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# -*-Perl-*-
## Bioperl Test Harness Script for Modules
##
# $Id: hmmer.t,v 1.12 2001/10/23 03:43:58 jason Exp $
# Before `make install' is performed this script should be runnable with
# `make test'. After `make install' it should work as `perl test.t'
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( $@ ) {
use lib 't';
}
use Test;
plan test => 24;
}
use Bio::Tools::HMMER::Domain;
use Bio::Tools::HMMER::Set;
use Bio::Tools::HMMER::Results;
use Bio::Root::IO;
my ($domain,$set,$homol,$rev,$res,$dom,@doms);
$domain = Bio::Tools::HMMER::Domain->new(-verbose=>1);
ok ref($domain), 'Bio::Tools::HMMER::Domain';
$domain->start(50);
$domain->end(200);
$domain->hstart(10);
$domain->hend(100);
$domain->seqbits(50);
$domain->bits(20);
$domain->evalue(0.0001);
$domain->seqname('silly');
# test that we can get out forward and reverse homol_SeqFeatures
$homol = $domain->feature2();
ok $homol->start(), 10;
$rev = $domain;
ok $rev->start(), 50;
$set = Bio::Tools::HMMER::Set->new();
$set->add_Domain($domain);
@doms = $set->each_Domain();
$dom = shift @doms;
ok $dom->start(), 50;
$set->bits(300);
$set->evalue(0.0001);
$set->name('sillyname');
$set->desc('a desc');
$set->accession('fakeaccesssion');
ok $set->bits(), 300;
ok $set->evalue(), 0.0001;
ok $set->name(), 'sillyname';
ok $set->desc, 'a desc';
ok $set->accession, 'fakeaccesssion';
$res = Bio::Tools::HMMER::Results->new( -file => Bio::Root::IO->catfile("t","data","hmmsearch.out") , -type => 'hmmsearch');
my $seen =0;
ok $res->hmmfile, "HMM";
ok $res->seqfile, "HMM.dbtemp.29591";
my $first = 0;
foreach $set ( $res->each_Set) {
foreach $domain ( $set->each_Domain ) {
#print STDERR "Got domain ",$domain->seqname," start ",$domain->start," end ",$domain->end,"\n";
# do nothing for the moment
$seen = 1;
}
}
ok $seen, 1;
ok $res->number, 1215, "\nBad number of domains. Expecting 1215. Got" . $res->number;
$res = Bio::Tools::HMMER::Results->new( -file =>
Bio::Root::IO->catfile("t","data",
"hmmpfam.out") ,
-type => 'hmmpfam');
ok ($res->number, 2);
# parse HMM 2.2 files
$res = Bio::Tools::HMMER::Results->new( -file =>
Bio::Root::IO->catfile("t","data",
"L77119.hmmer"),
-type => 'hmmpfam');
$seen =0;
ok $res->hmmfile, 'Pfam';
ok $res->seqfile, 'L77119.faa';
foreach $set ( $res->each_Set) {
# only one set anyways
ok($set->name, 'gi|1522636|gb|AAC37060.1|');
ok($set->desc, 'M. jannaschii predicted coding region MJECS02 [Methanococcus jannaschii]');
ok($set->accession, '[none]');
foreach $domain ( $set->each_Domain ) {
#print STDERR "Got domain ",$domain->seqname," start ",$domain->start," end ",$domain->end,"\n";
# do nothing for the moment
ok($domain->start, 280);
ok($domain->end, 481);
ok($domain->bits, -105.2);
ok($domain->evalue, 0.0022 );
}
}
ok ($res->number, 1);
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