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# -*-Perl-*-
## Bioperl Test Harness Script for Modules
## $Id: Clustalw.t,v 1.26.2.1 2002/03/11 01:44:30 jason Exp $
use strict;
BEGIN {
eval { require Test; };
if( $@ ) {
use lib 't';
}
use Test;
use vars qw($NTESTS);
$NTESTS = 10;
plan tests => $NTESTS;
}
use Bio::Tools::Run::Alignment::Clustalw;
use Bio::SimpleAlign;
use Bio::AlignIO;
use Bio::SeqIO;
use Bio::Root::IO;
END {
for ( $Test::ntest..$NTESTS ) {
skip("Clustalw program not found. Skipping. (Be sure you have clustalw > 1.4)",1);
}
}
ok(1);
my $verbose = -1;
my @params = ('ktuple' => 2, 'matrix' => 'BLOSUM',
-verbose => $verbose);
my $factory = Bio::Tools::Run::Alignment::Clustalw->new(@params);
ok $factory->isa('Bio::Tools::Run::Alignment::Clustalw');
my $ktuple = 3;
$factory->ktuple($ktuple);
my $new_ktuple = $factory->ktuple();
ok $new_ktuple, 3, " couldn't set factory parameter";
my $what_matrix = $factory->matrix();
ok $what_matrix, 'BLOSUM', "couldn't get factory parameter";
my $bequiet = 1;
$factory->quiet($bequiet); # Suppress clustal messages to terminal
my $inputfilename = Bio::Root::IO->catfile("t","data","cysprot.fa");
my $aln;
my $clustal_present = $factory->exists_clustal();
unless ($clustal_present) {
warn("Clustalw program not found. Skipping tests $Test::ntest to $NTESTS.\n");
exit 0;
}
ok ($factory->version >= 1.8, 1, "Code tested only on ClustalW versions > 1.8 ");
$aln = $factory->align($inputfilename);
ok ($aln->get_seq_by_pos(1)->get_nse, 'CATH_HUMAN/1-335',
"failed clustalw alignment using input file");
my $str = Bio::SeqIO->new(-file=> Bio::Root::IO->catfile("t","data","cysprot.fa"),
'-format' => 'Fasta');
my @seq_array =();
while ( my $seq = $str->next_seq() ) {
push (@seq_array, $seq) ;
}
$aln = $factory->align(\@seq_array);
ok ($aln->get_seq_by_pos(1)->get_nse, 'CATH_HUMAN/1-335',
"failed clustalw alignment using BioSeq array ");
my $profile1 = Bio::Root::IO->catfile("t","data","cysprot1a.msf");
my $profile2 = Bio::Root::IO->catfile("t","data","cysprot1b.msf");
$aln = $factory->profile_align($profile1,$profile2);
ok( $aln->get_seq_by_pos(2)->get_nse, 'CATH_HUMAN/1-335',
" failed clustalw profile alignment using input file" );
if ($factory->version > 1.82 ) {
my $str1 = Bio::AlignIO->new(-file=> Bio::Root::IO->catfile("t","data","cysprot1a.msf"));
my $aln1 = $str1->next_aln();
my $str2 = Bio::AlignIO->new(-file=> Bio::Root::IO->catfile("t","data","cysprot1b.msf"));
my $aln2 = $str2->next_aln();
$aln = $factory->profile_align($aln1,$aln2);
ok($aln->get_seq_by_pos(2)->get_nse, 'CATH_HUMAN/1-335');
$str1 = Bio::AlignIO->new(-file=> Bio::Root::IO->catfile("t","data","cysprot1a.msf"));
$aln1 = $str1->next_aln();
$str2 = Bio::SeqIO->new(-file=> Bio::Root::IO->catfile("t","data","cysprot1b.fa"));
my $seq = $str2->next_seq();
$aln = $factory->profile_align($aln1,$seq);
ok ($aln->get_seq_by_pos(2)->get_nse, 'CATH_HUMAN/1-335');
} else {
skip("skipping due to clustalw 1.81 & 1.82 profile align bug",1);
skip("skipping due to clustalw 1.81 & 1.82 profile align bug",1);
}
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