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1 # $Id: mase.pm,v 1.9 2002/10/22 07:38:25 lapp Exp $
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2 #
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3 # BioPerl module for Bio::AlignIO::mase
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4
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5 # based on the Bio::SeqIO::mase module
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6 # by Ewan Birney <birney@sanger.ac.uk>
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7 # and Lincoln Stein <lstein@cshl.org>
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8 #
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9 # and the SimpleAlign.pm module of Ewan Birney
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10 #
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11 # Copyright Peter Schattner
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12 #
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13 # You may distribute this module under the same terms as perl itself
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14 # _history
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15 # September 5, 2000
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16 # POD documentation - main docs before the code
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17
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18 =head1 NAME
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19
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20 Bio::AlignIO::mase - mase sequence input/output stream
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21
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22 =head1 SYNOPSIS
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23
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24 Do not use this module directly. Use it via the L<Bio::AlignIO> class.
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25
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26 =head1 DESCRIPTION
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27
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28 This object can transform L<Bio::Align::AlignI> objects to and from mase flat
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29 file databases.
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30
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31 =head1 FEEDBACK
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32
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33 =head2 Reporting Bugs
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34
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35 Report bugs to the Bioperl bug tracking system to help us keep track
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36 the bugs and their resolution.
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37 Bug reports can be submitted via email or the web:
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38
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39 bioperl-bugs@bio.perl.org
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40 http://bugzilla.bioperl.org/
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41
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42 =head1 AUTHORS - Peter Schattner
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43
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44 Email: schattner@alum.mit.edu
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45
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46
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47 =head1 APPENDIX
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48
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49 The rest of the documentation details each of the object
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50 methods. Internal methods are usually preceded with a _
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51
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52 =cut
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53
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54 # Let the code begin...
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55
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56 package Bio::AlignIO::mase;
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57 use vars qw(@ISA);
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58 use strict;
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59
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60 use Bio::AlignIO;
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61
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62 @ISA = qw(Bio::AlignIO);
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63
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64
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65 =head2 next_aln
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66
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67 Title : next_aln
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68 Usage : $aln = $stream->next_aln()
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69 Function: returns the next alignment in the stream.
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70 Returns : L<Bio::Align::AlignI> object
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71 Args : NONE
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72
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73 =cut
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74
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75 sub next_aln {
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76 my $self = shift;
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77 my $entry;
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78 my $name;
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79 my $start;
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80 my $end;
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81 my $seq;
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82 my $add;
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83 my $count = 0;
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84 my $seq_residues;
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85
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86 my $aln = Bio::SimpleAlign->new(-source => 'mase');
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87
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88
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89 while( $entry = $self->_readline) {
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90 $entry =~ /^;/ && next;
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91 if( $entry =~ /^(\S+)\/(\d+)-(\d+)/ ) {
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92 $name = $1;
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93 $start = $2;
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94 $end = $3;
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95 } else {
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96 $entry =~ s/\s//g;
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97 $name = $entry;
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98 $end = -1;
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99 }
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100
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101 $seq = "";
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102
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103 while( $entry = $self->_readline) {
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104 $entry =~ /^;/ && last;
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105 $entry =~ s/[^A-Za-z\.\-]//g;
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106 $seq .= $entry;
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107 }
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108 if( $end == -1) {
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109 $start = 1;
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110
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111 $seq_residues = $seq;
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112 $seq_residues =~ s/\W//g;
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113 $end = length($seq_residues);
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114 }
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115
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116 $add = new Bio::LocatableSeq('-seq'=>$seq,
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117 '-id'=>$name,
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118 '-start'=>$start,
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119 '-end'=>$end,
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120 );
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121
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122
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123 $aln->add_seq($add);
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124
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125
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126 # If $end <= 0, we have either reached the end of
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127 # file in <> or we have encountered some other error
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128 #
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129 if ($end <= 0) { undef $aln;}
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130
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131 }
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132
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133 return $aln;
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134 }
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135
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136
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137
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138 =head2 write_aln
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139
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140 Title : write_aln
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141 Usage : $stream->write_aln(@aln)
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142 Function: writes the $aln object into the stream in mase format ###Not yet implemented!###
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143 Returns : 1 for success and 0 for error
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144 Args : L<Bio::Align::AlignI> object
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145
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146
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147 =cut
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148
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149 sub write_aln {
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150 my ($self,@aln) = @_;
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151
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152 $self->throw("Sorry: mase-format output, not yet implemented! /n");
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153 }
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154
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155 1;
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