/usr/bin/sbe2mipe 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 | #!/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
sbe2mipe.pl - Inserts SBE data into MIPE file
CAUTION: DOES NOT WORK AT THE MOMENT!!
based on MIPE version v1.1
arguments: * mipe_file
* STDIN: tab-delimited list of data, in the following order:
PCR ID, SNP ID, SBE ID, SBE oligo, SBE specific, SBE tail, SBE strand, SBE remark
=head1 SYNOPSIS
sbe2mipe.pl my_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 $twig = XML::Twig->new( pretty_print => 'indented'
, keep_atts_order => 1
, TwigHandlers => { pcr => \&pcr }
);
my @assay_data = ( <STDIN> );
my %assay_passed;
foreach ( @assay_data ) {
chomp;
my ( $pcr_id_in, $snp_id_in, $assay_id_in, $assay_oligo_in, $assay_specific_in, $assay_tail_in, $assay_strand_in, $assay_remark_in ) = split /\t/, $_;
$assay_passed{$assay_id_in} = 0;
}
$twig->parsefile($file);
$twig->print;
foreach ( sort keys %assay_passed ) {
if ( $assay_passed{$_} == 0 ) {
print STDERR "Data for $_ not imported\n";
}
}
exit;
sub pcr {
my ( $twig, $pcr ) = @_;
my $pcr_id = $pcr->{att}->{id};
foreach my $input_line ( @assay_data ) {
chomp $input_line;
my ( $pcr_id_in, $snp_id_in, $assay_id_in, $assay_oligo_in, $assay_specific_in, $assay_tail_in, $assay_strand_in, $assay_remark_in ) = split /\t/, $input_line;
if ( $pcr_id =~ /$pcr_id_in/ ) {
my @snps = $pcr->next_elt('use')->children('snp');
foreach my $snp ( @snps ) {
if ( $snp->{att}->{id}; =~ /$snp_id_in/ ) {
my $assay = XML::Twig::Elt->new('assay', '');
my $type = XML::Twig::Elt->new('type', 'sbe');
$type->paste('last_child', $assay);
if ( defined $assay_id_in ) {
my $id = XML::Twig::Elt->new('id', $assay_id_in);
$id->paste('last_child', $assay);
};
if ( defined $assay_oligo_in ) {
my $oligo = XML::Twig::Elt->new('oligo', $assay_oligo_in);
$oligo->paste('last_child', $assay);
};
if ( defined $assay_specific_in ) {
my $specific = XML::Twig::Elt->new('specific', $assay_specific_in);
$specific->paste('last_child', $assay);
};
if ( defined $assay_tail_in ) {
my $tail = XML::Twig::Elt->new('tail', $assay_tail_in);
$tail->paste('last_child', $assay);
};
if ( defined $assay_strand_in ) {
my $strand = XML::Twig::Elt->new('strand', $assay_strand_in);
$strand->paste('last_child', $assay);
};
if ( defined $assay_remark_in ) {
my $remark = XML::Twig::Elt->new('remark', $assay_remark_in);
$remark->paste('last_child', $assay);
};
my $snp_id = $snp->{att}->{id};;
my @snp_pos = $snp->children('pos');
my $snp_pos = $snp_pos[0];
if ( defined $snp_pos ) {
$assay->paste('after', $snp_pos);
} elsif ( defined $snp_id ) {
$assay->paste('after', $snp_id);
} else {
$assay->paste('first_child', $snp_id);
};
$assay_passed{$assay_id_in} = 1;
}
}
}
}
}
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