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# -*-Perl-*- mode (to keep my emacs happy)
# $Id: SeqBuilder.t,v 1.2 2003/02/18 03:37:58 lapp Exp $
use strict;
use vars qw($DEBUG $TESTCOUNT);
BEGIN {
eval { require Test; };
if( $@ ) {
use lib 't';
}
use Test;
$TESTCOUNT = 101;
plan tests => $TESTCOUNT;
}
use Bio::Seq;
use Bio::SeqIO;
use Bio::Root::IO;
ok(1);
my $verbosity = -1; # Set to -1 for release version, so warnings aren't printed
my ($seqio,$seq); # predeclare variables for strict
# default mode
$seqio = Bio::SeqIO->new('-file'=> Bio::Root::IO->catfile(
"t","data","test.genbank"),
'-format' => 'GenBank');
ok $seqio;
$seqio->verbose($verbosity);
my $numseqs = 0;
my @loci = qw(U63596 U63595 M37762 NT_010368 L26462);
my @numfeas = (3,1,6,3,26);
while($seq = $seqio->next_seq()) {
ok ($seq->accession_number, $loci[$numseqs++]);
ok ($seq->annotation->get_Annotations());
ok (scalar($seq->top_SeqFeatures), $numfeas[$numseqs-1]);
ok ($seq->species->binomial);
ok ($seq->seq);
}
ok ($numseqs, 5);
# minimalistic mode
$seqio = Bio::SeqIO->new('-file'=> Bio::Root::IO->catfile(
"t","data","test.genbank"),
'-format' => 'GenBank');
ok $seqio;
$seqio->verbose($verbosity);
my $seqbuilder = $seqio->sequence_builder();
ok $seqbuilder;
ok $seqbuilder->isa("Bio::Factory::ObjectBuilderI");
$seqbuilder->want_none();
$seqbuilder->add_wanted_slot('display_id','accession_number','desc');
$numseqs = 0;
while($seq = $seqio->next_seq()) {
ok ($seq->accession_number, $loci[$numseqs++]);
ok (scalar(grep { ! ($_->tagname eq "keyword" ||
$_->tagname eq "date_changed" ||
$_->tagname eq "secondary_accession"); }
$seq->annotation->get_Annotations()), 0);
if($numseqs <= 3) {
ok (scalar($seq->top_SeqFeatures), 0);
} else {
ok (scalar($seq->top_SeqFeatures), $numfeas[$numseqs-1]);
}
ok ($seq->species, undef);
ok ($seq->seq, undef);
# switch on features for the last 2 seqs
$seqbuilder->add_wanted_slot('features') if $numseqs == 3;
}
ok ($numseqs, 5);
# everything but no sequence, and no features
$seqio = Bio::SeqIO->new('-file'=> Bio::Root::IO->catfile(
"t","data","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 = $seqio->next_seq()) {
ok ($seq->accession_number, $loci[$numseqs++]);
ok scalar($seq->annotation->get_Annotations());
if($numseqs <= 3) {
ok (scalar($seq->top_SeqFeatures), 0);
} else {
ok (scalar($seq->top_SeqFeatures), $numfeas[$numseqs-1]);
}
ok $seq->species->binomial;
ok ($seq->seq, undef);
# switch on features for the last 2 seqs
if($numseqs == 3) {
$seqbuilder->add_unwanted_slot(
grep { $_ ne 'features'; } $seqbuilder->remove_unwanted_slots());
}
}
ok ($numseqs, 5);
# skip sequences less than 100bp or accession like 'NT_*'
$seqio = Bio::SeqIO->new('-file'=> Bio::Root::IO->catfile(
"t","data","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()) {
$numseqs++;
ok ($seq->accession_number, $loci[$i]);
ok scalar($seq->annotation->get_Annotations());
ok (scalar($seq->top_SeqFeatures), $numfeas[$i]);
ok $seq->species->binomial;
ok $seq->seq;
$i += 2;
}
ok ($numseqs, 3);
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