/usr/bin/mipe2genotypes is in mipe 1.1-3.
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 | #!/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;
use Data::Dumper;
=head1 NAME
mipe2genotypes.pl - Generates list of genotypes from a MIPE file
included in output: PCR ID, list of SNP IDs, genotypes for each sample
based on MIPE version v1.1
arguments: * mipe_file
* (optional) list of PCR IDs
=head1 SYNOPSIS
mipe2genotypes.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 ( $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 ) {
print $pcr_id, "\n";
if ( not defined $pcr->first_child('use') ) {
print "\tNo use part defined\n";
} else {
my @snps = $pcr->first_child('use')->children('snp');
my %snps;
foreach my $snp ( @snps ) {
my $snp_id = $snp->{att}->{id};
my $snp_pos = $snp->first_child('pos')->text;
$snps{$snp_id} = $snp_pos;
}
my @samples = $pcr->first_child('use')->children('sample');
my %diplotypes;
foreach my $sample ( @samples ) {
my $sample_id = $sample->{att}->{id};
my @sample_snps = $sample->children('genotype');
foreach my $sample_snp ( @sample_snps ) {
my $sample_snp_id = $sample_snp->first_child('snp_id')->text;
my $sample_snp_amb = $sample_snp->first_child('amb')->text;
$diplotypes{$sample_id}{$snps{$sample_snp_id}} = $sample_snp_amb;
}
}
print join(';', ( sort { $a <=> $b } values %snps ) ), "\n";
foreach my $sample ( sort keys %diplotypes ) {
print $sample, "\t";
foreach my $snp_pos ( sort { $a <=> $b } values %snps ) {
print ( $diplotypes{$sample}{$snp_pos} || ' ' );
}
print "\n";
}
}
}
}
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