1# -*-Perl-*- 2## Bioperl Test Harness Script for Modules 3 4use strict; 5BEGIN { 6 use Bio::Root::Test; 7 test_begin(-tests => 8); 8 use_ok('Bio::Tools::Run::Alignment::Kalign'); 9 use_ok('Bio::AlignIO'); 10 use_ok('Bio::SeqIO'); 11} 12 13END { unlink qw(cysprot.dnd cysprot1a.dnd) } 14 15my @params = (); 16my $factory = Bio::Tools::Run::Alignment::Kalign->new(@params); 17my $inputfilename = test_input_file("cysprot.fa"); 18my $aln; 19 20SKIP: { 21 test_skip(-requires_executable => $factory, -tests => 5); 22 my $version = $factory->version; 23 is($version >= 2, 1, "Code tested only on kalign versions >= 2" ); 24 $aln = $factory->align($inputfilename); 25 ok($aln); 26 is( $aln->num_sequences, 7); 27 28 my $str = Bio::SeqIO->new('-file' => test_input_file("cysprot.fa"), 29 '-format' => 'Fasta'); 30 my @seq_array =(); 31 32 while ( my $seq = $str->next_seq() ) { 33 push (@seq_array, $seq) ; 34 } 35 36 my $seq_array_ref = \@seq_array; 37 38 $aln = $factory->align($seq_array_ref); 39 is $aln->num_sequences, 7; 40 my $s1_perid = $aln->average_percentage_identity; 41 is(int($s1_perid), 42); 42} 43 44