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comparison gfapts/gfap_r1.0_allvar_genomic_annotater.pl @ 0:f753b30013e6 draft

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author rdaveau
date Fri, 29 Jun 2012 10:20:55 -0400
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-1:000000000000 0:f753b30013e6
1 #!/usr/bin/perl
2
3 use strict;
4 use warnings FATAL => qw[ numeric uninitialized ];
5 use File::Basename;
6 use Getopt::Long;
7
8 sub sepind{
9 $_=shift @_ foreach my($str, $sep);
10 my($pos, @pos);
11 $pos=0;
12 while(1){
13 $pos=index($str, $sep, $pos);
14 last if($pos<0);
15 push @pos, $pos++;
16 }
17 return \@pos;
18 }
19
20 my($varfile, $buildver, $refseq_dir, $cosmic_dir, $refseq_release, $cosmic_release, $annovar_release, $outdir, $noncoding, $coding, $cos, $ogs, $mid, $pid, $cno, $pno);
21 my(@buffer, @header, @ogs, @mid, @cno, @pno, @sep, %buffer, %mid, %ogs, %opts);
22
23 GetOptions(\%opts, "varfile=s", "buildver=s", "refseq_dir=s", "refseq_release=s", "cosmic_dir=s", "cosmic_release=s", "annovar_release=s", "outdir=s", "noncoding=s", "coding=s");
24 $varfile = $opts{varfile};
25 $buildver = $opts{buildver};
26 $refseq_dir = $opts{refseq_dir};
27 $refseq_release = $opts{refseq_release};
28 $cosmic_dir = $opts{cosmic_dir};
29 $cosmic_release = $opts{cosmic_release};
30 $annovar_release = $opts{annovar_release};
31 $outdir = $opts{outdir};
32 $noncoding = $opts{noncoding};
33 $coding = $opts{coding};
34
35 my %legend=(
36 'unk' => 'undefined column',
37 'chr' => 'chromosome identifier',
38 'start' => "${buildver} 1-based start position",
39 'end' => "${buildver} 1-based end position",
40 'ref' => 'reference allele',
41 'alt' => 'alternate allele',
42 'annot' => 'ig:intergenic; pp:1kb-upstream; 5|3u:UTR; in:intronic; ss:splice; nc:ncRNA',
43 'ogs' => 'official gene symbol(s)',
44 'cos' => "gene listed in cosmic ${cosmic_release} release",
45 'mid' => "RefSeq mRNA identifier(s) from human.protein.gpff ${refseq_release} release",
46 'pid' => "RefSeq protein identifier(s) from human.protein.gpff ${refseq_release} release",
47 'c.x' => 'ATG-based variant descriptor in mRNA',
48 'p.x' => 'ATG-based variant descriptor in protein'
49 );
50
51 my $annovar_src_dir = 'inc/annovar';
52 my $annovar_db_dir = "db/annovar/${annovar_release}";
53
54 my $fname = readlink($varfile) || $varfile;
55 $fname = basename($fname);
56
57 `${annovar_src_dir}/annotate_variation.pl -buildver $buildver ${outdir}/${fname} $annovar_db_dir 2> /dev/null` and die $!;
58
59 open IN, "<${refseq_dir}/mid2pid_${refseq_release}.txt" or die $!;
60 while(<IN>){
61 next if /^#/;
62 /^(\S+)\s+(\S+)/;
63 $mid{$1}=$2;
64 }
65 close IN;
66
67 open IN, "<${cosmic_dir}/${buildver}_cosmic_ogs_${cosmic_release}.txt" or die $!;
68 chomp and $ogs{$_}++ while(<IN>);
69 close IN;
70
71 open IN, "<${outdir}/${fname}" or die $!;
72 while(<IN>){
73 last if $_!~/^#/;
74 last if $_!~/=/;
75 chomp;
76 /^#(\S+)\s{1}=\s{1}(.+)/;
77 push @header, $1;
78 $legend{$1}=$2;
79 }
80 if(!scalar(@header)){
