This file is indexed.

/usr/bin/bp_generate_histogram is in bioperl 1.6.924-3.

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
#!/usr/bin/perl 

eval 'exec /usr/bin/perl  -S $0 ${1+"$@"}'
    if 0; # not running under some shell

use strict;
use warnings;
use lib '.','./blib','../../blib/lib';
use Bio::DB::GFF;
use Getopt::Long;

my $usage = <<USAGE;
Usage: $0 [options] feature_type1 feature_type2...

Dump out a GFF-formatted histogram of the density of the indicated set
of feature types.

 Options:
   --dsn        <dsn>       Data source (default dbi:mysql:test)
   --adaptor    <adaptor>   Schema adaptor (default dbi::mysqlopt)
   --user       <user>      Username for mysql authentication
   --pass       <password>  Password for mysql authentication
   --bin        <bp>        Bin size in base pairs.
   --aggregator <list>      Comma-separated list of aggregators
   --sort                   Sort the resulting list by type and bin
   --merge                  Merge features with same method but different sources
USAGE
;

my ($DSN,$ADAPTOR,$AGG,$USER,$PASSWORD,$BINSIZE,$SORT,$MERGE);
GetOptions ('dsn:s'         => \$DSN,
	    'adaptor:s'     => \$ADAPTOR,
	    'user:s'        => \$USER,
	    'password:s'    => \$PASSWORD,
            'aggregators:s' => \$AGG,
            'bin:i'         => \$BINSIZE,
	    'sort'          => \$SORT,
	    'merge'         => \$MERGE,
	   ) or die $usage;

my @types = @ARGV or die $usage;

# some local defaults
$DSN     ||= 'dbi:mysql:test';
$ADAPTOR ||= 'dbi::mysqlopt';
$BINSIZE ||= 1_000_000;   # 1 megabase bins

my @options;
push @options,(-user=>$USER)     if defined $USER;
push @options,(-pass=>$PASSWORD) if defined $PASSWORD;
push @options,(-aggregator=>[split /\s+/,$AGG]) if defined $AGG;

my $db = Bio::DB::GFF->new(-adaptor=>$ADAPTOR,-dsn => $DSN,@options)
  or die "Can't open database: ",Bio::DB::GFF->error,"\n";

my @features = $db->features(-binsize=>$BINSIZE,-types=>\@types);

if ($MERGE) {
  my %MERGE;
  for my $f (@features) {
    my $name  = $f->name;
    my $class = $name->class;
    $name =~ s/^(.+:.+):.+$/$1/;
    $f->group(Bio::DB::GFF::Featname->new($class,$name));
    my $source = $f->source;
    $source =~ s/:.+$//;
    $f->source($source);
    if (my $already_there = $MERGE{$f->source,$f->abs_ref,$f->abs_start}) {
      $already_there->score($already_there->score + $f->score);
    } else {
      $MERGE{$f->source,$f->abs_ref,$f->abs_start} = $f;
    }
  }
  @features = values %MERGE;
}

# sort features by type, ref and start if requested
if ($SORT) {
  @features = sort {
    $a->type cmp $b->type
      || $a->abs_ref cmp $b->abs_ref
	|| $a->start <=> $b->start
      }
    @features;
}

for my $f (@features) {
  print $f->gff_string,"\n";
}


__END__

=head1 NAME

bp_generate_histogram.pl -- Generate a histogram of Bio::DB::GFF features

=head1 SYNOPSIS

  bp_generate_histogram.pl -d gadfly variation gene:curated

=head1 DESCRIPTION

Use this utility to generate feature density histograms from
Bio::DB::GFF databases.  The result is a GFF data file that is
suitable for loading with load_gff.pl.

=head2 OPTIONS

The following options are recognized:

  Option        Description
  ------        -----------

   --dsn        <dsn>       Data source (default dbi:mysql:test)
   --adaptor    <adaptor>   Schema adaptor (default dbi::mysqlopt)
   --user       <user>      Username for mysql authentication
   --pass       <password>  Password for mysql authentication
   --aggregator <list>      Comma-separated list of aggregators

=head1 BUGS

Please report them.

=head1 SEE ALSO

L<Bio::DB::GFF>

=head1 AUTHOR

Lincoln Stein E<lt>lstein@cshl.orgE<gt>

Copyright (c) 2001 Cold Spring Harbor Laboratory

This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself.  See DISCLAIMER.txt for
disclaimers of warranty.

=cut