/usr/bin/snpPosOnDesign is in mipe 1.1-4.
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 | #!/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
snpPosOnDesign.pl - Adds pos_design to SNP
based on MIPE version v1.1
arguments: * mipe_file
* STDIN: tab-delimited list of data, in the following order:
PCR ID, SNP ID
=head1 SYNOPSIS
snpPosOnDesign.pl your_file.mipe < my_data.txt
=head1 ADDITIONAL INFO
See http://mipe.sourceforge.net
=head1 AUTHOR
Jan Aerts (jan.aerts@bbsrc.ac.uk)
=cut
my $file = shift;
if ( not defined $file ) { die "Please provide filename\n" };
my $data = shift;
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 "Position of $_ on design sequence not calculated\n";
}
}
exit;
sub pcr {
my ( $twig, $pcr ) = @_;
my $pcr_id = $pcr->{att}->{id};
foreach my $input_line ( @snp_data ) {
chomp $input_line;
my ( $pcr_id_in, $snp_id_in ) = split /\t/, $input_line;
if ( $pcr_id =~ /$pcr_id_in/ ) {
my $revcomp = 0;
if ( defined $pcr->first_child('use') and defined $pcr->first_child('use')->first_child('seq') ) {
if ( defined $pcr->first_child('use')->first_child('revcomp') ) {
$revcomp = $pcr->first_child('use')->first_child('revcomp')->text;
}
my @snps = $pcr->first_child('use')->children('snp');
my $design_seq = uc($pcr->first_child('design')->first_child('seq')->text);
my $use_seq = uc($pcr->first_child('use')->first_child('seq')->text);
foreach my $snp ( @snps ) {
my $snp_id = $snp->->{att}->{id};
if ( $snp_id =~ /$snp_id_in/ and not defined $snp->first_child('pos_design') ) {
my $snp_pos_elt = $snp->first_child('pos');
my $snp_pos = $snp_pos_elt->text;
if ( $snp_pos > 10 and $snp_pos < ( (length $use_seq) - 10 ) ) {
my ( $snp_seq_left, $snp_seq_right, $snp_seq );
my $stars;
if ( $revcomp == 0 ) {
$snp_seq_left = substr($use_seq, $snp_pos - 11, 10);
$stars = ( $snp_seq_left =~ tr/*/*/ );
$snp_seq_left =~ s/\*//g;
( $snp_seq_right = substr($use_seq, $snp_pos, 10) ) =~ s/\*//g;
$snp_seq = $snp_seq_left . '.' . $snp_seq_right;
} else {
( $snp_seq_left = substr($use_seq, $snp_pos - 11, 10) ) =~ s/\*//g;
( $snp_seq_left = reverse $snp_seq_left ) =~ tr/acgtACGT/tgcaTGCA/;
$snp_seq_right = substr($use_seq, $snp_pos, 10);
$stars = ( $snp_seq_right =~ tr/*/*/ );
$snp_seq_right =~ s/\*//g;
( $snp_seq_right = reverse $snp_seq_right ) =~ tr/acgtACGT/tgcaTGCA/;
$snp_seq = $snp_seq_right . '.' . $snp_seq_left;
}
my %design_pos;
while ( $design_seq =~ /($snp_seq)/g ) {
$design_pos{($-[0]+11-$stars)} = $2;
}
if ( scalar keys %design_pos > 0 ) {
my $snp_design_pos_text = join ';', keys %design_pos;
my $snp_design_pos = XML::Twig::Elt->new('pos_design', $snp_design_pos_text);
$snp_design_pos->paste('after', $snp_pos_elt);
$snp_passed{$snp_id_in} = 1;
}
}
}
}
}
}
}
}
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