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comparison PsiCLASS-1.0.2/samtools-0.1.19/misc/sam2vcf.pl @ 0:903fc43d6227 draft default tip

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author lsong10
date Fri, 26 Mar 2021 16:52:45 +0000
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1 #!/usr/bin/perl -w
2 #
3 # VCF specs: http://www.1000genomes.org/wiki/doku.php?id=1000_genomes:analysis:vcf3.3
4 #
5 # Contact: pd3@sanger
6 # Version: 2010-04-23
7
8 use strict;
9 use warnings;
10 use Carp;
11
12 my $opts = parse_params();
13 do_pileup_to_vcf($opts);
14
15 exit;
16
17 #---------------
18
19 sub error
20 {
21 my (@msg) = @_;
22 if ( scalar @msg ) { croak(@msg); }
23 die
24 "Usage: sam2vcf.pl [OPTIONS] < in.pileup > out.vcf\n",
25 "Options:\n",
26 " -h, -?, --help This help message.\n",
27 " -i, --indels-only Ignore SNPs.\n",
28 " -r, --refseq <file.fa> The reference sequence, required when indels are present.\n",
29 " -R, --keep-ref Print reference alleles as well.\n",
30 " -s, --snps-only Ignore indels.\n",
31 " -t, --column-title <string> The column title.\n",
32 "\n";
33 }
34
35
36 sub parse_params
37 {
38 my %opts = ();
39
40 $opts{fh_in} = *STDIN;
41 $opts{fh_out} = *STDOUT;
42
43 while (my $arg=shift(@ARGV))
44 {
45 if ( $arg eq '-R' || $arg eq '--keep-ref' ) { $opts{keep_ref}=1; next; }
46 if ( $arg eq '-r' || $arg eq '--refseq' ) { $opts{refseq}=shift(@ARGV); next; }
47 if ( $arg eq '-t' || $arg eq '--column-title' ) { $opts{title}=shift(@ARGV); next; }
48 if ( $arg eq '-s' || $arg eq '--snps-only' ) { $opts{snps_only}=1; next; }
49 if ( $arg eq '-i' || $arg eq '--indels-only' ) { $opts{indels_only}=1; next; }
50 if ( $arg eq '-?' || $arg eq '-h' || $arg eq '--help' ) { error(); }
51
52 error("Unknown parameter \"$arg\". Run -h for help.\n");
53 }
54 return \%opts;
55 }
56
57 sub iupac_to_gtype
58 {
59 my ($ref,$base) = @_;
60 my %iupac = (
61 'K' => ['G','T'],
62 'M' => ['A','C'],
63 'S' => ['C','G'],
64 'R' => ['A','G'],
65 'W' => ['A','T'],
66 'Y' => ['C','T'],
67 );
68 if ( !exists($iupac{$base}) )
69 {
70 if ( $base ne 'A' && $base ne 'C' && $base ne 'G' && $base ne 'T' ) { error("FIXME: what is this [$base]?\n"); }
71 if ( $ref eq $base ) { return ('.','0/0'); }
72 return ($base,'1/1');
73 }
74 my $gt = $iupac{$base};
75 if ( $$gt[0] eq $ref ) { return ($$gt[1],'0/1'); }
76 elsif ( $$gt[1] eq $ref ) { return ($$gt[0],'0/1'); }
77 return ("$$gt[0],$$gt[1]",'1/2');
78 }
79
80
81 sub parse_indel
82 {
83 my ($cons) = @_;
84 if ( $cons=~/^-/ )
85 {
86 my $len = length($');
87 return "D$len";
88 }
89 elsif ( $cons=~/^\+/ ) { return "I$'"; }
90 elsif ( $cons eq '*' ) { return undef; }
91 error("FIXME: could not parse [$cons]\n");
92 }
93
94
95 # An example of the pileup format:
96 # 1 3000011 C C 32 0 98 1 ^~, A
97 # 1 3002155 * +T/+T 53 119 52 5 +T * 4 1 0
98 # 1 3003094 * -TT/-TT 31 164 60 11 -TT * 5 6 0
99 # 1 3073986 * */-AAAAAAAAAAAAAA 3 3 45 9 * -AAAAAAAAAAAAAA 7 2 0
100 #
101 sub do_pileup_to_vcf
102 {
103 my ($opts) = @_;
104
105 my $fh_in = $$opts{fh_in};
106 my $fh_out = $$opts{fh_out};
107 my ($prev_chr,$prev_pos,$prev_ref);
108 my $refseq;
109 my $ignore_indels = $$opts{snps_only} ? 1 : 0;
110 my $ignore_snps = $$opts{indels_only} ? 1 : 0;
111 my $keep_ref = $$opts{keep_ref} ? 1 : 0;
112 my $title = exists($$opts{title}) ? $$opts{title} : 'data';
113
114 print $fh_out
115 qq[##fileformat=VCFv3.3\n],
116 qq[##INFO=DP,1,Integer,"Total Depth"\n],
117 qq[##FORMAT=GT,1,String,"Genotype"\n],
118 qq[##FORMAT=GQ,1,Integer,"Genotype Quality"\n],
119 qq[##FORMAT=DP,1,Integer,"Read Depth"\n],
120 qq[#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\t$title\n]
121 ;
122
123 while (my $line=<$fh_in>)
124 {
125 chomp($line);
126 my (@items) = split(/\t/,$line);
127 if ( scalar @items<8 )
128 {
129 error("\nToo few columns, does not look like output of 'samtools pileup -c': $line\n");
130 }
131 my ($chr,$pos,$ref,$cons,$cons_qual,$snp_qual,$rms_qual,$depth,$a1,$a2) = @items;
132 $ref = uc($ref);
133 $cons = uc($cons);
134
135 my ($alt,$gt);
136 if ( $ref eq '*' )
137 {
138 # An indel is involved.
