This file is indexed.

/usr/bin/mipeCheckSanity is in mipe 1.1-3.

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
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
#!/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;
use Data::Dumper;

=head1 NAME

mipeCheckSanity.pl - Check sanity of MIPE file, focussing on contents (vs 'form', that can be checked using xmllint)
  based on MIPE version v0.9
  arguments: * mipe_file
             * (optional) list of PCR IDs

=head1 SYNOPSIS

mipe2genotypes.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 %amb_codes = ( M => ['A', 'C']
                , R => ['A', 'G']
		, W => ['A', 'T']
		, S => ['C', 'G']
		, Y => ['C', 'T']
		, K => ['G', 'T']
		, V => ['A', 'C', 'G']
		, H => ['A', 'C', 'T']
		, D => ['A', 'G', 'T']
		, B => ['C', 'G', 'T']
		, N => ['A', 'C', 'G', 'T']
		);


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->first_child('id')->text;
  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 ) {

    #####Check that there is a USE part
    if ( not defined $pcr->first_child('use') ) {
      print "WARNING\tCHECK01\t", $pcr->first_child('id')->text, "\tNo use part defined\n";
      next;
    }
  
  
    #####Check that snp_id in genotypes actually is defined as a SNP
    {
      my @snps = $pcr->first_child('use')->children('snp');
      my %snps;
      foreach my $snp ( @snps ) {
        $snps{$snp->first_child('id')->text} = 1;
      }
      my @samples = $pcr->first_child('use')->children('sample');
      foreach my $sample ( @samples ) {
        my @sample_snps = $sample->children('genotype');
        foreach my $sample_snp ( @sample_snps ) {
          if ( not defined $snps{$sample_snp->first_child('snp_id')->text} ) {
            print "ERROR\tCHECK02\t", $pcr_id, "\tSample ", $sample->first_child('id')->text, ": genotype SNP ID: ", $sample_snp->first_child('snp_id')->text, " not defined as SNP\n";
          }
        }
      }
    }
    
    #####Check if SBE primer sequence and SNP position are in concordance with piece of use 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_pos = $snp->first_child('pos')->text;
        my @assays = $snp->children('assay');
        foreach my $assay ( @assays ) {
	  if ( (uc $assay->first_child('type')->text) eq 'SBE' ) {
            my $sbe_specific = $assay->first_child('specific')->text;
            my $sbe_strand = $assay->first_child('strand')->text;
            if ( uc $sbe_strand =~ /^F/ ) {
              if ( not uc $sbe_specific eq uc substr($use_seq, ($snp_pos-(length $sbe_specific)-1), length $sbe_specific) ) {
                print "ERROR\tCHECK03\t", $pcr->first_child('id')->text, "\tSBE_SEQ does not comply with SNP pos and USE SEQ\t", $assay->first_child('id')->text, "\tSBE=", $sbe_specific, "\tUSE=", substr($use_seq, ($snp_pos-(length $sbe_specific)), length $sbe_specific), "\n";
              }
            } else {
              $sbe_specific = reverse $sbe_specific;
              $sbe_specific =~ tr/ACGTacgt/TGCAtgca/;
              if ( not uc $sbe_specific eq uc substr($use_seq, $snp_pos, length $sbe_specific) ) {
                print "ERROR\tCHECK03\t", $pcr->first_child('id')->text, "\tSBE_SEQ does not comply with SNP pos and USE SEQ\t", $assay->first_child('id')->text, "\tSBE=", $sbe_specific, "\tUSE=", substr($use_seq, $snp_pos, length $sbe_specific), "\n";
              }
            }
          }
	}
      }
    }
    
    #####Check if PCR primers can be found back in DESIGN sequence
    {
      my $design = $pcr->first_child('design');
      my $primer1_seq = uc $design->first_child('primer1')->first_child('seq')->text;
      ( my $primer2_seq = reverse uc $design->first_child('primer2')->first_child('seq')->text ) =~ tr/ACGTacgt/TGCAtgca/;
      my $design_seq = uc $design->first_child('seq')->text;
      if ( not $design_seq =~ /$primer1_seq/ ) {
        print "ERROR\tCHECK04\t", $pcr->first_child('id')->text, "\tPRIMER1_SEQ cannot be found back in DESIGN_SEQ\t", $primer1_seq, "\n";
      }
      if ( not $design_seq =~ /$primer2_seq/ ) {
        print "ERROR\tCHECK04\t", $pcr->first_child('id')->text, "\tPRIMER2_SEQ cannot be found back in DESIGN_SEQ\t", $primer2_seq, "\n";
      }
    }
        
    #####Check if SNP ambiguity code is in concordance with USE sequence
    {
      my $use_seq = $pcr->first_child('use')->first_child('seq')->text;
      my @snps = $pcr->first_child('use')->children('snp');
      foreach my $snp ( @snps ) {
        if ( not defined $snp->first_child('amb') ) { next };
        my $snp_id = $snp->first_child('id')->text;
	my $snp_pos = $snp->first_child('pos')->text;
	my $snp_amb = $snp->first_child('amb')->text;
        my $use_allele = substr($use_seq, $snp_pos-1, 1);
        my $good = 0;
	if ( uc $use_allele eq uc $snp_amb ) {
	  $good = 1;
	}
	if ( uc $use_allele eq 'N' ) {
	  $good = 1;
	}
	foreach my $amb_allele ( @{$amb_codes{$snp_amb}} ) {
	  if ( uc $amb_allele eq uc $use_allele ) {
	    $good = 1;
	  }
	}
	if ( not $good ) {
	  print "ERROR\tCHECK05\t", $pcr->first_child('id')->text, "\t", $snp->first_child('id')->text, "\tSNP ambiguity code (=", $snp_amb, ") does not comply with allele at SNP position in USE seq (=", $use_allele, ") (check CHECK03)\n";
	}
      }
    }
    
    #####Check for empty elements
    {
      if ( $pcr->first_child('id')->text eq '' ) {
        print "ERROR\tCHECK06\tNo PCR ID\n";
      }

      my @descendants = $pcr->descendants;
      foreach my $descendant ( @descendants ) {
        if ( scalar $descendant->descendants == 0 ) {
          if ( $descendant->text eq '' ) {
	    print "WARNING\tCHECK06\tEmpty element in ", $pcr->first_child('id')->text, "\n";
	  }
	}
      }
    }
  }
}