/usr/bin/mipe2snps is in mipe 1.1-6.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 | #!/usr/bin/perl
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later version.
#
# This library is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
# Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this library ('COPYING'); if not, write to the Free Software
# Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
use strict;
use warnings;
use XML::Twig;
=head1 NAME
mipe2snps.pl - Generates list of SNPs from a MIPE file
included in output: PCR ID, SNP ID, SNP pos, SNP amb, allele freqs, number of animals genotyped, SNP rank, flanking seqs, SNP remarks
based on MIPE version v1.1
arguments: * mipe_file
* (optional) list of PCR IDs
=head1 SYNOPSIS
mipe2snps.pl your_file.mipe <pcr_id1> <pcr_id2>
=head1 ADDITIONAL INFO
See http://mipe.sourceforge.net
=head1 AUTHOR
Jan Aerts (jan.aerts@bbsrc.ac.uk)
=cut
my %amb_codes = ( M => ['A', 'C']
, R => ['A', 'G']
, W => ['A', 'T']
, S => ['C', 'G']
, Y => ['C', 'T']
, K => ['G', 'T']
, V => ['A', 'C', 'G']
, H => ['A', 'C', 'T']
, D => ['A', 'G', 'T']
, B => ['C', 'G', 'T']
, N => ['A', 'C', 'G', 'T']
);
my ( $file, @pcr_ids ) = @ARGV;
if ( not defined $file ) { die "Please provide filename\n" };
my $twig = XML::Twig->new( TwigHandlers => { pcr => \&pcr }
, pretty_print => 'indented' );
$twig->parsefile($file);
exit;
sub pcr {
my ( $twig, $pcr ) = @_;
my $to_include = 0;
my $pcr_id = $pcr->{att}->{id};
if ( scalar @pcr_ids > 0 ) {
$to_include = 0;
foreach ( @pcr_ids ) {
if ( $pcr_id =~ /$_/i ) {
$to_include = 1;
}
}
} else {
$to_include = 1;
}
if ( $to_include ) {
if ( defined $pcr->first_child('use') ) {
my $use_seq;
my $snp_seq;
if ( defined $pcr->first_child('use')->first_child('seq') ) {
$use_seq = $pcr->first_child('use')->first_child('seq')->text;
}
my @snps = $pcr->first_child('use')->children('snp');
foreach my $snp ( @snps ) {
my $snp_id = $snp->{att}->{id};
my $snp_amb = ( defined $snp->first_child('amb') ) ? $snp->first_child('amb')->text : 'NO AMB';
my $snp_pos = ( defined $snp->first_child('pos') ) ? $snp->first_child('pos')->text : 'NO POS';
my $snp_pos_design = ( defined $snp->first_child('pos_design') ) ? $snp->first_child('pos_design')->text : 'NO POS_DESIGN';
my $snp_pos_source = ( defined $snp->first_child('pos_source') ) ? $snp->first_child('pos_source')->text : 'NO POS_SOURCE';
my $snp_rank = ( defined $snp->first_child('rank') ) ? $snp->first_child('rank')->text : 'NO RANK';
my @snp_remarks = $snp->children('remark');
my $snp_remark = 'NO REMARK';
my %occurences;
my $snp_minorallelefreq = 'NO FREQS';
my $number_of_samples = 0;
if ( defined $pcr->first_child('use')->first_child('sample') ) {
my @samples = $pcr->first_child('use')->children('sample');
foreach my $sample ( @samples ) {
my @genotypes = $sample->children('genotype');
foreach my $genotype ( @genotypes ) {
if ( $genotype->first_child('snp_id')->text eq $snp_id ) {
$number_of_samples++;
$occurences{$genotype->first_child('amb')->text}++;
}
}
}
my %freqs;
$snp_minorallelefreq = '';
foreach my $allele ( keys %occurences ) {
if ( $allele eq 'A' or $allele eq 'C' or $allele eq 'G' or $allele eq 'T' ) {
$freqs{$allele} = 2*$occurences{$allele};
} else{
foreach my $code ( keys %amb_codes ) {
if ( $allele eq $code ) {
foreach my $key ( @{$amb_codes{$code}} ) {
$freqs{$key} += $occurences{$allele};
}
}
}
}
}
my $total_alleles;
foreach my $allele ( keys %freqs ) {
$total_alleles += $freqs{$allele};
}
foreach my $allele ( keys %freqs ) {
$freqs{$allele} /= $total_alleles;
}
foreach my $allele ( sort { $freqs{$a} <=> $freqs{$b} } keys %freqs ) {
$snp_minorallelefreq .= $allele . '(' . sprintf("%.2f", $freqs{$allele}) . ');'
}
chop $snp_minorallelefreq;
}
if ( defined $use_seq and defined $snp->first_child('pos') ) {
my $_amb;
$snp_seq = substr($use_seq, $snp_pos - 11, 10);
if ( defined $snp->first_child('amb') ) {
$_amb = $snp->first_child('amb')->text;
} else {
$_amb = 'N';
}
$snp_seq .= $_amb;
$snp_seq .= substr($use_seq, $snp_pos, 10);
} else {
$snp_seq = 'UNKNOWN';
}
if ( scalar @snp_remarks > 0 ) {
my @remark_text;
foreach ( @snp_remarks ) {
push @remark_text, $_->text;
}
$snp_remark = join('; ', @remark_text);
}
print $pcr_id, "\t", $snp_id, "\t", $snp_pos, "\t", $snp_pos_design, "\t", $snp_pos_source, "\t", $snp_amb, "\t", $snp_minorallelefreq, "\t", $number_of_samples, "\t", $snp_rank, "\t", $snp_seq, "\t", $snp_remark, "\n";
}
}
}
}
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