/usr/lib/perl5/TFBS/SitePair.pm is in libtfbs-perl 0.5.svn.20100421-1build1.
This file is owned by root:root, with mode 0o644.
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 | package TFBS::SitePair;
use vars qw(@ISA);
use strict;
use Bio::SeqFeature::FeaturePair;
@ISA = qw(Bio::SeqFeature::FeaturePair);
# 'new' used to be inherited, but we need it now
sub new {
my ($caller, $site1, $site2) = @_;
#if ($Bio::Root::Root::VERSION < 1.4) {
#return $caller->SUPER::new($site1, $site2);
#}
#else {
return $caller->SUPER::new(-feature1 => $site1,
-feature2 => $site2);
#}
# ^ Version check commented out because from BioPerl 1.5.2
# version nrs are represented differently. // PE 2007-7-11
}
=head2 pattern
Title : pattern
Usage : my $pattern = $sitepair->pattern(); # gets the pattern
# sets the pattern to $pwm
Function: gets the pattern object associated with the site pair
Returns : pattern object, here TFBS::Matrix::PWM object
Args : none (get-only method)
=cut
sub pattern {
$_[0]->feature1->pattern();
}
=head2 GFF
Title : GFF
Usage : print $site->GFF();
: print $site->GFF($gff_formatter)
Function: returns a "standard" multiline GFF string
Returns : a string (multiline, newline terminated)
Args : a $gff_formatter function reference (optional)
=cut
sub GFF {
return join "\n", $_[0]->site1->GFF, $_[0]->site2->GFF;
}
=head2 site1
=head2 site2
Title : site1
site2
Usage : my $site1 = $sitepair->site1();
Function: Returns individual TFBS::Site objects, from the site pair
Returns : a TFBS::Site
Args : none
=cut
sub site1 {
$_[0]->feature1();
}
sub site2 {
$_[0]->feature2();
}
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