Bio::Restriction::IO bairoch
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Summary
Bio::Restriction::IO::bairoch - bairoch enzyme set
Package variables
No package variables defined.
Included modules
Bio::Restriction::Enzyme
Bio::Restriction::Enzyme::MultiCut
Bio::Restriction::Enzyme::MultiSite
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.
This parser is for the Bairoch format (aka MacVector, Vector NTI, PC/Gene
(Bairoch) format), REBASE format #19
Methods
readDescriptionCode
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
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 $/ = '//';
    while (defined(my $entry=$self->_readline()) ) {
        $self->debug("|$entry|\n");

        #
# Minimal information
#
my ($name) = $entry =~ /ID\s+(\S+)/; my ($site) = $entry =~ /RS\s+([^\n]+)/; next unless ($name && $site); # the standard sequence format for these guys is:
# GATC, 2;
# or, for enzymes that cut more than once
# GATC, 2; GTAC, 2;
# there are a couple of sequences that have multiple
# recognition sites.
my @sequences; if ($site =~ /\;/) { @sequences = split /\;/, $site; $self->debug(@sequences,"\n"); $site=shift @sequences; } my ($seq, $cut)=split /,\s+/, $site; $self->debug("SITE: |$site| GAVE: |$seq| and |$cut|\n"); if ($seq eq '?') { $self->warn("$name: no site. Skipping") if $self->verbose > 1; next; } # this is mainly an error check to make sure that I am adding what I think I am!
if ($seq !~ /[NGATC]/i) { $self->throw("Sequence $name has weird sequence: |$seq|"); } my $re; if ($cut eq "?") { $re = Bio::Restriction::Enzyme->new(-name=>$name, -seq => $seq); } else { if ($cut !~ /^-?\d+$/) { $self->throw("Cut site from $name is weird: |$cut|\n"); } $re = Bio::Restriction::Enzyme->new(-name=>$name, -cut => $cut, -seq => $seq ); } $renzs->enzymes($re); #
# prototype / isoschizomers
#
my ($prototype) = $entry =~ /PT\s+([^\n]+)/; if ($prototype) { #$re->isoschizomers(split /\,/, $isoschizomers);
#NOTE: Need to add a method so that we can add isoschosomers to enzymes that may not exist!
$re->is_prototype(0); } else { $re->is_prototype(1); } #
# methylation
#
my ($meth) = $entry =~ /MS\s+([^\n]+)/; my @meths; if ($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 =~ /OS\s+([^\n]+)/; $re->microbe($microbe) if $microbe; #
# source
#
#my ($source) = $entry =~ /<6>([^\n]+)/;
#$re->source($source) if $source;
#
# vendors
#
my ($vendors) = $entry =~ /CR\s+([^\n]+)/; $re->vendors(split /,\s*/, $vendors) if $vendors; #
# references
#
#my ($refs) = $entry =~ /<8>(.+)/s;
#$re->references(map {split /\n+/} $refs) if $refs;
#
# create special types of Enzymes
#
$self->warn("Current issues with multisite enzymes using bairoch format\n". "Recommend using itype2 or withrefm formats for now") if @sequences; #$self->_make_multisites($renzs, $re, \@sequences, \@meths) if @sequences;
} return $renzs;
}
writedescriptionprevnextTop
sub write {
    my ($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
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _