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# -*-Perl-*-
## Bioperl Test Harness Script for Modules
use strict;
BEGIN {
use Bio::Root::Test;
test_begin(-tests => 24);
use_ok('Bio::Tools::Run::FootPrinter');
use_ok('Bio::SeqIO');
}
SKIP: {
my $treefile = test_input_file("tree_of_life");
my @params = (
'size'=>10,
'sequence_type'=>'upstream',
'subregion_size'=>30,
'position_change_cost'=>5,
'triplet_filtering'=>1,
'pair_filtering'=>1,
'post_filtering'=>1,
'inversion_cost'=>1,
'tree' =>$treefile,
'details'=>0,
'verbose'=>0);
my $fact = Bio::Tools::Run::FootPrinter->new(@params);
test_skip(-requires_executable => $fact, -tests => 22);
is $fact->size, 10;
is $fact->sequence_type, 'upstream';
is $fact->subregion_size, 30;
is $fact->position_change_cost, 5;
is $fact->triplet_filtering,1;
is $fact->pair_filtering,1;
is $fact->post_filtering,1;
is $fact->inversion_cost,1;
is $fact->tree, $treefile;
my $input= test_input_file("FootPrinter.seq.fa");
my $in = Bio::SeqIO->new(-file => "$input" , '-format' => 'fasta');
my @seq;
while (my $seq = $in->next_seq){
push @seq, $seq; # 6 sequences
}
my @fp= $fact->run(@seq);
is @fp, 6;
my $first = shift @fp;
my @motifs = $first->sub_SeqFeature;
if (@motifs == 2) {
# older version of FootPrinter? or version 2.1 is buggy with its silly first
# motif of 1 bp below
is $motifs[0]->seq_id,'TETRAODON-motif1';
is $motifs[0]->seq->seq, 'tacaggatgca';
is $motifs[0]->start, 352;
is $motifs[0]->end, 362;
is $motifs[1]->seq_id,'TETRAODON-motif2';
is $motifs[1]->seq->seq, 'ccatatttgga';
is $motifs[1]->start, 363;
is $motifs[1]->end, 373;
ok 1 for 1..4;
}
elsif (@motifs == 3) {
is $motifs[0]->seq_id,'TETRAODON-motif1';
is $motifs[0]->seq->seq, 't';
is $motifs[0]->start, 352;
is $motifs[0]->end, 352;
is $motifs[1]->seq_id,'TETRAODON-motif2';
is $motifs[1]->seq->seq, 'acaggatgca';
is $motifs[1]->start, 353;
is $motifs[1]->end, 362;
is $motifs[2]->seq_id,'TETRAODON-motif3';
is $motifs[2]->seq->seq, 'ccatatttgga';
is $motifs[2]->start, 363;
is $motifs[2]->end, 373;
}
}
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