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comparison master2gd_snp.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
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1:1d8b23a21735 2:35c20b109be5
1 #!/usr/bin/perl -w
2 use strict;
3
4 #convert from master variant file to snp table (Webb format?)
5 #new format for version 2.0, also different format for cancer normal pairs
6 #set columns for 2.0 version Cancer format
7 my $aCnt1 = 21;
8 my $aCnt2 = 22;
9
10 #snp table format:
11 #1. chr
12 #2. position (0 based)
13 #3. ref allele
14 #4. second allele
15 #5. overall quality
16 #foreach individual (6-9, 10-13, ...)
17 #a. count of allele in 3
18 #b. count of allele in 4
19 #c. genotype call (-1, or count of ref allele)
20 #d. quality of genotype call (quality of non-ref allele from masterVar)
21
22 if (!@ARGV) {
23 print "usage: master2gd_snp.pl masterVar.txt[.gz|.bz2] [-tab=snpTable.txt -addColsOnly -build=hg19 -name=na ] > newSnpTable.txt\n";
24 exit;
25 }
26
27 my $in = shift @ARGV;
28 my $tab;
29 my $tabOnly;
30 my $build;
31 my $name;
32 foreach (@ARGV) {
33 if (/-tab=(.*)/) { $tab = $1; }
34 elsif (/-addColsOnly/) { $tabOnly = 1; }
35 elsif (/-build=(.*)/) { $build = $1; }
36 elsif (/-name=(.*)/) { $name = $1; }
37 }
38
39 #WARNING loads snp table in memory, this could take > 1G ram
40 my %old;
41 my $colcnt = 0;
42 my @head;
43 if ($tab) {
44 open(FH, $tab) or die "Couldn't open $tab, $!\n";
45 while (<FH>) {
46 chomp;
47 if (/^#/) { push(@head, $_); next; }
48 my @f = split(/\t/);
49 $old{"$f[0]:$f[1]"} = join("\t", @f);
50 $colcnt = scalar @f;
51 }
52 close FH or die "Couldn't close $tab, $!\n";
53 }
54
55 if ($in =~ /.gz$/) {
56 open(FH, "zcat $in |") or die "Couldn't open $in, $!\n";
57 }elsif ($in =~ /.bz2$/) {
58 open(FH, "bzcat $in |") or die "Couldn't open $in, $!\n";
59 }else {
60 open(FH, $in) or die "Couldn't open $in, $!\n";
61 }
62 prepHeader();
63 if (@head) { #keep old header, add new?
64 print join("\n", @head), "\n";
65 }
66 while (<FH>) {
67 chomp;
68 #FORMAT_VERSION 2.0
69 if (/^#FORMAT_VERSION\s+1\./) {
70 $aCnt1 = 16;
71 $aCnt2 = 17;
72 }
73 if (/^#/) { next; }
74 if (/^>/) { next; } #headers
75 if (/^\s*$/) { next; }
76 my @f = split(/\t/);
77 if (!$f[6]) { next; } #WHAT? most likely still zipped?
78 if ($f[6] ne 'snp') { next; } #table only has substitutions
79 if ($f[5] eq 'het-alt') { next; } #skip heterozygous with no ref match
80 if ($f[5] =~ /(hom|het)/) { #zygosity #haploid chrX and chrY?
81 my $a = $f[7]; #reference allele
82 my $a2;
83 my $freq;
84 my $freq2;
85 my $sc = -1;
86 my $alt;
87 my $g = 1; #genotype == ref allele count
88 if ($f[8] eq $f[9]) { #should be homozygous?
89 $a2 = $f[8];
90 $g = 0;
91 if ($f[10] && $f[10] ne '') { $sc = $f[10]; }#is this the best one to use? or smallest?
92 }else {
93 if ($a ne $f[8]) { $a2 = $f[8]; $alt = 8; }
94 elsif ($a ne $f[9]) { $a2 = $f[9]; $alt = 9; }
95 }
96 if (defined $f[10] && defined $f[11] && $alt) { #VAF score in 2.0 format
97 if ($f[$alt+2] && $f[$alt+2] ne '') { $sc = $f[$alt+2]; }
98 }
99 #version 1.12 columns 16 & 17, version 2.0 Cancer columns 21 & 22
100 if (defined $f[$aCnt1] && defined $f[$aCnt2] && $alt) {
101 if ($alt == 8) {
102 $freq = $f[$aCnt2];
103 $freq2 = $f[$aCnt1];
104 }elsif ($alt == 9) {
105 $freq = $f[$aCnt1];
106 $freq2 = $f[$aCnt2];
107 }
108 }elsif (defined $f[$aCnt1]) {
109 $freq = 0;
110 $freq2 = $f[$aCnt1];
111 }
112 #if starting a new table or new SNP in old table
113 #add option to only build on current table?
