/usr/bin/mipe2sbeprimers is in mipe 1.1-6.
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 | #!/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
mipe2sbeprimers.pl - Generates list of SBE primers from a MIPE file
included in output: PCR ID, SNP ID, SBE ID, SBE oligo, SBE strand, SBE tail, SBE specific, SBE remark
based on MIPE version v1.1
arguments: * mipe_file
* (optional) list of PCR IDs
=head1 SYNOPSIS
mipe2sbeprimers.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 ) {
if ( defined $pcr->first_child('use') ) {
my @snps = $pcr->first_child('use')->children('snp');
foreach my $snp ( @snps ) {
my $snp_id = $snp->{att}->{id};
my @assays = $snp->children('assay');
foreach my $assay ( @assays ) {
if ( (uc $assay->first_child('type')->text) eq 'SBE' ) {
my $sbe_id = $assay->{att}->{id};
my $sbe_oligo = ( defined $assay->first_child('oligo') ) ? $assay->first_child('oligo')->text : 'NO OLIGO';
my $sbe_specific = ( defined $assay->first_child('specific') ) ? $assay->first_child('specific')->text : 'NO SPECIFIC';
my $sbe_tail = ( defined $assay->first_child('tail') ) ? $assay->first_child('tail')->text : 'NO TAIL';
my $sbe_strand = ( defined $assay->first_child('strand') ) ? $assay->first_child('strand')->text : 'NO STRAND';
my $sbe_remark;
if ( scalar $assay->children('remark') > 0 ) {
foreach ( $assay->children('remark') ) {
$sbe_remark .= $_->text . ';';
}
chop $sbe_remark;
} else {
$sbe_remark = 'NO REMARK';
}
print $pcr_id, "\t", $snp_id, "\t", $sbe_id, "\t", $sbe_oligo, "\t", $sbe_strand, "\t", $sbe_tail, "\t", $sbe_specific, "\t", $sbe_remark, "\n";
}
}
}
}
}
}
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