Summary

Bio::Restriction::IO::itype2 - itype2 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 tab delimited, entry per line format which is fast to process.

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);

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

}

sub read {

    my $self = shift;

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

    # read until start of data
    while (defined( my $line = $self->_readline()) ) {
        next if $line =~ /^[ R]/;
        $self->_pushback($line);
        last;
    }

    # enzyme name [tab] prototype [tab] recognition sequence with
    # cleavage site [tab] methylation site and type [tab] commercial
    # source [tab] references

    while (defined(my $line = $self->_readline()) ) {
        $self->debug($line);
        chomp $line;

        my ($name, $prototype, $site, $meth, $vendor, $refs) = split /\t/, $line;
        # we need mininum name and site
        unless ($site) {
            $self->warn("Can not parse line with name [$name]") if $self->verbose > 0;
            next;
        }
        next unless $name;

        # four cut enzymes are not in this format
        my $precut;
        if ($site =~ m/^\((\d+\/\d+)\)[ATGCN]+/) {
            $precut=$1;
            $site =~ s/\($precut\)//;
        }
        # -------------- cut ---------------

        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 
        #

        $prototype ? $re->prototype_name($prototype) : $re->is_prototype;


        #
        # methylation
        #
        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;
            }
        }

        #
        # vendors
        #
        if ($vendor) {
            $re->vendors( split / */, $vendor);
        }

        #
        # references
        #
        $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 _