0
|
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
|