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Summary

Bio::Restriction::IO::prototype - prototype enzyme set

Package variables

Included modules

Inherit

Bio::Restriction::IO::base

Synopsis

Do not use this module directly. Use it via the Bio::Restriction::IO class.

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.

Methods

Methods description

 Title   : read
 Usage   : $renzs = $stream->read
 Function: reads all the restrction enzymes from the stream
 Returns : a Bio::Restriction::Restriction object
 Args    : none

 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

Methods code

sub read {

    my $self = shift;
    my $coll = Bio::Restriction::EnzymeCollection->new(-empty => 1);
    my ($seentop, $last_type);
    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 =~ 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;

}

sub write {

    my ($self,@h) = @_;
    $self->throw_not_implemented;
}

1;

}

General documentation

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

Please direct usage questions or support issues to the mailing list:
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.

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/

Rob Edwards, redwards@utmem.edu

Heikki Lehvaslaiho, heikki-at-bioperl-dot-org

The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _