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# -*-Perl-*- Test Harness script for Bioperl
# $Id$
use strict;
BEGIN {
use Bio::Root::Test;
test_begin(-tests => 25,
-requires_modules => [],
-requires_networking => 0,
);
use_ok('Bio::SeqIO::raw');
}
my $verbose = test_debug();
my $format = 'raw';
my $seqio_obj = Bio::SeqIO->new(-file => test_input_file("test.$format"),
-format => $format);
isa_ok($seqio_obj, 'Bio::SeqIO');
is $seqio_obj->variant, 'multiple';
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',
);
is ($seq_obj->seq(), $expected{'seq'}, 'sequence');
is ($seq_obj->length(), $expected{'length'}, 'length');
# checking the second sequence object
my $seq_obj2 = $seqio_obj->next_seq();
isa_ok($seq_obj2, 'Bio::Seq');
my %expected2 = ('seq' => 'MNKQRGTYSEVSLAQDPKRQQRKLKGNKISISGTKQEI' .
'FQVELNLQNASSDHQGNDKTYHCKGLLPPPEKLTAEVL' .
'GIICIVLMATVLKTIVLIPCIGVLEQNNFSLNRRMQKA' .
'RHCGHCPEEWITYSNSCYYIGKERRTWEERVCWPVLRR' .
'TLICFL',
'length' => '158',
);
is ($seq_obj2->seq(), $expected2{'seq'}, 'sequence');
is ($seq_obj2->length(), $expected2{'length'}, 'length');
# from testformats.pl
SKIP: {
test_skip(-tests => 2,
-requires_modules => [qw(Algorithm::Diff
IO::ScalarArray
IO::String)]);
use_ok('Algorithm::Diff', qw(diff LCS));
my ($file, $type) = ("test.$format", $format);
my $filename = test_input_file($file);
print "processing file $filename\n" if $verbose;
open my $FILE, '<', $filename or die "Could not read file '$filename': $!\n";
my @datain = <$FILE>;
close $FILE;
my $in = IO::String->new(join('', @datain));
my $seqin = Bio::SeqIO->new( -fh => $in,
-format => $type);
my $out = IO::String->new;
my $seqout = Bio::SeqIO->new( -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) {
use Data::Dumper; # should be safe for 5.005 and greater
foreach my $d ( @diffs ) {
print STDERR Dumper $d;
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";
}
}
# test raw variants
my @seq = qw(MVNSNQNQNGNSNGHDDDFPQDSITEPEHMRKLFIGGLDYRTTDENLKAHEKWGNIVDVV
VMKDPRTKRSRGFGFITYSHSSMIDEAQKSRPHKIDGRVEPKRAVPRQDIDSPNAGATVK
KLFVGALKDDHDEQSIRDYFQHFGNIVDNIVIDKETGKKRGFAFVEFDDYDPVDKVVLQK
QHQLNGKMVDVKKALPKNDQQGGGGGRGGPGGRAGGNRGNMGGGNYGNQNGGGNWNNGGN
NWGNNRGNDNWGNNSFGGGGGGGGGYGGGNNSWGNNNPWDNGNGGGNFGGGGNNWNGGND
FGGYQQNYGGGPQRGGGNFNNNRMQPYQGGGGFKAGGGNQGNYGNNQGFNNGGNNRRY);
$seqio_obj = Bio::SeqIO->new(-file => test_input_file("test2.raw"),
-format => 'raw');
is($seqio_obj->variant, 'multiple');
my $ct = 0;
while (my $seq = $seqio_obj->next_seq) {
is($seq->seq, $seq[$ct]);
$ct++;
}
is($ct, 6);
$seqio_obj = Bio::SeqIO->new(-file => test_input_file("test2.raw"),
-format => 'raw-single');
is($seqio_obj->variant, 'single');
my $seq = $seqio_obj->next_seq;
is($seq->seq, join('', @seq));
$seqio_obj = Bio::SeqIO->new(-file => test_input_file("test2.raw"),
-format => 'raw',
-variant => 'single');
is($seqio_obj->variant, 'single');
$seq = $seqio_obj->next_seq;
is($seq->seq, join('', @seq));
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