# $Id: bairoch.pm 16123 2009-09-17 12:57:27Z cjfields $
# BioPerl module for Bio::Restriction::IO::withrefm
#
# Please direct questions and support issues to <bioperl-l@bioperl.org> 
#
# Cared for by Rob Edwards <redwards@utmem.edu>
#
# Copyright Rob Edwards
#
# You may distribute this module under the same terms as perl itself
#

# POD documentation - main docs before the code

=head1 NAME

Bio::Restriction::IO::bairoch - bairoch enzyme set

=head1 SYNOPSIS

Do not use this module directly.  Use it via the Bio::Restriction::IO class.

=head1 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

=head1 FEEDBACK

=head2 Mailing Lists

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

=head2 Support 

Please direct usage questions or support issues to the mailing list:

I<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.

=head2 Reporting Bugs

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:

  http://bugzilla.open-bio.org/

=head1 AUTHOR

Rob Edwards, redwards@utmem.edu

=head1 CONTRIBUTORS

Heikki Lehvaslaiho, heikki-at-bioperl-dot-org

=head1 APPENDIX

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

=cut

# Let the code begin...

package Bio::Restriction::IO::bairoch;

use vars qw(%WITH_REFM_FIELD);
use strict;

use Bio::Restriction::Enzyme;
use Bio::Restriction::Enzyme::MultiCut;
use Bio::Restriction::Enzyme::MultiSite;
use Bio::Restriction::EnzymeCollection;

use Data::Dumper;

use base qw(Bio::Restriction::IO::base);

=head2 read

 Title   : read
 Usage   : $renzs = $stream->read
 Function: reads all the restrction enzymes from the stream
 Returns : a Bio::Restriction::Restriction object
 Args    : none

=cut

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;
}


=head2 write

 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

=cut

sub write {
    my ($self,@h) = @_;
    $self->throw_not_implemented;
}

1;
