3 # BioPerl module for Bio::Matrix::IO::phylip
5 # Please direct questions and support issues to <bioperl-l@bioperl.org>
7 # Cared for by Jason Stajich <jason-at-bioperl-dot.org>
9 # Copyright Jason Stajich
11 # You may distribute this module under the same terms as perl itself
13 # POD documentation - main docs before the code
17 Bio::Matrix::IO::phylip - A parser for PHYLIP distance matricies
22 my $parser = Bio::Matrix::IO->new(-format => 'phylip'
23 -file => 't/data/phylipdist.out');
24 my $matrix = $parser->next_matrix;
28 This is a parser for PHYLIP distance matrix output.
34 User feedback is an integral part of the evolution of this and other
35 Bioperl modules. Send your comments and suggestions preferably to
36 the Bioperl mailing list. Your participation is much appreciated.
38 bioperl-l@bioperl.org - General discussion
39 http://bioperl.org/wiki/Mailing_lists - About the mailing lists
43 Please direct usage questions or support issues to the mailing list:
45 L<bioperl-l@bioperl.org>
47 rather than to the module maintainer directly. Many experienced and
48 reponsive experts will be able look at the problem and quickly
49 address it. Please include a thorough description of the problem
50 with code and data examples if at all possible.
54 Report bugs to the Bioperl bug tracking system to help us keep track
55 of the bugs and their resolution. Bug reports can be submitted via
58 http://bugzilla.open-bio.org/
60 =head1 AUTHOR - Jason Stajich
62 Email jason-at-bioperl-dot.org
66 The rest of the documentation details each of the object methods.
67 Internal methods are usually preceded with a _
72 # Let the code begin...
75 package Bio
::Matrix
::IO
::phylip
;
76 use vars
qw($DEFAULTPROGRAM);
79 $DEFAULTPROGRAM = 'phylipdist';
81 use Bio::Matrix::PhylipDist;
83 use base qw(Bio::Matrix::IO);
88 Usage : my $obj = Bio::Matrix::IO::phylip->new();
89 Function: Builds a new Bio::Matrix::IO::phylip object
90 Returns : an instance of Bio::Matrix::IO::phylip
97 my($class,@args) = @_;
99 my $self = $class->SUPER::new
(@args);
100 my ($prog) = $self->_rearrange([qw(PROGRAM)], @args);
101 $self->{'_program'} = $prog || $DEFAULTPROGRAM;
109 Usage : my $matrix = $parser->next_matrix
110 Function: Get the next result set from parser data
111 Returns : L<Bio::Matrix::PhylipDist>
123 while ($entry=$self->_readline) {
124 if($#names >=0 && $entry =~/^\s+\d+\n$/){
125 $self->_pushback($entry);
127 } elsif($entry=~/^\s+(\d+)\n$/){
130 } elsif( $entry =~ s/^\s+(\-?\d+\.\d+)/$1/ ) {
131 my (@line) = split( /\s+/,$entry);
132 push @
{$values[-1]}, @line;
135 my ($n,@line) = split( /\s+/,$entry);
138 push @values, [@line];
140 if( scalar @names != $size ) {
141 $self->warn("The number of entries ".(scalar @names).
142 " is not the same $size");
144 $#names>=0 || return;
147 foreach my $name(@names){
149 foreach my $n(@names) {
150 $dist{$name}{$n} = [$i,$j];
155 my $matrix = Bio
::Matrix
::PhylipDist
->new
156 (-matrix_name
=> $self->{'_program'},
159 -values => \
@values);
166 Usage : $matio->write_matrix($matrix)
167 Function: Write out a matrix in the phylip distance format
169 Args : L<Bio::Matrix::PhylipDist>
175 my ($self,@matricies) = @_;
176 foreach my $matrix ( @matricies ) {
177 my @names = @
{$matrix->names};
178 my @values = @
{$matrix->_values};
179 my %matrix = %{$matrix->_matrix};
181 $str.= (" "x
4). scalar(@names)."\n";
182 foreach my $name (@names){
183 my $newname = $name. (" " x
(15-length($name)));
184 if( length($name) >= 15 ) { $newname .= " " }
187 foreach my $n (@names){
188 my ($i,$j) = @
{$matrix{$name}{$n}};
189 if($count < $#names){
190 $str.= $values[$i][$j]. " ";
193 $str.= $values[$i][$j];