Bio::Restriction::IO withrefm
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Summary
Bio::Restriction::IO::withrefm - withrefm enzyme set
Package variables
No package variables defined.
Included modules
Bio::Restriction::Enzyme
Bio::Restriction::EnzymeCollection
Data::Dumper
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
readDescriptionCode
_xln_subDescriptionCode
writeDescriptionCode
Methods description
readcode    nextTop
 Title   : read
Usage : $renzs = $stream->read
Function: reads all the restrction enzymes from the stream
Returns : a Bio::Restriction::Restriction object
Args : none
_xln_subcodeprevnextTop
 Title   : _xln_sub
Function: Translates withrefm coords to Bio::Restriction coords
Args : Bio::Restriction::Enzyme object, scalar integer (cut posn)
Note : Used internally; pass as a coderef to the B:R::Enzyme
constructor
writecodeprevnextTop
 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
readdescriptionprevnextTop
sub read {
    my $self = shift;

    my $renzs = Bio::Restriction::EnzymeCollection->new(-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 ( ! defined $site || $site eq '' or $site eq '?') { $self->warn("$name: no site. Skipping") if $self->verbose > 1; next; } # there are a couple of sequences that have multiple
# recognition sites eg M.PhiBssHII: ACGCGT,CCGCGG,RGCGCY,RCCGGY,GCGCGC
# TaqII : GACCGA(11/9),CACCCA(11/9)
my @sequences; if ($site =~ /\,/) { @sequences = split (/\,/, $site); $site=shift @sequences; } # this regexp now parses all possible components
# $1 : (s/t) or undef
# $2 : [site]
# $3 : (m/n) or undef /maj
no warnings; # avoid faulty 'uninitialized value' warnings
# occurring against the variables set by
# regexp matching (unless anyone has other ideas...)
my ($precut, $recog, $postcut) = ( $site =~ m/^(?:\((-?\w+\/-?\w+)\))?([\w^]+)(?:\((-?\w+\/-?\w+)\))?/ );
#
# prototype / isoschizomers
#
my ($isoschizomers) = $entry =~ /<2>([^\n]+)/; my @isos = split(/\,/,$isoschizomers); my $is_prototype = (@isos ? 1 : 0); #
# microbe
#
my ($microbe) = $entry =~ /<5>([^\n]+)/; #
# source
#
my ($source) = $entry =~ /<6>([^\n]+)/; #
# vendors
#
my ($vendors) = $entry =~ /<7>([^\n]+)/; my @vendors = split(/ */, $vendors); #
# references
#
my ($refs) = $entry =~ /<8>(.+)<1>/s; my @refs = map {split /\n+/} $refs; use warnings; # when enz is constructed, site() will contain original characters,
# but recog() will contain a regexp if required.../maj
my $re = Bio::Restriction::Enzyme->new( -name => $name, -site => $recog, -recog => $recog, -precut => $precut, -postcut => $postcut, -is_prototype => $is_prototype, -isoschizomers => [@isos], -source => $source, -vendors => [@vendors], -references => [@refs], -xln_sub =>\& _xln_sub ); #
# methylation: easier to set here during parsing/maj
#
my ($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
$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; } } # the _make_multicuts function now takes place in the
# Enzyme constructor / maj
#
# create special types of Enzymes
# (because of object cloning in _make_multisites, this happens
# after everything else is set /maj)
# (with the removal of the collection from the arglist, this
# call (or its code) could now be placed in the constructor,
# which is safer (since this has to happen last),
# but it requires the methylation info, which
# is more natural to get out here in the parsing./maj
$self->_make_multisites($re,\@ sequences,\@ meths,\& _xln_sub) if @sequences; $renzs->enzymes($re); } return $renzs;
}
_xln_subdescriptionprevnextTop
sub _xln_sub {
     my ($z,$c) = @_; 
    return ($c < 0 ? $c : length($z->string)+$c);
}
writedescriptionprevnextTop
sub write {
    my ($self,@h) = @_;
    $self->throw_not_implemented;
}

1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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
Support Top
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.
Reporting BugsTop
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/
AUTHORTop
Rob Edwards, redwards@utmem.edu
CONTRIBUTORSTop
Heikki Lehvaslaiho, heikki-at-bioperl-dot-org
Mark A. Jensen, maj-at-fortinbras-dot-us
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _