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#!/usr/local/bin/perl
# -*-Perl-*-
## Bioperl Test Harness Script for Modules
use strict;
BEGIN {
use Bio::Root::Test;
test_begin(-tests => 20);
use_ok('Bio::Tools::Run::Genewise');
use_ok('Bio::Root::IO');
use_ok('Bio::Seq');
}
my $verbose = test_debug() || -1;
my @params = ('-verbose' => $verbose,
'silent' => 1,
'quiet' => 1);
my $factory = Bio::Tools::Run::Genewise->new(@params);
SKIP:{
test_skip(-requires_executable => $factory, -tests => 17);
my $version = $factory->version;
warn("version is $version\n") if $verbose > 0;
isa_ok $factory,'Bio::Tools::Run::Genewise';
my $bequiet = 1;
$factory->quiet($bequiet); # Suppress pseudowise messages to terminal
#test with one file with 2 sequences
my $inputfilename = test_input_file('road.pep');
my $seqstream1 = Bio::SeqIO->new(-file => $inputfilename,
-format => 'fasta');
my $seq1 = Bio::Seq->new();
$seq1 = $seqstream1->next_seq();
$inputfilename = test_input_file('human.genomic');
my $seqstream2 = Bio::SeqIO->new(-file => $inputfilename,
-format => 'fasta');
my $seq2 = Bio::Seq->new();
$seq2 = $seqstream2->next_seq();
my ($genes) = $factory->predict_genes($seq1, $seq2);
my @transcripts = $genes->transcripts;
my @feat = $transcripts[0]->exons;
my $seqid = $feat[0]->seq_id;
is($seqid, 'HSHNRNPA');
my ($featpair)= $feat[0]->each_tag_value('supporting_feature');
is($featpair->feature2->seq_id,'roa1_drome');
is($featpair->feature1->seq_id,'HSHNRNPA');
if( defined $version && $version eq 'wise2-2-0' ) {
is($transcripts[0]->start, 1386);
is($transcripts[0]->end, 3963);
is($feat[0]->start, 1386);
is($feat[0]->end, 1493);
is($feat[0]->strand,1);
is($featpair->feature2->start,26);
is($featpair->feature2->end,61);
is($featpair->feature2->strand,1);
is($featpair->feature2->score,'253.10');
is($featpair->feature1->start,1386);
is($featpair->feature1->end,1493);
is($featpair->feature1->strand,1);
is($featpair->feature1->score,'253.10');
} else {
warn("These tests may fail because I'm not sure about your genewise version -- using wise 2.2.3-rc7 values\n");
is($transcripts[0]->start, 1386);
is($transcripts[0]->end, 4304);
is($feat[0]->start, 1386);
is($feat[0]->end, 1493);
is($feat[0]->strand,1);
is($featpair->feature2->start,26);
is($featpair->feature2->end,61);
is($featpair->feature2->strand,1);
is($featpair->feature2->score,'319.10');
is($featpair->feature1->start,1386);
is($featpair->feature1->end,1493);
is($featpair->feature1->strand,1);
is($featpair->feature1->score,'319.10');
}
}