Bio/Restriction/IO/prototype.pm

   1 # $Id: prototype.pm 14572 2008-02-29 05:52:03Z cjfields $
   2 #
   3 # BioPerl module for Bio::Restriction::IO::prototype
   4 #
   5 # Cared for by Chris Fields
   6 #
   7 # Copyright Chris Fields
   8 #
   9 # You may distribute this module under the same terms as perl itself
  10
  11 # POD documentation - main docs before the code
  12
  13 =head1 NAME
  14
  15 Bio::Restriction::IO::prototype - prototype enzyme set
  16
  17 =head1 SYNOPSIS
  18
  19 Do not use this module directly.  Use it via the Bio::Restriction::IO class.
  20
  21 =head1 DESCRIPTION
  22
  23 This is a parser for the proto/neo file REBASE format, which contains
  24 prototype information as well as (in the neo file) neoschizomer data.
  25
  26 =head1 FEEDBACK
  27
  28 =head2 Mailing Lists
  29
  30 User feedback is an integral part of the evolution of this and other
  31 Bioperl modules. Send your comments and suggestions preferably to the
  32 Bioperl mailing lists Your participation is much appreciated.
  33
  34   bioperl-l@bioperl.org                  - General discussion
  35   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  36
  37 =head2 Reporting Bugs
  38
  39 Report bugs to the Bioperl bug tracking system to help us keep track
  40 the bugs and their resolution.  Bug reports can be submitted via the
  41 web:
  42
  43   http://bugzilla.open-bio.org/
  44
  45 =head1 AUTHOR
  46
  47 Rob Edwards, redwards@utmem.edu
  48
  49 =head1 CONTRIBUTORS
  50
  51 Heikki Lehvaslaiho, heikki-at-bioperl-dot-org
  52
  53 =head1 APPENDIX
  54
  55 The rest of the documentation details each of the object
  56 methods. Internal methods are usually preceded with a _
  57
  58 =cut
  59
  60 # Let the code begin...
  61
  62 package Bio::Restriction::IO::prototype;
  63
  64 use vars qw(%WITH_REFM_FIELD);
  65 use strict;
  66
  67 #use Bio::Restriction::IO;
  68 use Bio::Restriction::Enzyme;
  69 use Bio::Restriction::EnzymeCollection;
  70
  71 use Data::Dumper;
  72
  73 use base qw(Bio::Restriction::IO::base);
  74
  75 sub new {
  76     my($class, @args) = @_;
  77     my $self = bless {}, $class;
  78     $self->_initialize(@args);
  79     return $self;
  80 }
  81
  82 sub _initialize {
  83     my($self,@args) = @_;
  84     my ($verbose) =
  85             $self->_rearrange([qw(
  86                                   VERBOSE
  87                                  )], @args);
  88     $verbose || 0;
  89     $self->verbose($verbose);
  90     return unless $self->SUPER::_initialize(@args);
  91 }
  92
  93 =head2 read
  94
  95  Title   : read
  96  Usage   : $renzs = $stream->read
  97  Function: reads all the restrction enzymes from the stream
  98  Returns : a Bio::Restriction::Restriction object
  99  Args    : none
 100
 101 =cut
 102
 103 sub read {
 104     my $self = shift;
 105     my $coll = Bio::Restriction::EnzymeCollection->new(-empty => 1);
 106     my ($seentop, $last_type);
 107     while (defined (my $line = $self->_readline)) {
 108         chomp $line;
 109         next unless $line;
 110         if ($line =~ /TYPE\s+(I)+/) {
 111             $last_type = $1;
 112             $seentop ||= 1;
 113             next;
 114         }
 115         next unless $seentop;
 116         my @data = split /\s+/,$line,2;
 117         next if $data[0] =~ /^[-\s]*$/;
 118         # neo
 119         my ($enzyme, $is_neo, $is_proto, $site);
 120         if ($data[0] =~ /^\s+(\S+)\s+(\S+)/) {
 121             ($enzyme, $site, $is_proto, $is_neo) = ($1, $2, 0, 1);
 122         } else {
 123             ($enzyme, $site, $is_proto, $is_neo) = ($data[0], $data[1], 1, 0);
 124         }
 125         $site =~ s/\s+//g;
 126
 127         my $precut;
 128         if ($site =~ m/^\((\d+\/\d+)\)[RYATGCN]+/) {
 129             $precut=$1;
 130             $site =~ s/\($precut\)//;
 131         }
 132
 133         my ($cut, $comp_cut);
 134         ($site, $cut, $comp_cut) = $self->_cuts_from_site($site);
 135
 136         my $re = Bio::Restriction::Enzyme->new(
 137             -type => $last_type,
 138             -site => $site,
 139             -name => $enzyme,
 140             -is_prototype => $is_proto,
 141             -is_neoschizomer => $is_neo);
 142
 143         if ($cut) {
 144             $re->cut($self->_coordinate_shift_to_cut(length($site), $cut));
 145             $re->complementary_cut($self->_coordinate_shift_to_cut(length($site), $comp_cut));
 146         }
 147
 148         $coll->enzymes($re);
 149     }
 150     return $coll->enzymes;
 151 }
 152
 153 =head2 write
 154
 155  Title   : write
 156  Usage   : $stream->write($renzs)
 157  Function: writes restriction enzymes into the stream
 158  Returns : 1 for success and 0 for error
 159  Args    : a Bio::Restriction::Enzyme
 160            or a Bio::Restriction::EnzymeCollection object
 161
 162 =cut
 163
 164 sub write {
 165     my ($self,@h) = @_;
 166     $self->throw_not_implemented;
 167 }
 168
 169 1;