#
# BioPerl module for Bio::Restriction::IO::prototype
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Chris Fields
#
# Copyright Chris Fields
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Restriction::IO::prototype - prototype enzyme set
=head1 SYNOPSIS
Do not use this module directly. Use it via the Bio::Restriction::IO class.
=head1 DESCRIPTION
This is a parser for the proto/neo file REBASE format, which contains
prototype information as well as (in the neo file) neoschizomer data.
=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 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://github.com/bioperl/bioperl-live/issues
=head1 AUTHOR
Rob Edwards, redwards@utmem.edu
=head1 CONTRIBUTORS
Heikki Lehvaslaiho, heikki-at-bioperl-dot-org
=head1 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Restriction::IO::prototype;
use vars qw(%WITH_REFM_FIELD);
use strict;
use Bio::Restriction::Enzyme;
use Bio::Restriction::EnzymeCollection;
use Data::Dumper;
use base qw(Bio::Restriction::IO::base);
=head2 read
Title : read
Usage : $renzs = $stream->read
Function: reads all the restrction enzymes from the stream
Returns : a Bio::Restriction::Restriction object
Args : none
=cut
sub read {
my $self = shift;
my $coll = Bio::Restriction::EnzymeCollection->new(-empty => 1);
my ($seentop, $last_type);
ENZYME:
while (defined (my $line = $self->_readline)) {
chomp $line;
next unless $line;
if ($line =~ /TYPE\s+(I)+/) {
$last_type = $1;
$seentop ||= 1;
next;
}
next unless $seentop;
my @data = split /\s+/,$line,2;
next if $data[0] =~ /^[-\s]*$/;
# neo
my ($enzyme, $is_neo, $is_proto, $site);
if ($data[0] =~ /^\s+(\S+)\s+(\S+)/) {
($enzyme, $site, $is_proto, $is_neo) = ($1, $2, 0, 1);
} else {
($enzyme, $site, $is_proto, $is_neo) = ($data[0], $data[1], 1, 0);
}
$site =~ s/\s+//g;
my $precut;
if ($site =~ /,/) {
$self->warn("Split site support not available for Bio::Restriction::Enzyme yet, ".
"skipping $enzyme [$site]");
next ENZYME;
}
if ($site =~ m/^\((\d+\/\d+)\)[RYATGCN]+/) {
$precut=$1;
$site =~ s/\($precut\)//;
}
my ($cut, $comp_cut);
($site, $cut, $comp_cut) = $self->_cuts_from_site($site);
my $re = Bio::Restriction::Enzyme->new(
-type => $last_type,
-site => $site,
-name => $enzyme,
-is_prototype => $is_proto,
-is_neoschizomer => $is_neo);
if ($cut) {
$re->cut($self->_coordinate_shift_to_cut(length($site), $cut));
$re->complementary_cut($self->_coordinate_shift_to_cut(length($site), $comp_cut));
}
$coll->enzymes($re);
}
return $coll->enzymes;
}
=head2 write
Title : write
Usage : $stream->write($renzs)
Function: writes restriction enzymes into the stream
Returns : 1 for success and 0 for error
Args : a Bio::Restriction::Enzyme
or a Bio::Restriction::EnzymeCollection object
=cut
sub write {
my ($self,@h) = @_;
$self->throw_not_implemented;
}
1;