/usr/share/perl5/Bio/SeqFeature/Amplicon.pm is in libbio-perl-perl 1.6.923-1.
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# BioPerl module for Bio::SeqFeature::Amplicon
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Copyright Florent Angly
#
# You may distribute this module under the same terms as perl itself
=head1 NAME
Bio::SeqFeature::Amplicon - Amplicon feature
=head1 SYNOPSIS
# Amplicon with explicit sequence
use Bio::SeqFeature::Amplicon;
my $amplicon = Bio::SeqFeature::Amplicon->new(
-seq => $seq_object,
-fwd_primer => $primer_object_1,
-rev_primer => $primer_object_2,
);
# Amplicon with implicit sequence
use Bio::Seq;
my $template = Bio::Seq->new( -seq => 'AAAAACCCCCGGGGGTTTTT' );
$amplicon = Bio::SeqFeature::Amplicon->new(
-start => 6,
-end => 15,
);
$template->add_SeqFeature($amplicon);
print "Amplicon start : ".$amplicon->start."\n";
print "Amplicon end : ".$amplicon->end."\n";
print "Amplicon sequence: ".$amplicon->seq->seq."\n";
# Amplicon sequence should be 'CCCCCGGGGG'
=head1 DESCRIPTION
Bio::SeqFeature::Amplicon extends L<Bio::SeqFeature::Subseq> to represent an
amplicon sequence and optional primer sequences.
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via
the web:
https://redmine.open-bio.org/projects/bioperl/
=head1 AUTHOR
Florent Angly <florent.angly@gmail.com>
=head1 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
=cut
package Bio::SeqFeature::Amplicon;
use strict;
use base qw(Bio::SeqFeature::SubSeq);
=head2 new
Title : new()
Usage : my $amplicon = Bio::SeqFeature::Amplicon( -seq => $seq_object );
Function: Instantiate a new Bio::SeqFeature::Amplicon object
Args : -seq , the sequence object or sequence string of the amplicon (optional)
-fwd_primer , a Bio::SeqFeature primer object with specified location on amplicon (optional)
-rev_primer , a Bio::SeqFeature primer object with specified location on amplicon (optional)
Returns : A Bio::SeqFeature::Amplicon object
=cut
sub new {
my ($class, @args) = @_;
my $self = $class->SUPER::new(@args);
my ($fwd_primer, $rev_primer) =
$self->_rearrange([qw(FWD_PRIMER REV_PRIMER)], @args);
$fwd_primer && $self->fwd_primer($fwd_primer);
$rev_primer && $self->rev_primer($rev_primer);
return $self;
}
sub _primer {
# Get or set a primer. Type is either 'fwd' or 'rev'.
my ($self, $type, $primer) = @_;
if (defined $primer) {
if ( not(ref $primer) || not $primer->isa('Bio::SeqFeature::Primer') ) {
$self->throw("Expected a primer object but got a '".ref($primer)."'\n");
}
if ( not defined $self->location ) {
$self->throw("Location of $type primer on amplicon is not known. ".
"Use start(), end() or location() to set it.");
}
$primer->primary_tag($type.'_primer');
$self->add_SeqFeature($primer);
}
return (grep { $_->primary_tag eq $type.'_primer' } $self->get_SeqFeatures)[0];
}
=head2 fwd_primer
Title : fwd_primer
Usage : my $primer = $feat->fwd_primer();
Function: Get or set the forward primer. When setting it, the primary tag
'fwd_primer' is added to the primer and its start, stop and strand
attributes are set if needed, assuming that the forward primer is
at the beginning of the amplicon and the reverse primer at the end.
Args : A Bio::SeqFeature::Primer object (optional)
Returns : A Bio::SeqFeature::Primer object
=cut
sub fwd_primer {
my ($self, $primer) = @_;
return $self->_primer('fwd', $primer);
}
=head2 rev_primer
Title : rev_primer
Usage : my $primer = $feat->rev_primer();
Function: Get or set the reverse primer. When setting it, the primary tag
'rev_primer' is added to the primer.
Args : A Bio::SeqFeature::Primer object (optional)
Returns : A Bio::SeqFeature::Primer object
=cut
sub rev_primer {
my ($self, $primer) = @_;
return $self->_primer('rev', $primer);
}
1;
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