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comparison VCFToolFilter/VCFToolsFilter.pl @ 24:21d878747ac6 draft default tip

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author dereeper
date Mon, 23 Mar 2015 05:53:20 -0400
parents 1b672da89d00
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23:a1ab979f4551 24:21d878747ac6
1
2 #!/usr/bin/perl
3
4 use strict;
5 use Switch;
6 use Getopt::Long;
7 use Bio::SeqIO;
8
9 my $usage = qq~Usage:$0 <args> [<opts>]
10
11 where <args> are:
12
13 -i, --input <VCF input>
14 -o, --out <Output basename>
15
16 <opts> are:
17
18 -s, --samples <Samples to be analyzed. Comma separated list>
19 -c, --chromosomes <Chromosomes to be analyzed. Comma separated list>
20 -e, --export <Output format (VCF/freq/plink. Default: VCF>
21 -f, --frequency <Minimum MAF. Default: 0.001>
22 -m, --max_freq <Maximum MAF. Default: 0.5>
23 -a, --allow_missing <Allowed missing data proportion per site. Must be comprised between 0 and 1. Default: 0>
24 -n, --nb_alleles <Accepted number of alleles (min,max). Default: 2,4>
25 -t, --type <Type of polymorphisms to keep (ALL/SNP/INDEL). Default: ALL>
26 -b, --bounds <Lower bound and upper bound for a range of sites to be processed (start,end). Default: 1, 100000000>
27 ~;
28 $usage .= "\n";
29
30 my ($input,$out);
31
32
33 #my $indel_size_max = 500;
34 #my $indel_size_min = 1;
35 my $frequency_max = 0.5;
36 my $frequency_min = 0.001;
37 my $pos_max = 100000000000;
38 my $pos_min = 0;
39 my $filter_snp_type = "all";
40
41 my $missing_data = 0;
42 my $export = "VCF";
43 my $type = "ALL";
44 my $nb_alleles;
45 my $bounds;
46 my $samples;
47 my $chromosomes;
48
49 GetOptions(
50 "input=s" => \$input,
51 "out=s" => \$out,
52 "samples=s" => \$samples,
53 "chromosomes=s" => \$chromosomes,
54 "frequency=s" => \$frequency_min,
55 "max_freq=s" => \$frequency_max,
56 "allow_missing=s"=> \$missing_data,
57 "export=s" => \$export,
58 "type=s" => \$type,
59 "nb_alleles=s" => \$nb_alleles,
60 "bounds=s" => \$bounds,
61 );
62
63
64 die $usage
65 if ( !$input || !$out);
66
67 if ($samples && $samples =~/^([\w\,]+)\s*$/){
68 $samples = $1;
69 }
70 elsif ($samples){
71 die "Error: Samples must be a comma separated list of string\n";
72 }
73 if ($chromosomes && $chromosomes =~/^([\w\,]+)\s*$/){
74 $chromosomes = $1;
75 }
76 elsif($chromosomes){
77 die "Error: Chromosomes must be a comma separated list of string\n";
78 }
79 if ($bounds && $bounds =~/^([\d\,]+)\s*$/){
80 $bounds = $1;
81 }
82 elsif($bounds){
83 die "Error: Bounds must be a comma separated list of integers\n";
84 }
85
86 if ($frequency_min && $frequency_min =~/^([\d\.]+)\s*$/){
87 $frequency_min = $1;
88 }
89 elsif ($frequency_min){
90 die "Error: frequency must be an integer\n";
91 }
92 if ($frequency_max && $frequency_max =~/^([\d\.]+)\s*$/){
93 $frequency_max = $1;
94 }
95 elsif($frequency_max){
96 die "Error: frequency must be an integer\n";
97 }
98 if ($missing_data && $missing_data =~/^([\d\.]+)\s*$/){
99 $missing_data = $1;
100 }
101 elsif ($missing_data){
102 die "Error: Missing data must be an integer\n";
103 }
104 if ($nb_alleles && $nb_alleles =~/^([\d\.\,]+)\s*$/){
105 $nb_alleles = $1;
106 }
107 elsif($nb_alleles){
108 die "Error: Nb alleles must be two integers\n";
109 }
110 if ($export && $export =~/^([\w]+)\s*$/){
111 $export = $1;
112 }
113 elsif($export){
114 die "Error: Export must be a string\n";
115 }
116 if ($type && $type =~/^([\w]+)\s*$/){
117 $type = $1;
118 }
119 elsif($type){
120 die "Error: Type must be a string\n";
121 }
122
123
124 my @dnasamples;
125 if ($samples)
126 {
127 @dnasamples = split(",",$samples);
128 }
129 my @nalleles;
130 if ($nb_alleles)
131 {
132 @nalleles = split(",",$nb_alleles);
133 }
134 my @boundaries;
135 if ($bounds)
136 {
137 @boundaries = split(",",$bounds);
138 }
139 my @chromosomes_list;
140 if ($chromosomes)
141 {
142 @chromosomes_list = split(",",$chromosomes);
143 }
144
145
146 my $experiment = "chromosomes";
147 my $table = "";
148 my %genes;
149 my @snp_ids;
150 my @snp_ids_and_positions;
151 my @snp_ids_and_positions_all;
152 my $gene;
153 my $snp_num = 0;
154 my %ref_sequences;
155 my %snps_of_gene;
156
157
158
159
160 my $indiv_cmd = "";
161 if (@dnasamples)
162 {
163 $indiv_cmd = "--indv " . join(" --indv ",@dnasamples);
164 }
165
166 my $chrom_cmd = "";
167 if (@chromosomes_list)
168 {
169 $chrom_cmd = "--chr " . join(" --chr ",@chromosomes_list);
170 }
171
172 my $export_cmd = "--recode";
173 if ($export eq "freq")
174 {
175 $export_cmd = "--freq";
176 }
177 if ($export eq "plink")
178 {
179 $export_cmd = "--plink";
180 }
181
182
183
184 my $nb_alleles_cmd = "--min-alleles 1 --max-alleles 4";
185 if (@nalleles)
186 {
187 $nb_alleles_cmd = "--min-alleles $nalleles[0] --max-alleles $nalleles[1]";
188 }
189 my $bounds_cmd = "--from-bp 1 --to-bp 100000000";
190 if (@boundaries)
191 {
192 $bounds_cmd = "--from-bp $boundaries[0] --to-bp $boundaries[1]";
193 }
194
195
196 my $type_cmd = "";
197 if ($type eq "INDEL")
198 {
199 $type_cmd = "--keep-only-indels";
200 }
201 if ($type eq "SNP")
202 {
203 $type_cmd = "--remove-indels";
204 }
205
206
207 system("vcftools --vcf $input --out $out --keep-INFO-all --remove-filtered-all $type_cmd $export_cmd $chrom_cmd $indiv_cmd $nb_alleles_cmd --maf $frequency_min --max-maf $frequency_max --max-missing $missing_data >>vcftools.log 2>&1");
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