139 if ( $ignore_indels )
140 {
141 $prev_ref = $ref;
142 $prev_pos = $pos;
143 $prev_chr = $chr;
144 next;
145 }
146
147 if (!defined $prev_chr || $chr ne $prev_chr || $pos ne $prev_pos)
148 {
149 if ( !$$opts{refseq} ) { error("Cannot do indels without the reference.\n"); }
150 if ( !$refseq ) { $refseq = Fasta->new(file=>$$opts{refseq}); }
151 $ref = $refseq->get_base($chr,$pos);
152 $ref = uc($ref);
153 }
154 else { $ref = $prev_ref; }
155
156 # One of the alleles can be a reference and it can come in arbitrary order. In some
157 # cases */* can be encountered. In such a case, look in the additional columns.
158 my ($al1,$al2) = split(m{/},$cons);
159 if ( $al1 eq $al2 && $al1 eq '*' ) { $al1=$a1; $al2=$a2; }
160 my $alt1 = parse_indel($al1);
161 my $alt2 = parse_indel($al2);
162 if ( !$alt1 && !$alt2 ) { error("FIXME: could not parse indel:\n", $line); }
163 if ( !$alt1 )
164 {
165 $alt=$alt2;
166 $gt='0/1';
167 }
168 elsif ( !$alt2 )
169 {
170 $alt=$alt1;
171 $gt='0/1';
172 }
173 elsif ( $alt1 eq $alt2 )
174 {
175 $alt="$alt1";
176 $gt='1/1';
177 }
178 else
179 {
180 $alt="$alt1,$alt2";
181 $gt='1/2';
182 }
183 }
184 else
185 {
186 if ( $ignore_snps || (!$keep_ref && $ref eq $cons) )
187 {
188 $prev_ref = $ref;
189 $prev_pos = $pos;
190 $prev_chr = $chr;
191 next;
192 }
193
194 # SNP
195 ($alt,$gt) = iupac_to_gtype($ref,$cons);
196 }
197
198 print $fh_out "$chr\t$pos\t.\t$ref\t$alt\t$snp_qual\t0\tDP=$depth\tGT:GQ:DP\t$gt:$cons_qual:$depth\n";
199
200 $prev_ref = $ref;
201 $prev_pos = $pos;
202 $prev_chr = $chr;
203 }
204 }
205
206
207 #------------- Fasta --------------------
208 #
209 # Uses samtools to get a requested base from a fasta file. For efficiency, preloads
210 # a chunk to memory. The size of the cached sequence can be controlled by the 'size'
211 # parameter.
212 #
213 package Fasta;
214
215 use strict;
216 use warnings;
217 use Carp;
218
219 sub Fasta::new
220 {
221 my ($class,@args) = @_;
222 my $self = {@args};
223 bless $self, ref($class) || $class;
224 if ( !$$self{file} ) { $self->throw(qq[Missing the parameter "file"\n]); }
225 $$self{chr} = undef;
226 $$self{from} = undef;
227 $$self{to} = undef;
228 if ( !$$self{size} ) { $$self{size}=10_000_000; }
229 bless $self, ref($class) || $class;
230 return $self;
231 }
232
233 sub read_chunk
234 {
235 my ($self,$chr,$pos) = @_;
236 my $to = $pos + $$self{size};
237 my $cmd = "samtools faidx $$self{file} $chr:$pos-$to";
238 my @out = `$cmd`;
239 if ( $? ) { $self->throw("$cmd: $!"); }
240 my $line = shift(@out);
241 if ( !($line=~/^>$chr:(\d+)-(\d+)/) ) { $self->throw("Could not parse: $line"); }
242 $$self{chr} = $chr;
243 $$self{from} = $1;
244 $$self{to} = $2;
245 my $chunk = '';
246 while ($line=shift(@out))
247 {
248 chomp($line);
249 $chunk .= $line;
250 }
251 $$self{chunk} = $chunk;
252 return;
253 }
254
255 sub get_base
256 {
257 my ($self,$chr,$pos) = @_;
258 if ( !$$self{chr} || $chr ne $$self{chr} || $pos<$$self{from} || $pos>$$self{to} )
259 {
260 $self->read_chunk($chr,$pos);
261 }
262 my $idx = $pos - $$self{from};
263 return substr($$self{chunk},$idx,1);
264 }
265
266 sub throw
267 {
268 my ($self,@msg) = @_;
269 croak(@msg);
270 }