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# -*-Perl-*- Test Harness script for Bioperl
# $Id$
use strict;
BEGIN {
use Bio::Root::Test;
test_begin(-tests => 14);
use_ok('Bio::Matrix::PSM::IO');
}
# Test psiblast reading functionality.
my $psmIO = Bio::Matrix::PSM::IO->new(-format => 'psiblast',
-file => test_input_file('atp1.matrix'));
ok $psmIO;
my $psm = $psmIO->next_psm;
ok $psm;
# Verify that getting IUPAC sequence is functional
my $IUPAC = 'MEMSINPSEISSIIKEQIENYDTKAEVSEVGTVLSVGDGIARVYGLDNVMAGEMVEFPSGVKGMALNLEEDNVGVVLLGDDTGIKEGDLVKRTGKIVEVPVGEALLGRVVDPLGNPIDAKGPIKTDERRPVEVKAPGIIPRKSVHEPLQTGLKAIDSLVPIGRGQRELIIGDRQTGKTAIAIDTIINQKRINDESTDEGKKVYCIYVAIGQKRSTVAQVVQTLREAGALEYTIIVAATAAAPAPAQYLSAYAGCAIGEAFADNGAAACIIHDDLSRQAVAYAIISLLLRRPPGREAYPGDVFYLHSRLLERAAKLSDELGGGSLTALPIIETQAGDVSAYIPTNVISITDGQIFLETDLFNSGIRPAINVGLSVSRVGSAAQIKAMKKVAGSLKLELAQYRELAAFAQFGSDLDAATQAQLNRGARLTELLKQPQYSPLPVEEQVVILYAGVNGYLDDIPVEDIRDFEKELLEYLKSNHPEILESIRTGKLSDEIEKALKEAIKEFV';
is $psm->IUPAC, $IUPAC;
## Lets try to compress and uncompress the log odds and the
## frequencies, see if there is no considerable loss of data.
SKIP: {
skip('TODO: Module incomplete',10);
my $fA=$psm->get_compressed_freq('A');
my @check=Bio::Matrix::PSM::SiteMatrix::_uncompress_string($fA,1,1);
my @A=$psm->get_array('A');
my ($var,$max) = (0,0);
for (my $i = 0; $i<@check;$i++) {
my $diff=abs(abs($check[$i])-abs($A[$i]));
$var += $diff;
$max=$diff if ($diff>$max);
}
my $avg=$var/@check;
cmp_ok $avg,'<',0.01; #Loss of data under 1 percent
is $psm->sequence_match_weight('CAGAAAAATAAAATGGCCACCACCC'),2015;
my $lA=$psm->get_compressed_logs('A');
@check=Bio::Matrix::PSM::SiteMatrix::_uncompress_string($lA,1000,2);
@A=$psm->get_logs_array('A');
($var,$max) = (0,0);
for (my $i = 0;$i<@check;$i++) {
my $diff=abs(abs($check[$i])-abs($A[$i]));
$var += $diff;
$max=$diff if ($diff>$max);
}
$avg=$var/@check;
cmp_ok $avg,'<',10; #Loss of data under 1 percent
my $matrix=$psm->matrix;
ok $matrix;
my $psm2=$psm;
$psm2->matrix($matrix);
is $psm,$psm2;
is $IUPAC,'CAGAAAAATWVAATYCCCACCHCCC';
is $IUPAC,$psm2->IUPAC;
is $IUPAC,$matrix->IUPAC;
my $instances=$psm->instances;
ok $instances;
foreach my $instance (@{$instances}) {
my $id=$instance->primary_id;
is $instance->strand,1;
last if (ok $id);
}
}
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