Mercurial > repos > miller-lab > snp_analysis_conversion

comparison gd_snp2vcf.pl @ 2:35c20b109be5

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
comparison
equal deleted inserted replaced
1:1d8b23a21735 2:35c20b109be5
1 #!/usr/bin/perl -w
2 use strict;
3
4 #convert from gd_snp file to vcf file (with dbSNP fields)
5
6 #gd_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: gd_snp2vcf.pl file.gd_snp[.gz|.bz2] -geno=8[,12:16,20...] -handle=HANDLE -batch=BATCHNAME -ref=REFERENCEID [-bioproj=XYZ -biosamp=ABC -pop=POPID[,POPID2...] -chrCol=9 -posCol=9 ] > snpsForSubmission.vcf\n";
20 exit;
21 }
22
23 my $in = shift @ARGV;
24 my $genoCols = '';
25 my $handle;
26 my $batch;
27 my $bioproj;
28 my $biosamp;
29 my $ref;
30 my $pop;
31 my $cr = 0; #allow to use alternate reference?
32 my $cp = 1;
33 my $meta;
34 foreach (@ARGV) {
35 if (/-geno=([0-9,]+)/) { $genoCols .= "$1:"; }
36 elsif (/-handle=(.*)/) { $handle = $1; }
37 elsif (/-batch=(.*)/) { $batch = $1; }
38 elsif (/-bioproj=(.*)/) { $bioproj = $1; }
39 elsif (/-biosamp=(.*)/) { $biosamp = $1; }
40 elsif (/-ref=(.*)/) { $ref = $1; }
41 elsif (/-population=(\S+)/) { $pop = $1; }
42 elsif (/-chrCol=(\d+)/) { $cr = $1 - 1; }
43 elsif (/-posCol=(\d+)/) { $cp = $1 - 1; }
44 elsif (/-metaOut=(.*)/) { $meta = $1; }
45 }
46 if ($cr < 0 or $cp < 0) { die "ERROR the column numbers should be 1 based.\n"; }
47
48 #remove trailing delimiters
49 $genoCols =~ s/,:/:/g;
50 $genoCols =~ s/[,:]$//;
51
52 my @gnc = split(/,|:/, $genoCols);
53
54 if ($in =~ /.gz$/) {
55 open(FH, "zcat $in |") or die "Couldn't open $in, $!\n";
56 }elsif ($in =~ /.bz2$/) {
57 open(FH, "bzcat $in |") or die "Couldn't open $in, $!\n";
58 }else {
59 open(FH, $in) or die "Couldn't open $in, $!\n";
60 }
61 my @head = prepHeader();
62 if (@head) {
63 print join("\n", @head), "\n";
64 #now column headers
65 print "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO";
66 if (defined $pop) {
67 $pop =~ s/,$//;
68 my $t = $pop;
69 $t =~ s/,/\t/g;
70 print "\tFORMAT\t$t";
71 }
72 print "\n";
73 }
74 while (<FH>) {
75 chomp;
76 if (/^#/) { next; }
77 if (/^\s*$/) { next; }
78 my @f = split(/\t/);
79 #vcf columns: chrom pos id ref alt qual filter info
80 # info must have VRT=[0-9] 1==SNV 2=indel 6=NoVariation 8=MNV ...
81 my $vrt = 1;
82 if ($f[2] !~ /^[ACTG]$/ or $f[3] !~ /^[ACTG]$/) {
83 die "Sorry this can only do SNV's at this time\n";
84 }
85 if (scalar @gnc == 1) { #single genotype column
86 if (!defined $f[4] or $f[4] == -1) { $f[4] = '.'; }
87 if ($f[$gnc[0]-1] == 2) { $vrt = 6; } #reference match
88 print "$f[$cr]\t$f[$cp]\t$f[$cr];$f[$cp]\t$f[2]\t$f[3]\t$f[4]\t.\tVRT=$vrt\n";
89 #TODO? put read counts in comment?
