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  • Committer: Package Import Robot
  • Author(s): Charles Plessy
  • Date: 2013-09-22 13:39:48 UTC
  • mfrom: (3.1.11 sid)
  • Revision ID: package-import@ubuntu.com-20130922133948-c6z62zegjyp7ztou
Tags: 1.6.922-1
http://bugs.debian.org/722910
* New upstream release.
* Replaces and Breaks grinder (<< 0.5.3-3~) because of overlaping contents.
  Closes: #722910
* Stop Replacing and Breaking bioperl ( << 1.6.9 ): not needed anymore. 

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