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# -*-Perl-*- Test Harness script for Bioperl
# $Id: masta.t 15112 2008-12-08 18:12:38Z sendu $
use strict;
BEGIN {
use lib '.';
use Bio::Root::Test;
test_begin(-tests => 16);
use_ok('Bio::Matrix::PSM::IO');
}
#Let's try masta formats here
my $mio = Bio::Matrix::PSM::IO->new(-format=>'masta',
-file=>test_input_file('masta.dat'));
my $masta_w_dat = test_output_file();
my $wmio=Bio::Matrix::PSM::IO->new(-format=>'masta',
-file=>">".$masta_w_dat);
$wmio->_flush_on_write(1);
ok $mio;
ok $wmio;
my @cons;
my $carry;
while (my $site=$mio->next_matrix) {
ok $site;
push @cons,$site->consensus;
$carry=$site if ($site->id eq 'm1logs');
}
is $cons[0],'CAGAAAAATNGAATNCCCACCCCCC';
is $cons[1],'CAGAAAAATAGAATCCCCACCCCCC';
is $cons[2],'CAGAAAAATNNAATNCCCACCNCCC';
$wmio->write_psm($carry,'PWM');
$carry->id('m1freq');
$wmio->write_psm($carry,'PFM');
$carry->id('m1seq');
$wmio->write_psm($carry,'SEQ');
$wmio->DESTROY;
my $chio=Bio::Matrix::PSM::IO->new(-format=>'masta',
-file=>$masta_w_dat);
ok $chio;
my $site=$chio->next_matrix;
is $site->id,'m1logs';
is $site->consensus,'CAGAAAAATAGAATCCCCACCCCCC';
$site=$chio->next_matrix;
is $site->id,'m1freq';
is $site->consensus,'CAGAAAAATAGAATCCCCACCCCCC';
$site=$chio->next_matrix;
is $site->id,'m1seq';
is $site->consensus,'CAGAAAAATAGAATCCCCACCCCCC';
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