90 }elsif ($pop) { #do as population
91 my @cols;
92 foreach my $gp (split(/:/,$genoCols)) { #foreach population
93 my @g = split(/,/, $gp);
94 my $totChrom = 2*(scalar @g);
95 my $totRef = 0;
96 foreach my $i (@g) { if ($f[$i-1] == -1) { next; } $totRef += $f[$i-1]; }
97 if ($totChrom == $totRef) { $vrt = 6; }
98 if ($totRef > $totChrom) { die "ERROR likely the wrong column was chosen for genotype\n"; }
99 my $altCnt = $totChrom - $totRef;
100 push(@cols, "$totChrom:$altCnt");
101 }
102 print "$f[$cr]\t$f[$cp]\t$f[$cr];$f[$cp]\t$f[2]\t$f[3]\t$f[4]\t.\tVRT=$vrt\tNA:AC\t", join("\t", @cols), "\n";
103 }else { #leave allele counts off
104 my $totChrom = 2*(scalar @gnc);
105 my $totRef = 0;
106 foreach my $i (@gnc) { if ($f[$i-1] == -1) { next; } $totRef += $f[$i-1]; }
107 if ($totChrom == $totRef) { $vrt = 6; }
108 print "$f[$cr]\t$f[$cp]\t$f[$cr];$f[$cp]\t$f[2]\t$f[3]\t$f[4]\t.\tVRT=$vrt\n";
109 }
110 }
111 close FH or die "Couldn't close $in, $!\n";
112
113 if ($meta) {
114 open(FH, ">", $meta) or die "Couldn't open $meta, $!\n";
115 print FH "TYPE: CONT\n",
116 "HANDLE: $handle\n",
117 "NAME: \n",
118 "FAX: \n",
119 "TEL: \n",
120 "EMAIL: \n",
121 "LAB: \n",
122 "INST: \n",
123 "ADDR: \n",
124 "||\n",
125 "TYPE: METHOD\n",
126 "HANDLE: $handle\n",
127 "ID: \n",
128 "METHOD_CLASS: Sequence\n",
129 "TEMPLATE_TYPE: \n",
130 "METHOD:\n",
131 "||\n";
132 if ($pop) {
133 my @p = split(/,/, $pop);
134 foreach my $t (@p) {
135 print FH
136 "TYPE: POPULATION\n",
137 "HANDLE: $handle\n",
138 "ID: $t\n",
139 "POPULATION: \n",
140 "||\n";
141 }
142 }
143 print FH "TYPE: SNPASSAY\n",
144 "HANDLE: $handle\n",
145 "BATCH: $batch\n",
146 "MOLTYPE: \n",
147 "METHOD: \n",
148 "ORGANISM: \n",
149 "||\n",
150 "TYPE: SNPPOPUSE | SNPINDUSE\n",
151 "HANDLE: $handle\n",
152 "BATCH: \n",
153 "METHOD: \n",
154 "||\n";
155
156 close FH or die "Couldn't close $meta, $!\n";
157 }
158
159 exit 0;
160
161 #parse old header and add or create new
162 sub prepHeader {
163 my @h;
164 $h[0] = '##fileformat=VCFv4.1';
165 my ($day, $mo, $yr) = (localtime)[3,4,5];
166 $mo++;
167 $yr+=1900;
168 $h[1] = '##fileDate=' . "$yr$mo$day";
169 $h[2] = "##handle=$handle";
170 $h[3] = "##batch=$batch";
171 my $i = 4;
172 if ($bioproj) { $h[$i] = "##bioproject_id=$bioproj"; $i++; }
173 if ($biosamp) { $h[$i] = "##biosample_id=$biosamp"; $i++; }
174 $h[$i] = "##reference=$ref"; ##reference=GCF_999999.99
175 #$i++;
176 #$h[$i] = '##INFO=<ID=LID, Number=1,Type=string, Description="Unique local variation ID or name for display. The LID provided here combined with the handle must be unique for a particular submitter.">'
177 $i++;
178 $h[$i] = '##INFO=<ID=VRT,Number=1,Type=Integer,Description="Variation type,1 - SNV: single nucleotide variation,2 - DIV: deletion/insertion variation,3 - HETEROZYGOUS: variable, but undefined at nucleotide level,4 - STR: short tandem repeat (microsatellite) variation, 5 - NAMED: insertion/deletion variation of named repetitive element,6 - NO VARIATON: sequence scanned for variation, but none observed,7 - MIXED: cluster contains submissions from 2 or more allelic classes (not used) ,8 - MNV: multiple nucleotide variation with all eles of common length greater than 1,9 - Exception">';
179 #sometimes have allele freqs?
180 if (defined $pop) {
181 $i++;
182 $h[$i] = "##FORMAT=<ID=NA,Number=1,Type=Integer,Description=\"Number of alleles for the population.\"";
183 $i++;
184 $h[$i] = '##FORMAT=<ID=AC,Number=.,Type=Integer,Description="Allele count for each alternate allele.">';
185 my @p = split(/,/, $pop);
186 foreach my $t (@p) {
187 $i++;
188 $h[$i] = "##population_id=$t";
189 }
190 }
191 #PMID?
192 ##INFO=<ID=PMID,Number=.,Type=Integer,Description="PubMed ID linked to variation if available.">
193
194 return @h;
195 }
196 ####End
197