 my $alt; | |
| 125 if ($f[4] == 1) { #should be homozygous | |
| 126 if ($f[3] eq $f[$ref]) { $g = 2; $freq = $f[5]; $alt = 'N'; } | |
| 127 else { $g = 0; $freq2 = $f[5]; $alt = $f[3]; } #matches alternate | |
| 128 $sc = $f[6]; | |
| 129 }else { | |
| 130 my $a = 0; #index of a alleles, freq, scores | |
| 131 my $b = 1; #same for b | |
| 132 my @all = split(/\//, $f[3]); | |
| 133 if ($f[$ref] ne $all[0] && $f[$ref] ne $all[1]) { next; } #must match one | |
| 134 if ($f[$ref] eq $all[1]) { #switch indexes | |
| 135 $a = 1; | |
| 136 $b = 0; | |
| 137 } | |
| 138 my @fr = split(/,/, $f[5]); | |
| 139 $freq = $fr[$a]; | |
| 140 $freq2 = $fr[$b]; | |
| 141 my @s = split(/,/, $f[6]); | |
| 142 $sc = $s[$b]; | |
| 143 $alt = $all[$b]; | |
| 144 } | |
| 145 #print initial columns | |
| 146 print "$f[0]\t$f[1]\t$f[$ref]\t$alt\t-1"; | |
| 147 #pad for other individuals if needed | |
| 148 my $i = 5; | |
| 149 while ($i < $colcnt) { | |
| 150 print "\t-1\t-1\t-1\t-1"; | |
| 151 $i += 4; | |
| 152 } | |
| 153 #add new columns | |
| 154 print "\t$freq\t$freq2\t$g\t$sc\n"; | |
| 155 } | |
| 156 } | |
| 157 close FH or die "Couldn't close $in, $!\n"; | |
| 158 | |
| 159 #if adding to a snp table, now we need to finish those not in the latest set | |
| 160 foreach my $k (keys %old) { | |
| 161 if ($old{$k} ne '') { #not printed yet | |
| 162 print $old{$k}, "\t-1\t-1\t-1\t-1\n"; #plus blank for this one | |
| 163 } | |
| 164 } | |
| 165 | |
| 166 exit; | |
| 167 | |
| 168 #parse old header and add or create new | |
| 169 sub prepHeader { | |
| 170 if (!$build) { $build = 'hg19'; } #set default | |
| 171 my @cnames; | |
| 172 my @ind; | |
| 173 my $n; | |
| 174 if (@head) { #parse previous header | |
| 175 my $h = join("", @head); #may split between lines | |
| 176 if ($h =~ /"column_names":\[(.*?)\]/) { | |
| 177 my @t = split(/,/, $1); | |
| 178 foreach (@t) { s/"//g; } | |
| 179 @cnames = @t; | |
| 180 $n = $cnames[$#cnames]; | |
| 181 $n =~ s/Q//; | |
| 182 $n++; | |
| 183 } | |
| 184 if ($h =~ /"dbkey":"(.*?)"/) { $build = $1; } | |
| 185 if ($h =~ /"individuals":\[(.*)\]/) { | |
| 186 my $t = $1; | |
| 187 $t =~ s/\]\].*/]/; #remove if there is more categories | |
| 188 @ind = split(/,/, $t); | |
| 189 } | |
| 190 }else { #start new header | |
| 191 @cnames = ("chr", "pos", "A", "B", "Q"); | |
| 192 $n = 1; | |
| 193 } | |
| 194 #add current | |
| 195 if (!$name) { $name= 'na'; } | |
| 196 my $stcol = $colcnt + 1; | |
| 197 if ($stcol == 1) { $stcol = 6; } #move past initial columns | |
| 198 push(@ind, "[\"$name\",$stcol]"); | |
| 199 push(@cnames, "${n}A", "${n}B", "${n}G", "${n}Q"); | |
| 200 #reassign head | |
| 201 undef @head; | |
| 202 foreach (@cnames) { $_ = "\"$_\""; } #quote name | |
| 203 $head[0] = "#{\"column_names\":[" . join(",", @cnames) . "],"; | |
| 204 $head[1] = "#\"individuals\":[" . join(",", @ind) . "],"; | |
| 205 $head[2] = "#\"dbkey\":\"$build\",\"pos\":2,\"rPos\":2,\"ref\":1,\"scaffold\":1,\"species\":\"$build\"}"; | |
| 206 } | |
| 207 ####End | |
| 208 |