Summary

Bio::Restriction::IO::withrefm - withrefm 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 the most complete format of the REBASE files, and basically
includes all the data on each of the restriction enzymes.

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 new {

    my($class, @args) = @_;
    my $self = bless {}, $class;
    $self->_initialize(@args);
    return $self;

}

sub _initialize {

    my($self,@args) = @_;
    my ($verbose) =
            $self->_rearrange([qw(
                                  VERBOSE
                                 )], @args);
    $verbose || 0;
    $self->verbose($verbose);

    return unless $self->SUPER::_initialize(@args);

}

sub read {

    my $self = shift;

    my $renzs = new Bio::Restriction::EnzymeCollection(-empty => 1);

    local $/ = '<1>';
    while (defined(my $entry=$self->_readline()) ) {

        # not an entry.
        next unless $entry =~ /<2>/;

        #$self->debug("|$entry|\n");

        #
        # Minimal information
        #
        my ($name) = $entry =~ /^(\S+)/;
        my ($site) = $entry =~ /<3>([^\n]+)/;


        if ($site eq ''  or $site eq '?') {
            $self->warn("$name: no site. Skipping") if $self->verbose > 1;
            next;
        }

        my $precut;
        if ($site =~ m/^\((\w+\/\w+)\)\w+\((\w+\/\w+)\)/) {
            $precut = $1;
            $site =~ s/\($precut\)//;
        }

        # there are a couple of sequences that have multiple
        # recognition sites eg M.PhiBssHII: ACGCGT,CCGCGG,RGCGCY,RCCGGY,GCGCGC


        my @sequences;
        if ($site =~ /\,/) {
            @sequences = split /\,/, $site;
            $site=shift @sequences;
        }

        my ($cut, $comp_cut);
        ($site, $cut, $comp_cut) = $self->_cuts_from_site($site);

        my $re = new Bio::Restriction::Enzyme(-name=>$name,
                                              -site => $site
                                             );
        $renzs->enzymes($re);

        if ($cut) {
            $re->cut($self->_coordinate_shift_to_cut(length($site), $cut));
            $re->complementary_cut($self->_coordinate_shift_to_cut(length($site), $comp_cut));
        }

        #
        # prototype / isoschizomers
        #

        my ($isoschizomers) = $entry =~ /<2>([^\n]+)/;

        if ($isoschizomers) {
            $re->isoschizomers(split /\,/, $isoschizomers);
            $re->is_prototype(0);
        } else {
            $re->is_prototype(1);
        }

        #
        # methylation
        #

        my ($meth) = $entry =~ /<4>([^\n]+)/;
        my @meths;
        if ($meth) {
            # this can be either X(Y) or X(Y),X2(Y2)
            # where X is the base and y is the type of methylation
            if ( $meth =~ /(\S+)\((\d+)\),(\S+)\((\d+)\)/ ) { # two msites per site
                #my ($p1, $m1, $p2, $m2) = ($1, $2, $3, $4);
                $re->methylation_sites($self->_meth($re,$1, $2),
                                       $self->_meth($re,$3,$4));
            }
            elsif ($meth =~ /(\S+)\((\d+)\)/ ) { # one msite per site or more sites
                #print Dumper $meth;
                $re->methylation_sites( $self->_meth($re,$1,$2) );
                @meths = split /, /, $meth;
                $meth=shift @meths;
            } else {
                $self->warn("Unknown methylation format [$meth]") if $self->verbose >0;
            }
        }

        #
        # microbe
        #
        my ($microbe) = $entry =~ /<5>([^\n]+)/;
        $re->microbe($microbe) if $microbe;

        #
        # source
        #
        my ($source) = $entry =~ /<6>([^\n]+)/;
        $re->source($source) if $source;

        #
        # vendors
        #
        my ($vendors) = $entry =~ /<7>([^\n]+)/;
        $re->vendors(split / */, $vendors) if $vendors;

        #
        # references
        #
        my ($refs) = $entry =~ /<8>(.+)/s;
        $re->references(map {split /\n+/} $refs) if $refs;


        #
        # create special types of Enzymes
        #
        $self->_make_multisites($renzs, $re,\@ sequences,\@ meths) if @sequences;

        $self->_make_multicuts($renzs, $re, $precut) if $precut;

    }

    return $renzs;

}

sub write {

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

}

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://bio.perl.org/MailList.html        - About the mailing lists

Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via email
or the web:

  bioperl-bugs@bio.perl.org
  http://bugzilla.bioperl.org/

Rob Edwards, redwards@utmem.edu

Heikki Lehvaslaiho, heikki@ebi.ac.uk

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