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# -*-Perl-*- Test Harness script for Bioperl
# $Id$
use strict;
BEGIN {
use Bio::Root::Test;
test_begin(-tests => 63);
use_ok ('Bio::Matrix::PSM::IO');
}
my $mmt= "chr04q 170164 170208 strong - 0 Motif 3 occurrance in chr04q
chr04q 215755 215799 strong + 0 Motif 4 occurrance in chr04q
chr04q 532530 532574 strong + 2 Motif 2 occurrance in chr04q
chr04q 539492 539536 strong - 1 Motif 1 occurrance in chr04q
chr04q 586113 586157 strong + 2 Motif 2 occurrance in chr04q
chr04q 698245 698289 strong - 0 Motif 4 occurrance in chr04q
chr04q 804412 804456 strong - 0 Motif 3 occurrance in chr04q
chr04q 858870 858914 strong - 2 Motif 3 occurrance in chr04q
chr04q 861561 861605 strong - 2 Motif 3 occurrance in chr04q
chr04q 916898 916942 strong - 1 Motif 1 occurrance in chr04q
chr04q 1146916 1146960 strong - 0 Motif 1 occurrance in chr04q
chr04q 1315772 1315816 strong + 1 Motif 1 occurrance in chr04q
chr04q 1636119 1636163 strong + 2 Motif 3 occurrance in chr04q
chr04q 1636200 1636244 strong + 2 Motif 1 occurrance in chr04q
chr04q 1636437 1636481 strong + 2 Motif 4 occurrance in chr04q
chr04q 1637361 1637405 strong + 2 Motif 2 occurrance in chr04q
chr04q 1652447 1652491 strong + 1 Motif 4 occurrance in chr04q";
my @mmt=split(/\n/,$mmt);
#Let's try meme here
my $psmIO = Bio::Matrix::PSM::IO->new(-format=>'meme',
-file=>test_input_file('meme.dat'));
ok $psmIO;
my @inputfile=grep(/datafile/i,$psmIO->unstructured);
ok @inputfile;
my $release=$psmIO->release;
ok $release;
my @ids=$psmIO->hid;
is @ids,4;
my %weights=$psmIO->weight;
ok %weights;
my %seq = $psmIO->seq;
is %seq,'0';#Meme doesn't have seq
is $psmIO->version,'3.0';
my $psm = $psmIO->next_psm;
ok $psm;
#Lets try to compress and uncompress the log odds and the frequencies, see if there is no
#considerable loss of data.
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
#print $avg,"\n";
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;
my %psm_header=$psm->header;
is $psm_header{IC},38.1;
is $psm_header{sites},4;
is $psm_header{width},25;
is $psm_header{e_val},'1.2e-002';
#Quick check if returned object works
my $IUPAC=$psm->IUPAC;
is $IUPAC,'CMKWMAAAKWVAWTYCMCASCHCCM';
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);
}
ok $psm->header('e_val');
#Meme parser should be OK if tests passed
#Now we are going to try transfac
$psmIO = Bio::Matrix::PSM::IO->new(-format=>'transfac',
-file=> test_input_file('transfac.dat'));
ok $psmIO;
my $version=$psmIO->version;
ok !$version;
is $psmIO->release, '6.4--2002-12-02';
$psm = $psmIO->next_psm;
ok $psm;
# Lets try to compress and uncompress the the frequencies, see if
# there is no considerable loss of data.
$fA=$psm->get_compressed_freq('A');
@check=Bio::Matrix::PSM::SiteMatrix::_uncompress_string($fA,1,1);
@A=$psm->get_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,'<',0.01; #Loss of data under 1 percent
%weights = $psmIO->weight;
ok !$weights{''};
%seq = $psmIO->seq;
is scalar keys %seq, 0;
#Quick check if returned object works
$IUPAC = $psm->IUPAC;
is $IUPAC,'VVDCAKSTGBYD';
#Now we are going to try mast
$psmIO = Bio::Matrix::PSM::IO->new(-format=>'mast',
-file=>test_input_file('mast.dat'));
ok $psmIO;
@inputfile = grep(/datafile/i,$psmIO->unstructured);
ok !@inputfile;
is( $psmIO->release, '2002/04/02 0:11:59');
@ids = $psmIO->hid;
is @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;
is $psmIO->version, '3.0';
my $mmastIO=Bio::Matrix::PSM::IO->new(-format=>'mast',-file=>test_input_file('mixedmast.dat'));
$psm = $mmastIO->next_psm;
my $lastinstances = $psm->instances();
my $i=0;
foreach my $hit (@$lastinstances) {
$hit -> end ( $hit-> start () + length ($hit->seq) - 1 ) ; # fix an old bug in InstanceSite.pm
my $d=join("\t",$hit->{accession_number},$hit -> start () , $hit-> end (),$hit -> score (),
$hit -> strand == 1 ? '+' : '-' , $hit -> frame, $hit -> desc ( ));
is $d,$mmt[$i];
$i++;
last if ($hit -> start == 1652447);
}
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