lib/Bio/Matrix/IO/mlagan.pm

   1 #
   2 # BioPerl module for Bio::Matrix::IO::mlagan
   3 #
   4 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   5 #
   6 # Cared for by Sendu Bala <bix@sendu.me.uk>
   7 #
   8 # Copyright Sendu Bala
   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::Matrix::IO::mlagan - A parser for the mlagan substitution matrix
  17
  18 =head1 SYNOPSIS
  19
  20   use Bio::Matrix::IO;
  21   my $parser = Bio::Matrix::IO->new(-format => 'mlagan',
  22                                    -file   => 'nucmatrix.txt');
  23   my $matrix = $parser->next_matrix;
  24   my $gap_open = $parser->gap_open;
  25   my $gap_continue = $parser->gap_continue;
  26
  27 =head1 DESCRIPTION
  28
  29 Use to read in and write out substitution matrix files suitable for use by
  30 mlagan.
  31
  32 =head1 FEEDBACK
  33
  34 =head2 Mailing Lists
  35
  36 User feedback is an integral part of the evolution of this and other
  37 Bioperl modules. Send your comments and suggestions preferably to
  38 the Bioperl mailing list.  Your participation is much appreciated.
  39
  40   bioperl-l@bioperl.org                  - General discussion
  41   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  42
  43 =head2 Support
  44
  45 Please direct usage questions or support issues to the mailing list:
  46
  47 I<bioperl-l@bioperl.org>
  48
  49 rather than to the module maintainer directly. Many experienced and
  50 reponsive experts will be able look at the problem and quickly
  51 address it. Please include a thorough description of the problem
  52 with code and data examples if at all possible.
  53
  54 =head2 Reporting Bugs
  55
  56 Report bugs to the Bioperl bug tracking system to help us keep track
  57 of the bugs and their resolution. Bug reports can be submitted via
  58 the web:
  59
  60   https://github.com/bioperl/bioperl-live/issues
  61
  62 =head1 AUTHOR - Sendu Bala
  63
  64 Email bix@sendu.me.uk
  65
  66 =head1 APPENDIX
  67
  68 The rest of the documentation details each of the object methods.
  69 Internal methods are usually preceded with a _
  70
  71 =cut
  72
  73 # Let the code begin...
  74
  75 package Bio::Matrix::IO::mlagan;
  76
  77 use strict;
  78
  79 use Bio::Matrix::Mlagan;
  80 use base qw(Bio::Matrix::IO);
  81
  82 =head2 new
  83
  84  Title   : new
  85  Usage   : my $obj = Bio::Matrix::IO::mlagan->new();
  86  Function: Builds a new Bio::Matrix::IO::mlagan object
  87  Returns : an instance of Bio::Matrix::IO::mlagan
  88  Args    :
  89
  90 =cut
  91
  92 =head2 next_matrix
  93
  94  Title   : next_matrix
  95  Usage   : my $matrix = $obj->next_matrix();
  96  Function: parses a matrix file
  97  Returns : L<Bio::Matrix::Mlagan>
  98  Args    : none
  99
 100 =cut
 101
 102 sub next_matrix {
 103     my $self = shift;
 104
 105     my (@matrix, $gap_open, $gap_cont);
 106     while (defined ($_ = $self->_readline)) {
 107         if (/^[ACGTN\.]/) {
 108             my (undef, @values) = split;
 109             push(@matrix, \@values);
 110         }
 111         elsif (/^[-\d]/) {
 112             ($gap_open, $gap_cont) = split;
 113             last;
 114         }
 115     }
 116
 117     @matrix == 6 || $self->throw("Something wrong with file, was it the correct format?");
 118
 119     my $matrix = Bio::Matrix::Mlagan->new(-values => \@matrix,
 120                                           -gap_open => $gap_open,
 121                                           -gap_continue => $gap_cont);
 122
 123     return $matrix;
 124 }
 125
 126 =head2 write_matrix
 127
 128  Title   : write_matrix
 129  Usage   : $obj->write_matrix($matrix)
 130  Function: Write out a matrix in mlagan format
 131  Returns : n/a
 132  Args    : L<Bio::Matrix::Generic>
 133
 134 =cut
 135
 136 sub write_matrix {
 137     my ($self, $matrix) = @_;
 138     $matrix || $self->throw("Matrix required as input");
 139     my $gap_open = $matrix->gap_open;
 140     my $gap_continue = $matrix->gap_continue;
 141
 142     unless (defined $gap_open && defined $gap_continue) {
 143         $self->throw("gap_open() and gap_continue() in the supplied matrix object must both be set");
 144     }
 145
 146     $self->_print("     A    C    G    T    .    N\n");
 147
 148     foreach my $char (qw(A C G T . N)) {
 149         my @row = $matrix->get_row($char);
 150         my $row = $char;
 151         foreach my $val (@row) {
 152             $row .= " " x (5 - length($val)) . $val;
 153         }
 154
 155         $self->_print($row."\n");
 156     }
 157
 158     $self->_print("\n$gap_open $gap_continue");
 159
 160     return;
 161 }
 162
 163 1;