/usr/bin/removeSnpFromMipe is in mipe 1.1-5.
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 | #!/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
removeSnpFromMipe.pl - Removes SNP data from MIPE file
based on MIPE version v0.9
arguments: * mipe_file
* STDIN: tab-delimited list of data, in the following order:
PCR ID, SNP ID
=head1 SYNOPSIS
removeSnpFromMipe.pl my_file.mipe < my_data.txt
=head1 AUTHOR
Jan Aerts (jan.aerts@wur.nl)
=cut
my $file = shift;
if ( not defined $file ) { die "Please provide filename\n" };
my $twig = XML::Twig->new( pretty_print => 'indented'
# , keep_atts_order => 1
, TwigHandlers => { pcr => \&pcr }
);
my @snp_data = ( <STDIN> );
my %snp_passed;
foreach ( @snp_data ) {
chomp;
my ( $pcr_id_in, $snp_id_in ) = split /\t/, $_;
$snp_passed{$snp_id_in} = 0;
}
$twig->parsefile($file);
$twig->print;
foreach ( sort keys %snp_passed ) {
if ( $snp_passed{$_} == 0 ) {
print STDERR "Data for $_ could not be removed from MIPE file; $_ not present\n";
}
}
sub pcr {
my ( $twig, $pcr ) = @_;
my $pcr_id = $pcr->first_child('id')->text;
foreach my $input_line ( @snp_data ) {
chomp $input_line;
my ( $pcr_id_in, $snp_id_in ) = split /\t/, $input_line;
if ( $pcr_id eq $pcr_id_in ) {
my @snps = $pcr->next_elt('use')->children('snp');
foreach my $snp ( @snps ) {
if ( $snp->first_child('id')->text eq $snp_id_in ) {
$snp->delete;
$snp_passed{$snp_id_in} = 1;
}
}
my @samples = $pcr->next_elt('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_in ) {
$genotype->delete;
}
}
}
}
}
}
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