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
|
#!/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
snpPosOnSource.pl - Adds pos_source 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
snpPosOnSource.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 source 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('design')->first_child('pos') ) {
if ( defined $pcr->first_child('use')->first_child('revcomp') ) {
$revcomp = $pcr->first_child('use')->first_child('revcomp');
}
my @snps = $pcr->first_child('use')->children('snp');
foreach my $snp ( @snps ) {
my $snp_id = $snp->{att}->{id};
if ( $snp_id =~ /$snp_id_in/ and defined $snp->first_child('pos_design') and not defined $snp->first_child('pos_source') ) {
my $snp_pos_design = $snp->first_child('pos_design');
my ( $source_start, $source_stop ) = split /-/, $pcr->first_child('design')->first_child('pos')->text;
my $snp_pos_source_text = $snp_pos_design->text + $source_start - 1;
my $snp_pos_source_elt = XML::Twig::Elt->new('pos_source', $snp_pos_source_text);
$snp_pos_source_elt->paste('after', $snp_pos_design);
$snp_passed{$snp_id_in} = 1;
}
}
}
}
}
}
|