114 if (!$tab) {
115 print "$f[2]\t$f[3]\t$a\t$a2\t-1";
116 }elsif (!$tabOnly && !exists $old{"$f[2]:$f[3]"}) {
117 print "$f[2]\t$f[3]\t$a\t$a2\t-1";
118 }elsif (exists $old{"$f[2]:$f[3]"}) {
119 print $old{"$f[2]:$f[3]"};
120 $old{"$f[2]:$f[3]"} = ''; #unset so we know it is printed
121 }elsif ($tabOnly && !exists $old{"$f[2]:$f[3]"}) {
122 next; #skip this one entirely
123 }
124 if ($colcnt && !exists $old{"$f[2]:$f[3]"}) {
125 #new SNP pad for missing individuals
126 my $i = 5;
127 while ($i < $colcnt) {
128 print "\t-1\t-1\t-1\t-1";
129 $i += 4;
130 }
131 }
132 #add columns for individual
133 print "\t$freq\t$freq2\t$g\t$sc\n";
134 }elsif ($f[5] eq 'hap') {
135 my $g = 0;
136 my $freq = 0;
137 my $freq2 = 0;
138 if (defined $f[10]) { $freq2 = $f[10]; }
139 my $sc = -1;
140 if (defined $f[$aCnt1] && $f[$aCnt1] ne '') { $sc = $f[$aCnt1]; }
141 if ($f[8]) {
142 if (!$tab) {
143 print "$f[2]\t$f[3]\t$f[7]\t$f[8]\t-1";
144 }elsif (!$tabOnly && !exists $old{"$f[2]:$f[3]"}) {
145 print "$f[2]\t$f[3]\t$f[7]\t$f[8]\t-1";
146 }elsif (exists $old{"$f[2]:$f[3]"}) {
147 print $old{"$f[2]:$f[3]"};
148 $old{"$f[2]:$f[3]"} = ''; #unset so we know it is printed
149 }elsif ($tabOnly && !exists $old{"$f[2]:$f[3]"}) {
150 next; #skip this one entirely
151 }
152 if ($colcnt && !exists $old{"$f[2]:$f[3]"}) {
153 #new SNP pad for missing individuals
154 my $i = 5;
155 while ($i < $colcnt) {
156 print "\t-1\t-1\t-1\t-1";
157 $i += 4;
158 }
159 }
160 #add columns for individual
161 print "\t$freq\t$freq2\t$g\t$sc\n";
162 }
163 }
164 }
165 close FH or die "Couldn't close $in, $!\n";
166
167 #if adding to a snp table, now we need to finish those not in the latest set
168 foreach my $k (keys %old) {
169 if ($old{$k} ne '') { #not printed yet
170 print $old{$k}, "\t-1\t-1\t-1\t-1\n"; #plus blank for this one
171 }
172 }
173
174 exit;
175
176 #parse old header and add or create new
177 sub prepHeader {
178 if (!$build) { $build = 'hg19'; } #set default
179 my @cnames;
180 my @ind;
181 my $n;
182 if (@head) { #parse previous header
183 my $h = join("", @head); #may split between lines
184 if ($h =~ /"column_names":\[(.*?)\]/) {
185 my @t = split(/,/, $1);
186 foreach (@t) { s/"//g; }
187 @cnames = @t;
188 $n = $cnames[$#cnames];
189 $n =~ s/Q//;
190 $n++;
191 }
192 if ($h =~ /"dbkey":"(.*?)"/) { $build = $1; }
193 if ($h =~ /"individuals":\[(.*)\]/) {
194 my $t = $1;
195 $t =~ s/\]\].*/]/; #remove if there is more categories
196 @ind = split(/,/, $t);
197 }
198 }else { #start new header
199 @cnames = ("chr", "pos", "A", "B", "Q");
200 $n = 1;
201 }
202 #add current
203 if (!$name) { $name= 'na'; }
204 my $stcol = $colcnt + 1;
205 if ($stcol == 1) { $stcol = 6; } #move past initial columns
206 push(@ind, "[\"$name\",$stcol]");
207 push(@cnames, "${n}A", "${n}B", "${n}G", "${n}Q");
208 #reassign head
209 undef @head;
210 foreach (@cnames) { $_ = "\"$_\""; } #quote name
211 $head[0] = "#{\"column_names\":[" . join(",", @cnames) . "],";
212 $head[1] = "#\"individuals\":[" . join(",", @ind) . "],";
213 $head[2] = "#\"dbkey\":\"$build\",\"pos\":2,\"rPos\":2,\"ref\":1,\"scaffold\":1,\"species\":\"$build\"}";
214 }
215 ####End
216
217 ##example header
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",
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",
220 #34],["Ruil_40",38],["Ruil_47F",42]],"pos":2,"rPos":2,"ref":1,"scaffold":1,"species":"hg19"}
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