t/masta.t

   1 # -*-Perl-*- Test Harness script for Bioperl
   2 # $Id$
   3
   4 use strict;
   5
   6 BEGIN {
   7     use lib 't/lib';
   8     use BioperlTest;
   9
  10     test_begin(-tests => 16);
  11
  12         use_ok('Bio::Matrix::PSM::IO');
  13 }
  14
  15 #Let's try masta formats here
  16 my $mio =  Bio::Matrix::PSM::IO->new(-format=>'masta',
  17                                       -file=>test_input_file('masta.dat'));
  18 my $masta_w_dat = test_output_file();
  19 my $wmio=Bio::Matrix::PSM::IO->new(-format=>'masta',
  20                                       -file=>">".$masta_w_dat);
  21 $wmio->_flush_on_write(1);
  22 ok $mio;
  23 ok $wmio;
  24 my @cons;
  25 my $carry;
  26 while (my $site=$mio->next_matrix) {
  27         ok $site;
  28         push @cons,$site->consensus;
  29         $carry=$site if ($site->id eq 'm1logs');
  30 }
  31 is $cons[0],'CAGAAAAATNGAATNCCCACCCCCC';
  32 is $cons[1],'CAGAAAAATAGAATCCCCACCCCCC';
  33 is $cons[2],'CAGAAAAATNNAATNCCCACCNCCC';
  34
  35 $wmio->write_psm($carry,'PWM');
  36 $carry->id('m1freq');
  37 $wmio->write_psm($carry,'PFM');
  38 $carry->id('m1seq');
  39 $wmio->write_psm($carry,'SEQ');
  40 $wmio->DESTROY;
  41 my $chio=Bio::Matrix::PSM::IO->new(-format=>'masta',
  42                                       -file=>$masta_w_dat);
  43 ok $chio;
  44 my $site=$chio->next_matrix;
  45 is $site->id,'m1logs';
  46 is $site->consensus,'CAGAAAAATAGAATCCCCACCCCCC';
  47 $site=$chio->next_matrix;
  48 is $site->id,'m1freq';
  49 is $site->consensus,'CAGAAAAATAGAATCCCCACCCCCC';
  50 $site=$chio->next_matrix;
  51 is $site->id,'m1seq';
  52 is $site->consensus,'CAGAAAAATAGAATCCCCACCCCCC';