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1 # $Id: mapmaker.pm,v 1.5 2002/10/22 07:45:16 lapp Exp $
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2 #
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3 # BioPerl module for Bio::MapIO::mapmaker
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4 #
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5 # Cared for by Jason Stajich <jason@bioperl.org>
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6 #
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7 # Copyright Jason Stajich
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8 #
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9 # You may distribute this module under the same terms as perl itself
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10
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11 # POD documentation - main docs before the code
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12
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13 =head1 NAME
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14
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15 Bio::MapIO::mapmaker - A Mapmaker Map reader
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16
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17 =head1 SYNOPSIS
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18
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19 # do not use this object directly it is accessed through the Bio::MapIO system
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20
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21 use Bio::MapIO;
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22 my $mapio = new Bio::MapIO(-format => "mapmaker",
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23 -file => "mapfile.map");
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24 while( my $map = $mapio->next_map ) {
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25 # get each map
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26 foreach my $marker ( $map->each_element ) {
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27 # loop through the markers associated with the map
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28 }
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29 }
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30
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31 =head1 DESCRIPTION
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32
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33 This object contains code for parsing and processing Mapmaker output
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34 and creating L<Bio::Map::MapI> objects from it.
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35
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36 =head1 FEEDBACK
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37
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38 =head2 Mailing Lists
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39
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40 User feedback is an integral part of the evolution of this and other
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41 Bioperl modules. Send your comments and suggestions preferably to
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42 the Bioperl mailing list. Your participation is much appreciated.
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43
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44 bioperl-l@bioperl.org - General discussion
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45 http://bioperl.org/MailList.shtml - About the mailing lists
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46
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47 =head2 Reporting Bugs
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48
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49 Report bugs to the Bioperl bug tracking system to help us keep track
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50 of the bugs and their resolution. Bug reports can be submitted via
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51 email or the web:
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52
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53 bioperl-bugs@bioperl.org
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54 http://bugzilla.bioperl.org/
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55
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56 =head1 AUTHOR - Jason Stajich
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57
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58 Email jason@bioperl.org
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59
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60 Describe contact details here
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61
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62 =head1 CONTRIBUTORS
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63
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64 Additional contributors names and emails here
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65
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66 =head1 APPENDIX
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67
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68 The rest of the documentation details each of the object methods.
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69 Internal methods are usually preceded with a _
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70
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71 =cut
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72
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73
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74 # Let the code begin...
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75
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76
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77 package Bio::MapIO::mapmaker;
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78 use vars qw(@ISA);
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79 use strict;
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80
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81 use Bio::MapIO;
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82 use Bio::Map::SimpleMap;
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83 use Bio::Map::LinkagePosition;
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84 use Bio::Map::Marker;
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85
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86 @ISA = qw(Bio::MapIO );
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87
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88 =head2 next_map
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89
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90 Title : next_tree
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91 Usage : my $map = $factory->next_map;
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92 Function: Get a map from the factory
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93 Returns : L<Bio::Map::MapI>
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94 Args : none
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95
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96 =cut
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97
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98 sub next_map{
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99 my ($self) = @_;
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100 my ($ready,$map) = (0,new Bio::Map::SimpleMap('-name' => '',
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101 '-units' => 'cM',
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102 '-type' => 'Genetic'));
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103 my @markers;
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104 my $runningDistance = 0;
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105 while( defined($_ = $self->_readline()) ) {
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106 if ( $ready || /^\s+Markers\s+Distance/ ) {
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107 unless ( $ready ) { $ready = 1; next }
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108 } else { next }
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109
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110 last if ( /-{5,}/); # map terminator is -------
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111 s/ +/\t/;
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112 my ($number,$name,$distance) = split;
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113 $runningDistance += $distance;
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114 $runningDistance = '0.0' if $runningDistance == 0;
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115 # print "$_|$number-$name-$distance---------";
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116 my $pos = new Bio::Map::LinkagePosition (-order => $number,
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117 -map => $map,
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118 -value => $runningDistance
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119 );
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120 my $marker = new Bio::Map::Marker(-name=> $name,
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121 -position => $pos,
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122 );
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123 $marker->position($pos);
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124 # use Data::Dumper; print Dumper($marker); exit;
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125 # print $marker->position->value, "\n";
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126 # use Data::Dumper; print Dumper($pos);
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127 # $map->add_element(new Bio::Map::Marker('-name'=> $name,
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128 # '-position' => $pos,
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129 # ));
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130 }
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131 # return undef if( ! $ready );
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132 return $map;
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133 }
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134
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135 =head2 write_map
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136
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137 Title : write_tree
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138 Usage : $factory->write_map($map);
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139 Function: Write a map out through the factory
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140 Returns : none
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141 Args : Bio::Map::MapI
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142
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143 =cut
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144
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145 sub write_map{
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146 my ($self,@args) = @_;
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147 $self->throw_not_implemented();
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148 }
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149
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150 1;
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