# -*-Perl-*- Test Harness script for Bioperl
# $Id$
use strict;
BEGIN {
use lib '.';
use Bio::Root::Test;
test_begin(-tests => 69,
-requires_modules => [qw(DB_File
Storable
Fcntl)]);
use_ok('Bio::Index::Fasta');
use_ok('Bio::Index::Qual');
use_ok('Bio::Index::SwissPfam');
use_ok('Bio::Index::EMBL');
use_ok('Bio::Index::GenBank');
use_ok('Bio::Index::Stockholm');
use_ok('Bio::Index::Swissprot');
use_ok('Bio::DB::InMemoryCache');
use_ok('Bio::DB::InMemoryCache');
}
my $ind = Bio::Index::Fasta->new(-filename => 'Wibbl',
-write_flag => 1,
-verbose => 0);
$ind->make_index(test_input_file('multifa.seq'));
$ind->make_index(test_input_file('seqs.fas'));
ok ( -e "Wibbl" || -e "Wibbl.pag" );
my $seq = $ind->fetch('HSEARLOBE');
is($seq->length,321);
is($seq->primary_id(),'HSEARLOBE');
$seq = $ind->fetch('HSMETOO');
is($seq->length,134);
is($seq->primary_id(),'HSMETOO');
$seq = $ind->fetch('MMWHISK');
is($seq->length,62);
is($seq->primary_id(),'MMWHISK');
$seq = $ind->fetch('gi|238775|bbs|65126');
is($seq->length,70);
my $stream = $ind->get_PrimarySeq_stream();
$seq = $stream->next_seq;
isa_ok $seq, 'Bio::PrimarySeqI';
$ind = Bio::Index::Fasta->new(-filename => 'multifa_index',
-write_flag => 1,
-verbose => 0);
$ind->make_index(test_input_file('multifa.seq.qual'));
ok ( -e "multifa_index" );
$ind = Bio::Index::Qual->new(-filename => 'multifa_qual_index',
-write_flag => 1,
-verbose => 0);
$ind->make_index(test_input_file('multifa.seq.qual'));
ok ( -e "multifa_qual_index" );
ok ( defined($seq) );
isa_ok $seq, 'Bio::SeqI';
$seq = $ind->fetch('HSEARLOBE');
is($seq->length,321);
is($seq->primary_id(),'HSEARLOBE');
$seq = $ind->fetch('HSMETOO');
is($seq->length,134);
is($seq->primary_id(),'HSMETOO');
$seq = $ind->fetch('MMWHISK');
is($seq->length,62);
is($seq->primary_id(),'MMWHISK');
$seq = $ind->fetch('NONEXISTENT_SEQ');
ok(! defined $seq);
$ind = Bio::Index::SwissPfam->new(-filename => 'Wibbl2',
-write_flag =>1);
$ind->make_index(test_input_file('swisspfam.data'));
ok ( -e "Wibbl2" || -e "Wibbl2.pag" );
$ind = Bio::Index::EMBL->new(-filename => 'Wibbl3',
-write_flag =>1);
$ind->make_index(test_input_file('test.embl'));
ok ( -e "Wibbl3" || -e "Wibbl3.pag" );
is ($ind->fetch('AL031232')->length, 4870);
$ind = Bio::Index::Swissprot->new(-filename => 'Wibbl4',
-write_flag => 1);
$ind->make_index(test_input_file('roa1.swiss'));
ok ( -e "Wibbl4" || -e "Wibbl4.pag" );
$seq = $ind->fetch('ROA1_HUMAN');
is ($seq->display_id(), 'ROA1_HUMAN');
$seq = $ind->fetch('P09651');
is ($seq->display_id(), 'ROA1_HUMAN');
# test id_parser
$ind = Bio::Index::Swissprot->new(-filename => 'Wibbl4',
-write_flag => 1);
$ind->id_parser(\&get_id);
$ind->make_index(test_input_file('roa1.swiss'));
ok ( -e "Wibbl4" || -e "Wibbl4.pag" );
$seq = $ind->fetch('X12671');
is ($seq->length,371);
my $gb_ind = Bio::Index::GenBank->new(-filename => 'Wibbl5',
-write_flag =>1,
