Bio::Restriction::IO itype2
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Summary
Bio::Restriction::IO::itype2 - itype2 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 tab delimited, entry per line format which is fast to process.
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::IO object
Args : none
Internally creates a hash of enzyme information which is passed on to
Bio::Restriction::Enzyme::new.
_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);

    # 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 ---------------
# this regexp now parses all possible components
# $1 : (s/t) or undef
# $2 : [site]
# $3 : (m/n) or undef /maj
my ($precut, $recog, $postcut) = ( $site =~ m/^(?:\((\w+\/\w+)\))?([\w^]+)(?:\((\w+\/\w+)\))?/ );
my @sequences; if ($site =~ /\,/) { @sequences = split( /\,/, $site); $site=shift @sequences; } #
# prototype
#
# presence of a name means the prototype isoschizomer, absence means
# this enzyme is the prototype
my $is_prototype = ($prototype ? 1 : 0); #
# vendors
#
my @vendors; @vendors = ( split / */, $vendor) if $vendor; #
# references
#
my @refs; @refs = map {split /\n+/} $refs if $refs; # 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, -prototype => $prototype, -vendors => [@vendors], -references => [@refs], -xln_sub =>\& _xln_sub ); #
# methylation
#
# [easier to set here during parsing than in constructor] /maj
my @meths; if ($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; } } #
# create special types of Enzymes
#
$self->_make_multisites( $re,\@ sequences,\@ meths) 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 _