81 @header=('chr', 'start', 'end', 'ref', 'alt');
82 $_=readline(IN);
83 @_=split /\t/, $_;
84 $_=$#_-4;
85 push @header, ('unk')x$_ if($_!=0);
86 }
87 close IN;
88 push @header, ('annot', 'ogs', 'cos');
89 open OUT, ">${outdir}/${fname}.nc" or die $!;
90 print OUT "#", join(' = ', $_, $legend{$_}), "\n" foreach @header;
91 print OUT "#", join("\t", @header), "\n";
92 open IN, "<${outdir}/${fname}.variant_function" or die $!;
93 while(<IN>){
94 next if /exonic/;
95 s/^downstream/ig/;
96 s/;downstream//;
97 s/,/:/g;
98 s/(UTR(3|5))|(upstream)|(intronic)|(splicing)|(ncRNA)|(intergenic)/$1?"${2}u":$3?'pp':$4?'in':$5?'ss':$6?'nc':'ig'/eg;
99 chomp;
100 @buffer=split /\t/, $_;
101 $buffer[1]='na' if $buffer[0] eq 'ig';
102 $buffer[1]=~s/([^;]+);(?:\S+)$/$1/ if $buffer[0]!~/;/;
103 print OUT join("\t", @buffer[2..$#buffer, 0..1], ($buffer[1] eq 'na')?'na':(exists $ogs{$buffer[1]})?'TRUE':'FALSE'), "\n";
104 }
105 close IN;
106 close OUT;
107
108 $legend{annot}='fd:frameshift deletion; fi:frameshift insertion; nd:nonframeshift deletion; ni:nonframeshift insertion; bs:block substitution; ss:synonymous SNV; ns:nonsynonymous SNV; sg:stopgain; sl:stoploss; na:unknown';
109 push @header, ('mid', 'pid', 'c.x', 'p.x');
110
111 open IN, "${outdir}/${fname}.exonic_variant_function" or die $!;
112 open OUT, ">${outdir}/${fname}.cds" or die $!;
113 print OUT "#", join(' = ', $_, $legend{$_}), "\n" foreach @header;
114 print OUT "#", join("\t", @header), "\n";
115 while(<IN>){
116 next if /unknown/;
117 s/^\S+\s+//;
118 chomp;
119 %buffer=();
120 @{$_}=() foreach (\@ogs, \@mid, \@cno, \@pno, \@sep);
121 @buffer=split /\t/, $_;
122 $buffer[0]=~s/(nonf\w+\s{1}(d|i|s)\w+)|(\w+\s{1}(d|i)\w+)|(stop(\w){1}.+)|(^(n|s).+)|(.+)/$1?(($2 eq 's')?'b':'n').$2:$3?"f$4":$5?"s$6":$7?"${8}s":'na'/eg;
123 foreach (split /,/, $buffer[1]){
124 @_=split /:/, $_;
125 splice(@_, 2, 1);
126 $_=shift(@_) || 'na' foreach ($ogs, $mid, $cno, $pno);
127 $buffer{ogs}->{$ogs}->{$cno}->{$mid}++;
128 $buffer{ono}->{$cno}=$pno;
129 }
130 $cos=0;
131 foreach $ogs (@ogs=keys %{$buffer{ogs}}){
132 push @cno, join('|', (@_=keys %{$buffer{ogs}->{$ogs}}));
133 unshift @pno, $buffer{ono}->{$_} foreach reverse @_;
134 $pno=join('|', @pno[0..$#_]);
135 splice(@pno, 0, $#_+1);
136 push @pno, $pno;
137 foreach $cno (@_){
138 push @mid, join(':', keys %{$buffer{ogs}->{$ogs}->{$cno}});
139 }
140 $cos++ if exists $ogs{$ogs};
141 }
142 $mid=join('|', @mid);
143 $cno=join(';', @cno);
144 if($#ogs!=0){
145 (my $sep=$cno)=~s/[^;\|:]+//g;
146 @_=@{sepind($mid, '|')}[@{sepind($sep, ';')}];
147 substr($mid, $_, 1)=';' foreach @_;
148 }
149 ($pid=$mid)=~s/([^;\|:]+)/$mid{$1} || 'na'/eg;
150 push @buffer, shift @buffer, join(';', @ogs), ($cos!=0)?'TRUE':'FALSE', $mid, $pid, $cno, join(';', @pno);
151 shift @buffer;
152 print OUT join("\t", @buffer), "\n";
153 }
154 close IN;
155 close OUT;
156 system "rm $noncoding $coding ${outdir}/${fname}*variant_function ${outdir}/${fname}*invalid*; ln -s ${outdir}/${fname}.nc $noncoding; ln -s ${outdir}/${fname}.cds $coding" and die $!;