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# -*-Perl-*- Test Harness script for Bioperl
# $Id$
use strict;
BEGIN {
use Bio::Root::Test;
test_begin(-tests => 137);
use_ok('Bio::SeqIO');
}
my $verbosity = test_debug;
my ($seqio, $seq); # predeclare variables for strict
# default mode
ok $seqio = Bio::SeqIO->new('-file' => test_input_file('test.genbank'),
'-format' => 'GenBank');
$seqio->verbose($verbosity);
my $numseqs = 0;
my @loci = qw(U63596 U63595 M37762 NT_010368 L26462);
my @numfeas = (3,1,6,3,26);
while ($seq = $seqio->next_seq) {
is $seq->accession_number, $loci[$numseqs++];
ok $seq->annotation->get_Annotations;
is scalar($seq->top_SeqFeatures), $numfeas[$numseqs-1];
ok $seq->species->binomial;
ok $seq->seq;
ok $seq->desc;
ok $seq->id;
}
is $numseqs, 5;
# minimalistic mode
$seqio = Bio::SeqIO->new('-file' => test_input_file('test.genbank'),
'-format' => 'GenBank');
ok $seqio;
$seqio->verbose($verbosity);
ok my $seqbuilder = $seqio->sequence_builder;
isa_ok $seqbuilder, "Bio::Factory::ObjectBuilderI";
$seqbuilder->want_none;
$seqbuilder->add_wanted_slot('display_id','accession_number','desc');
$numseqs = 0;
while ($seq = $seqio->next_seq) {
is $seq->accession_number, $loci[$numseqs++];
is scalar(grep { ! ($_->tagname eq "keyword" ||
$_->tagname eq "date_changed" ||
$_->tagname eq "secondary_accession"); }
$seq->annotation->get_Annotations), 0;
if ($numseqs <= 3) {
is scalar($seq->top_SeqFeatures), 0;
}
else {
is scalar($seq->top_SeqFeatures), $numfeas[$numseqs-1];
}
is $seq->species, undef;
is $seq->seq, undef;
ok $seq->desc;
ok $seq->id;
# switch on features for the last 2 seqs
$seqbuilder->add_wanted_slot('features') if $numseqs == 3;
}
is $numseqs, 5;
# everything but no sequence, and no features
$seqio = Bio::SeqIO->new('-file' => test_input_file('test.genbank'),
'-format' => 'GenBank');
ok $seqio;
$seqio->verbose($verbosity);
$seqbuilder = $seqio->sequence_builder;
# want-all is default
$seqbuilder->add_unwanted_slot('seq','features');
$numseqs = 0;
while ($seq = $seqio->next_seq) {
is $seq->accession_number, $loci[$numseqs++];
ok scalar($seq->annotation->get_Annotations);
if ($numseqs <= 3) {
is scalar($seq->top_SeqFeatures), 0;
}
else {
is scalar($seq->top_SeqFeatures), $numfeas[$numseqs-1];
}
ok $seq->species->binomial;
is $seq->seq, undef;
ok $seq->desc;
ok $seq->id;
# switch on features for the last 2 seqs
if ($numseqs == 3) {
$seqbuilder->add_unwanted_slot(
grep { $_ ne 'features'; } $seqbuilder->remove_unwanted_slots
);
}
}
is $numseqs, 5;
# skip sequences less than 100bp or accession like 'NT_*'
$seqio = Bio::SeqIO->new('-file' => test_input_file('test.genbank'),
'-format' => 'GenBank');
ok $seqio;
$seqio->verbose($verbosity);
$seqbuilder = $seqio->sequence_builder;
# we could have as well combined the two conditions into one, but we want to
# test the implicit AND here
$seqbuilder->add_object_condition(sub {
my $h = shift;
return 0 if($h->{'-length'} < 100);
return 1;
});
$seqbuilder->add_object_condition(sub {
my $h = shift;
return 0 if($h->{'-display_id'} =~ /^NT_/);
return 1;
});
$numseqs = 0;
my $i = 0;
while ($seq = $seqio->next_seq) {
$numseqs++;
is $seq->accession_number, $loci[$i];
ok scalar($seq->annotation->get_Annotations);
is scalar($seq->top_SeqFeatures), $numfeas[$i];
ok $seq->species->binomial;
ok $seq->seq;
ok $seq->desc;
ok $seq->id;
$i += 2;
}
is $numseqs, 3;
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