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 use strict;
  77
  78 use Bio::Matrix::Mlagan;
  79 use base qw(Bio::Matrix::IO);
  80
  81 =head2 new
  82
  83  Title   : new
  84  Usage   : my $obj = Bio::Matrix::IO::mlagan->new();
  85  Function: Builds a new Bio::Matrix::IO::mlagan object
  86  Returns : an instance of Bio::Matrix::IO::mlagan
  87  Args    :
  88
  89 =cut
  90
  91 =head2 next_matrix
  92
  93  Title   : next_matrix
  94  Usage   : my $matrix = $obj->next_matrix();
  95  Function: parses a matrix file
  96  Returns : L<Bio::Matrix::Mlagan>
  97  Args    : none
  98
  99 =cut
 100
 101 sub next_matrix {
 102     my $self = shift;
 103
 104     my (@matrix, $gap_open, $gap_cont);
 105     while (defined ($_ = $self->_readline)) {
 106         if (/^[ACGTN\.]/) {
 107             my (undef, @values) = split;
 108             push(@matrix, \@values);
 109         }
 110         elsif (/^[-\d]/) {
 111             ($gap_open, $gap_cont) = split;
 112             last;
 113         }
 114     }
 115
 116     @matrix == 6 || $self->throw("Something wrong with file, was it the correct format?");
 117
 118     my $matrix = Bio::Matrix::Mlagan->new(-values => \@matrix,
 119                                           -gap_open => $gap_open,
 120                                           -gap_continue => $gap_cont);
 121
 122     return $matrix;
 123 }
 124
 125 =head2 write_matrix
 126
 127  Title   : write_matrix
 128  Usage   : $obj->write_matrix($matrix)
 129  Function: Write out a matrix in mlagan format
 130  Returns : n/a
 131  Args    : L<Bio::Matrix::Generic>
 132
 133 =cut
 134
 135 sub write_matrix {
 136     my ($self, $matrix) = @_;
 137     $matrix || $self->throw("Matrix required as input");
 138     my $gap_open = $matrix->gap_open;
 139     my $gap_continue = $matrix->gap_continue;
 140
 141     unless (defined $gap_open && defined $gap_continue) {
 142         $self->throw("gap_open() and gap_continue() in the supplied matrix object must both be set");
 143     }
 144
 145     $self->_print("     A    C    G    T    .    N\n");
 146
 147     foreach my $char (qw(A C G T . N)) {
 148         my @row = $matrix->get_row($char);
 149         my $row = $char;
 150         foreach my $val (@row) {
 151             $row .= " " x (5 - length($val)) . $val;
 152         }
 153
 154         $self->_print($row."\n");
 155     }
 156
 157     $self->_print("\n$gap_open $gap_continue");
 158
 159     return;
 160 }
 161
 162 1;