t/Matrix/IO/masta.t

   1 # -*-Perl-*- Test Harness script for Bioperl
   2 # $Id$
   3
   4 use strict;
   5
   6 BEGIN {
   7     use Bio::Root::Test;
   8
   9     test_begin(-tests => 16);
  10
  11         use_ok('Bio::Matrix::PSM::IO');
  12 }
  13
  14 #Let's try masta formats here
  15 my $mio =  Bio::Matrix::PSM::IO->new(-format=>'masta',
  16                                       -file=>test_input_file('masta.dat'));
  17 my $masta_w_dat = test_output_file();
  18 my $wmio=Bio::Matrix::PSM::IO->new(-format=>'masta',
  19                                       -file=>">".$masta_w_dat);
  20 $wmio->_flush_on_write(1);
  21 ok $mio;
  22 ok $wmio;
  23 my @cons;
  24 my $carry;
  25 while (my $site=$mio->next_matrix) {
  26         ok $site;
  27         push @cons,$site->consensus;
  28         $carry=$site if ($site->id eq 'm1logs');
  29 }
  30 is $cons[0],'CAGAAAAATNGAATNCCCACCCCCC';
  31 is $cons[1],'CAGAAAAATAGAATCCCCACCCCCC';
  32 is $cons[2],'CAGAAAAATNNAATNCCCACCNCCC';
  33
  34 $wmio->write_psm($carry,'PWM');
  35 $carry->id('m1freq');
  36 $wmio->write_psm($carry,'PFM');
  37 $carry->id('m1seq');
  38 $wmio->write_psm($carry,'SEQ');
  39 $wmio->DESTROY;
  40 my $chio=Bio::Matrix::PSM::IO->new(-format=>'masta',
  41                                       -file=>$masta_w_dat);
  42 ok $chio;
  43 my $site=$chio->next_matrix;
  44 is $site->id,'m1logs';
  45 is $site->consensus,'CAGAAAAATAGAATCCCCACCCCCC';
  46 $site=$chio->next_matrix;
  47 is $site->id,'m1freq';
  48 is $site->consensus,'CAGAAAAATAGAATCCCCACCCCCC';
  49 $site=$chio->next_matrix;
  50 is $site->id,'m1seq';
  51 is $site->consensus,'CAGAAAAATAGAATCCCCACCCCCC';