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# -*-Perl-*- Test Harness script for Bioperl
# $Id: fasta.t 16090 2009-09-15 21:57:56Z cjfields $
use strict;
BEGIN {
use lib '.';
use Bio::Root::Test;
test_begin(-tests => 22,
-requires_modules => [],
-requires_networking => 0,
);
use_ok('Bio::SeqIO::fasta');
}
my $verbose = test_debug();
my $format = 'fasta';
my $seqio_obj = Bio::SeqIO->new(-file => test_input_file("test.$format"),
-format => $format);
isa_ok($seqio_obj, 'Bio::SeqIO');
my @methods = qw(next_seq write_seq);
foreach my $method (@methods) {
can_ok($seqio_obj, $method) ||
diag "$method method not implemented for $format";
}
# checking the first sequence object
my $seq_obj = $seqio_obj->next_seq();
isa_ok($seq_obj, 'Bio::Seq');
my %expected = ('seq' => 'MVNSNQNQNGNSNGHDDDFPQDSITEPEHMRKLFIGGL' .
'DYRTTDENLKAHEKWGNIVDVVVMKDPRTKRSRGFGFI' .
'TYSHSSMIDEAQKSRPHKIDGRVEPKRAVPRQDIDSPN' .
'AGATVKKLFVGALKDDHDEQSIRDYFQHFGNIVDNIVI' .
'DKETGKKRGFAFVEFDDYDPVDKVVLQKQHQLNGKMVD' .
'VKKALPKNDQQGGGGGRGGPGGRAGGNRGNMGGGNYGN' .
'QNGGGNWNNGGNNWGNNRGNDNWGNNSFGGGGGGGGGY' .
'GGGNNSWGNNNPWDNGNGGGNFGGGGNNWNGGNDFGGY' .
'QQNYGGGPQRGGGNFNNNRMQPYQGGGGFKAGGGNQGN' .
'YGNNQGFNNGGNNRRY',
'length' => '358',
'primary_id' => 'roa1_drome',
'description' => qr(Rea guano receptor type III),
);
is ($seq_obj->seq(), $expected{'seq'}, 'sequence');
is ($seq_obj->length(), $expected{'length'}, 'length');
is ($seq_obj->primary_id(), $expected{'primary_id'}, 'primary_id');
like ($seq_obj->description(), $expected{'description'}, 'description');
# checking the second sequence object
my $seq_obj2 = $seqio_obj->next_seq();
isa_ok($seq_obj2, 'Bio::Seq');
my %expected2 = ('seq' => 'MVNSNQNQNGNSNGHDDDFPQDSITEPEHMRKLFIGGL' .
'DYRTTDENLKAHEKWGNIVDVVVMKDPTSTSTSTSTST' .
'STSTSTMIDEAQKSRPHKIDGRVEPKRAVPRQDIDSPN' .
'AGATVKKLFVGALKDDHDEQSIRDYFQHLLLLLLLDLL' .
'LLDLLLLDLLLFVEFDDYDPVDKVVLQKQHQLNGKMVD' .
'VKKALPKNDQQGGGGGRGGPGGRAGGNRGNMGGGNYGN' .
'QNGGGNWNNGGNNWGNNRGNDNWGNNSFGGGGGGGGGY' .
'GGGNNSWGNNNPWDNGNGGGNFGGGGNNWNGGNDFGGY' .
'QQNYGGGPQRGGGNFNNNRMQPYQGGGGFKAGGGNQGN' .
'YGNNQGFNNGGNNRRY',
'length' => '358',
'primary_id' => 'roa2_drome',
'description' => qr(Rea guano ligand),
);
is ($seq_obj2->seq(), $expected2{'seq'}, 'sequence');
is ($seq_obj2->length(), $expected2{'length'}, 'length');
is ($seq_obj2->primary_id(), $expected2{'primary_id'}, 'primary_id');
like ($seq_obj2->description(), $expected2{'description'}, 'description');
# from testformats.pl
SKIP: {
test_skip(-tests => 4, -requires_modules => [qw(Algorithm::Diff
IO::ScalarArray
IO::String)]);
use_ok('Algorithm::Diff');
eval "use Algorithm::Diff qw(diff LCS);";
use_ok('IO::ScalarArray');
use_ok('IO::String');
my ($file, $type) = ("test.$format", $format);
my $filename = test_input_file($file);
print "processing file $filename\n" if $verbose;
open(FILE, "< $filename") or die("cannot open $filename");
my @datain = <FILE>;
my $in = new IO::String(join('', @datain));
my $seqin = new Bio::SeqIO( -fh => $in,
-format => $type);
my $out = new IO::String;
my $seqout = new Bio::SeqIO( -fh => $out,
-format => $type);
my $seq;
while( defined($seq = $seqin->next_seq) ) {
$seqout->write_seq($seq);
}
$seqout->close();
$seqin->close();
my $strref = $out->string_ref;
my @dataout = map { $_."\n"} split(/\n/, $$strref );
my @diffs = &diff( \@datain, \@dataout);
is(@diffs, 0, "$format format can round-trip");
if(@diffs && $verbose) {
foreach my $d ( @diffs ) {
foreach my $diff ( @$d ) {
chomp($diff->[2]);
print $diff->[0], $diff->[1], "\n>", $diff->[2], "\n";
}
}
print "in is \n", join('', @datain), "\n";
print "out is \n", join('',@dataout), "\n";
}
}
# bug 1508
# test genbank, gcg, ace against fasta (should throw an exception on each)
for my $file (qw(roa1.genbank test.gcg test.ace test.raw)) {
my $in = Bio::SeqIO->new(-file => test_input_file($file),
-format => 'fasta');
throws_ok {$in->next_seq}
qr/The sequence does not appear to be FASTA format/, "dies with $file";
}
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