/usr/bin/mipe2putativesbeprimers 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
mipe2putativesbeprimers.pl - Generates list of putative SBE primers from a MIPE file
included in output: PCR ID, SNP ID, putative forward SBE primer, putative reverse SBE primer
based on MIPE version v1.1
arguments: * mipe_file
* (optional) list of PCR IDs
=head1 SYNOPSIS
mipe2putativesbeprimers.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 $sbe_length = 35;
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') ) {
if ( defined $pcr->first_child('use')->first_child('seq') ) {
my $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};
if ( $snp->first_child('pos')->text > 0 ) {
my $snp_pos = $snp->first_child('pos')->text;
my $fw_start = ( $snp_pos > $sbe_length) ? $snp_pos - $sbe_length - 1 : 0;
my $fw_length = ( $snp_pos > $sbe_length ) ? $sbe_length : $snp_pos - 1;
my $rev_start = $snp_pos;
my $rev_length = $sbe_length;
my $fw_primer = substr($use_seq, $fw_start, $fw_length);
my $rev_primer = substr($use_seq, $rev_start, $rev_length);
( $rev_primer = reverse $rev_primer ) =~ tr/actgACTG/tgacTGAC/;
print $pcr_id, "\t", $snp_id, "\t", $fw_primer, "\t", $rev_primer, "\n";
} else {
print $pcr_id, "\t", $snp_id, "\tSNP POSITION BEFORE START OF SEQUENCE\n";
}
}
}
}
}
}
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