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# -*-Perl-*-
#Some simple tests for meme and transfac parsers
use strict;
BEGIN {
# to handle systems with no installed Test module
# we include the t dir (where a copy of Test.pm is located)
# as a fallback
eval { require Test; };
if( $@ ) {
use lib 't';
}
use Test;
plan tests => 42;
}
use Bio::Matrix::PSM::IO;
ok(1);
#Let's try meme here
my $psmIO = new Bio::Matrix::PSM::IO(-format=>'meme',
-file=>Bio::Root::IO->catfile(qw(t data meme.dat)));
ok $psmIO;
my @inputfile=grep(/datafile/i,$psmIO->unstructured);
ok @inputfile;
my $release=$psmIO->release;
ok $release;
my @ids=$psmIO->hid;
ok @ids,4;
my %weights=$psmIO->weight;
ok %weights;
my %seq = $psmIO->seq;
ok %seq,'0';#Meme doesn't have seq
ok $psmIO->version,'3.0';
my $psm = $psmIO->next_psm;
ok $psm;
my $matrix=$psm->matrix;
ok $matrix;
my $psm2=$psm;
$psm2->matrix($matrix);
ok $psm,$psm2;
my %psm_header=$psm->header;
ok $psm_header{IC},38.1;
ok $psm_header{sites},4;
ok $psm_header{width},25;
ok $psm_header{e_val},'1.2e-002';
#Quick check if returned object works
my $IUPAC=$psm->IUPAC;
ok $IUPAC,'CAGAAAAATWVAATYCCCACCHCCC';
ok $IUPAC,$psm2->IUPAC;
ok $IUPAC,$matrix->IUPAC;
my $instances=$psm->instances;
ok $instances;
foreach my $instance (@{$instances}) {
my $id=$instance->primary_id;
last if (ok $id);
}
ok $psm->header('e_val');
#Meme parser should be OK if tests passed
#Now we are going to try transfac
$psmIO = new Bio::Matrix::PSM::IO(-format=>'transfac',
-file=> Bio::Root::IO->catfile(qw(t data transfac.dat)));
ok $psmIO;
my $version=$psmIO->version;
ok !$version;
ok $psmIO->release, '6.4--2002-12-02';
@ids = $psmIO->hid;
ok @ids, '1';
$psm = $psmIO->next_psm;
ok $psm;
%weights = $psmIO->weight;
ok !$weights{''};
%seq = $psmIO->seq;
ok scalar keys %seq, 0;
#Quick check if returned object works
$IUPAC = $psm->IUPAC;
ok $IUPAC,'NNNNNNNNNNNN';
#Now we are going to try mast
$psmIO = new Bio::Matrix::PSM::IO(-format=>'mast',
-file=>Bio::Root::IO->catfile(qw(t data mast.dat)));
ok $psmIO;
@inputfile = grep(/datafile/i,$psmIO->unstructured);
ok !@inputfile;
ok( $psmIO->release, '2002/04/02 0:11:59');
@ids = $psmIO->hid;
ok @ids,4;
%weights = $psmIO->weight;
ok !%weights; #Mast doesn't have weights
ok %seq = $psmIO->seq;
foreach my $id ($psmIO->hid) {
ok $seq{$id};
}
ok $psm=$psmIO->next_psm;
my %instances=$psmIO->instances;
ok %instances;
ok $psmIO->version, '3.0';
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