-verbose => 0);
$gb_ind->make_index(test_input_file('roa1.genbank'));
ok ( -e "Wibbl5" || -e "Wibbl5.pag" );
$seq = $gb_ind->fetch('AI129902');
is ($seq->length, 37);
is ($seq->species->binomial, 'Homo sapiens');
$seq = $gb_ind->fetch(3598416);
is ($seq->seq,"CTCCGCGCCAACTCCCCCCACCCCCCCCCCACACCCC");
my $cache = Bio::DB::InMemoryCache->new( -seqdb => $gb_ind );
ok ( $cache->get_Seq_by_id('AI129902') );
SKIP: {
test_skip(-tests => 22, -requires_module => 'Bio::DB::FileCache');
$cache = Bio::DB::FileCache->new(-seqdb => $gb_ind,
-keep => 1,
-file => 'filecache.idx');
# problem:
my $seq = $cache->get_Seq_by_id('AI129902');
ok ( $seq);
is ( $seq->length, 37);
is ( lc($seq->seq()), 'ctccgcgccaactccccccaccccccccccacacccc');
my ( $f1 ) = $seq->get_SeqFeatures();
is ( ($f1->get_tag_values('sex'))[0], 'female');
is ( ($f1->get_tag_values('lab_host'))[0], 'DH10B');
my $species = $seq->species;
ok( $species );
is( $species->binomial, 'Homo sapiens');
is( $species->species(), 'sapiens');
is( $species->genus(), 'Homo');
# changes in GenBank file SOURCE line
# this is now the abbreviated name
ok defined($species->name('abbreviated'));
is ($species->name('abbreviated')->[0], 'human');
$cache = undef;
$cache = Bio::DB::FileCache->new(-seqdb => $gb_ind,
-keep => 0,
-file => 'filecache.idx');
$seq = $cache->get_Seq_by_id('AI129902');
ok ( $seq);
is ( $seq->length, 37);
is ( lc($seq->seq()), 'ctccgcgccaactccccccaccccccccccacacccc');
( $f1 ) = $seq->get_SeqFeatures();
is ( ($f1->get_tag_values('sex'))[0], 'female');
is ( ($f1->get_tag_values('lab_host'))[0], 'DH10B');
$species = $seq->species;
ok( $species );
is( $species->binomial, 'Homo sapiens');
is( $species->species(), 'sapiens');
is( $species->genus(), 'Homo');
# changes in GenBank file SOURCE line
# this is now the abbreviated name
ok defined($species->name('abbreviated'));
is ($species->name('abbreviated')->[0], 'human');
}
# test id_parser
$gb_ind = Bio::Index::GenBank->new(-filename => 'Wibbl5',
-write_flag =>1,
-verbose => 0);
$gb_ind->id_parser(\&get_id);
$gb_ind->make_index(test_input_file('roa1.genbank'));
ok ( -e "Wibbl5" || -e "Wibbl5.pag" );
$seq = $gb_ind->fetch('alpha D-globin');
is ($seq->length,141);
# test Stockholm
my $st_ind = Bio::Index::Stockholm->new(-filename => 'Wibbl6',
-write_flag => 1,
-verbose => 0);
isa_ok $st_ind, 'Bio::Index::Stockholm';
$st_ind->make_index(test_input_file('testaln.stockholm'));
ok ( -e "Wibbl6" );
my $aln = $st_ind->fetch_aln('PF00244');
isa_ok($aln,'Bio::SimpleAlign');
sub get_id {
my $line = shift;
return $1 if ($line =~ /product="([^"]+)"/);
return $1 if ($line =~ /^DR\s+EMBL;\s+([^;]+)/);
}
END {
cleanup();
}
sub cleanup {
for my $root ( qw( Wibbl Wibbl2 Wibbl3 Wibbl4 Wibbl5 Wibbl6
multifa_index multifa_qual_index ) ) {
unlink $root if( -e $root );
unlink "$root.pag" if( -e "$root.pag");
unlink "$root.dir" if( -e "$root.dir");
}
}