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# -*-Perl-*- Test Harness script for Bioperl
# $Id: Perl.t 15112 2008-12-08 18:12:38Z sendu $
use strict;
BEGIN {
use lib '.';
use Bio::Root::Test;
test_begin(-tests => 29,
-requires_module => 'IO::String');
use_ok('Bio::Perl');
}
# Bio::Perl isn't OO so we don't see Bio::Perl->new() here
my ($seq_object,$filename,@seq_object_array);
# will guess file format from extension
$filename = test_input_file('cysprot1.fa');
ok ($seq_object = read_sequence($filename));
isa_ok $seq_object, 'Bio::SeqI';
# forces genbank format
$filename = test_input_file('AF165282.gb');
ok ($seq_object = read_sequence($filename,'genbank'));
isa_ok $seq_object, 'Bio::SeqI';
# reads an array of sequences
$filename = test_input_file('amino.fa');
is (@seq_object_array = read_all_sequences($filename,'fasta'), 2);
isa_ok $seq_object_array[0], 'Bio::SeqI';
isa_ok $seq_object_array[1], 'Bio::SeqI';
$filename = test_output_file();
ok write_sequence(">$filename",'genbank',$seq_object);
ok ($seq_object = new_sequence("ATTGGTTTGGGGACCCAATTTGTGTGTTATATGTA","myname","AL12232"));
isa_ok $seq_object, 'Bio::SeqI';
my $trans;
ok ($trans = translate($seq_object));
isa_ok $trans, 'Bio::SeqI';
ok ($trans = translate("ATTGGTTTGGGGACCCAATTTGTGTGTTATATGTA"));
isa_ok $trans, 'Bio::PrimarySeqI';
ok ($trans = translate_as_string($seq_object));
is $trans, 'IGLGTQFVCYM';
$trans = '';
ok ($trans = translate_as_string("ATTGGTTTGGGGACCCAATTTGTGTGTTATATGTA"));
is $trans, 'IGLGTQFVCYM';
# we need to keep tests that depend on net connection at the end
# these now run only with BIOPERLDEBUG set
SKIP: {
test_skip(-tests => 10, -requires_networking => 1);
# swissprot
SKIP: {
eval {
$seq_object = get_sequence('swissprot',"ROA1_HUMAN");
};
if ($@) {
skip("problem connecting to SwissProt:$@",2);
} else {
ok $seq_object;
isa_ok $seq_object, 'Bio::SeqI';
}
}
# embl
SKIP: {
eval {
$seq_object = get_sequence('embl',"BUM");
};
if ($@) {
skip("problem connecting to EMBL:$@",2);
} else {
ok $seq_object;
isa_ok $seq_object, 'Bio::SeqI';
}
}
# genbank
SKIP: {
eval {
$seq_object = get_sequence('genbank',"AI129902");
};
if ($@) {
skip("problem connecting to GenBank:$@",2);
} else {
ok $seq_object;
isa_ok $seq_object, 'Bio::SeqI';
}
}
# refseq
SKIP: {
eval {
$seq_object = get_sequence('genbank',"NM_006732");
};
if( $@ ) {
skip("problem connecting to RefSeq:$@",2);
} else {
ok $seq_object;
isa_ok $seq_object, 'Bio::SeqI';
}
}
# genpept
SKIP: {
eval {
$seq_object = get_sequence('genpept',"AAC06201");
};
if ($@) {
skip("problem connecting to RefSeq:$@",2);
} else {
ok $seq_object;
isa_ok $seq_object, 'Bio::SeqI';
}
}
}
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