Bio/MapIO/mapmaker.pm

   1 #
   2 # BioPerl module for Bio::MapIO::mapmaker
   3 #
   4 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   5 #
   6 # Cared for by Jason Stajich <jason@bioperl.org>
   7 #
   8 # Copyright Jason Stajich
   9 #
  10 # You may distribute this module under the same terms as perl itself
  11
  12 # POD documentation - main docs before the code
  13
  14 =head1 NAME
  15
  16 Bio::MapIO::mapmaker - A Mapmaker Map reader
  17
  18 =head1 SYNOPSIS
  19
  20 # do not use this object directly it is accessed through the Bio::MapIO system
  21
  22     use Bio::MapIO;
  23     my $mapio = Bio::MapIO->new(-format => "mapmaker",
  24                                               -file   => "mapfile.map");
  25     while ( my $map = $mapio->next_map ) {  # get each map
  26             foreach my $marker ( $map->each_element ) {
  27                # loop through the markers associated with the map
  28             }
  29     }
  30
  31 =head1 DESCRIPTION
  32
  33 This object contains code for parsing and processing Mapmaker output
  34 and creating L<Bio::Map::MapI> objects from it.
  35
  36 =head1 FEEDBACK
  37
  38 =head2 Mailing Lists
  39
  40 User feedback is an integral part of the evolution of this and other
  41 Bioperl modules. Send your comments and suggestions preferably to
  42 the Bioperl mailing list.  Your participation is much appreciated.
  43
  44   bioperl-l@bioperl.org                  - General discussion
  45   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  46
  47 =head2 Support
  48
  49 Please direct usage questions or support issues to the mailing list:
  50
  51 I<bioperl-l@bioperl.org>
  52
  53 rather than to the module maintainer directly. Many experienced and
  54 reponsive experts will be able look at the problem and quickly
  55 address it. Please include a thorough description of the problem
  56 with code and data examples if at all possible.
  57
  58 =head2 Reporting Bugs
  59
  60 Report bugs to the Bioperl bug tracking system to help us keep track
  61 of the bugs and their resolution. Bug reports can be submitted via the
  62 web:
  63
  64   https://github.com/bioperl/bioperl-live/issues
  65
  66 =head1 AUTHOR - Jason Stajich
  67
  68 Email jason@bioperl.org
  69
  70 =head1 APPENDIX
  71
  72 The rest of the documentation details each of the object methods.
  73 Internal methods are usually preceded with a _
  74
  75 =cut
  76
  77 # Let the code begin...
  78
  79 package Bio::MapIO::mapmaker;
  80 use strict;
  81
  82 use Bio::Map::SimpleMap;
  83 use Bio::Map::LinkagePosition;
  84 use Bio::Map::Marker;
  85
  86 use base qw(Bio::MapIO);
  87
  88 =head2 next_map
  89
  90  Title   : next_map
  91  Usage   : my $map = $factory->next_map;
  92  Function: Get one or more map objects from the Mapmaker input
  93  Returns : Bio::Map::MapI
  94  Args    : none
  95
  96 See L<Bio::Map::MapI>
  97
  98 =cut
  99
 100 sub next_map{
 101    my ($self) = @_;
 102    my $map = Bio::Map::SimpleMap->new(-name  => '',
 103                                                                                                   -units => 'cM',
 104                                                                                                   -type  => 'Genetic');
 105
 106         # Mapmaker input can be free-form, like the result of a copy-paste
 107         # from a terminal, with no particular format before or after the
 108         # map data. The $in_map variable is a flag that's set to 1 when
 109         # we're reading map data lines and set back to 0 when we're finished.
 110    my ($in_map,$runningDistance);
 111
 112    while ( defined ($_ = $self->_readline()) ) {
 113                 if ( /^\s+Markers\s+Distance/ ) {
 114                         $in_map = 1;
 115                         next;
 116                 }
 117                 next unless $in_map;
 118
 119                 s/ +/\t/;
 120                 my ($number,$name,$distance) = split;
 121                 $runningDistance += $distance unless ($distance =~ /-+/);
 122                 $runningDistance = '0.0' if ($runningDistance == 0 || $distance =~ /-+/);
 123
 124                 my $pos = Bio::Map::LinkagePosition->new(-order => $number,
 125                                                                                                                          -map   => $map,
 126                                                                                                                          -value => $runningDistance );
 127                 my $marker = Bio::Map::Marker->new(-name     => $name,
 128                                                                                                          -position => $pos );
 129
 130                 if ($distance =~ /-+/) { # last marker
 131                         $in_map = 0;
 132                         return $map;
 133                 }
 134         }
 135 }
 136
 137 =head2 write_map
 138
 139  Title   : write_map
 140  Usage   : $factory->write_map($map);
 141  Function: Write a map out through the factory
 142  Returns : none
 143  Args    : Bio::Map::MapI
 144
 145 =cut
 146
 147 sub write_map{
 148    my ($self,@args) = @_;
 149    $self->throw_not_implemented();
 150 }
 151
 152 1;