BioPerl

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Bio/DB/WebDBSeqI.pm  view on Meta::CPAN

 Usage   : $self->retrieval_type($type);
           my $type = $self->retrieval_type
 Function: Get/Set a proxy for retrieval_type (pipeline, io_string or tempfile)
 Returns : string representing retrieval type
 Args    : $value - the value to store

This setting affects how the data stream from the remote web server is
processed and passed to the Bio::SeqIO layer. Three types of retrieval
types are currently allowed:

   pipeline  Perform a fork in an attempt to begin streaming
             while the data is still downloading from the remote
             server.  Disk, memory and speed efficient, but will
             not work on Windows or MacOS 9 platforms.

   io_string Store downloaded database entry(s) in memory.  Can be
             problematic for batch downloads because entire set
             of entries must fit in memory.  Alll entries must be
             downloaded before processing can begin.

   tempfile  Store downloaded database entry(s) in a temporary file.

Bio/DB/WebDBSeqI.pm  view on Meta::CPAN

      close STDIN; close STDOUT;
      setsid() or $self->throw('Could not detach from parent');
    }
  } else {
    #PARENT
    $pipe->reader();
  }
  return ( $pid, $pipe );
}

# send web request to specified filehandle, or stdout, for streaming purposes
sub _stream_request {
  my $self    = shift;
  my $request = shift;
  my $dest_fh = shift || \*STDOUT;

  # fork so as to pipe output of fetch process through to
  # postprocess_data method call.
  my ($child,$fetch) = $self->_open_pipe();

  if ($child) {

t/LocalDB/Qual.t  view on Meta::CPAN

is $truncobj->length, 3;
ok my $revobj = $obj->revcom;
isa_ok $revobj, 'Bio::Seq::PrimaryQual::Qual';
isa_ok $revobj, 'Bio::Seq::PrimaryQual';
is ref($revobj->qual), 'ARRAY';
is $revobj->length, 14;
undef $obj;
undef $truncobj;
undef $revobj;

# using get_PrimarySeq_stream streaming
ok my $stream = $db->get_PrimaryQual_stream;
ok $stream = $db->get_PrimarySeq_stream;
isa_ok $stream, 'Bio::DB::Indexed::Stream';
ok my $streamqual = $stream->next_seq;
isa_ok $streamqual, 'Bio::Seq::PrimaryQual';

# using newFh streaming
ok my $fh = Bio::DB::Qual->newFh($test_dbdir);
my $fhqual = <$fh>;
isa_ok $fhqual, 'Bio::Seq::PrimaryQual';
undef $fh;

# tied-hash access
my (%h,$dna1,$dna2);
ok tie(%h,'Bio::DB::Qual',$test_dbdir);
ok $h{$seqid};
ok $dna1 = $h{"$seqid:1,10"};

t/SeqIO/Handler.t  view on Meta::CPAN

my $location = $features[1]->location;
ok($location->isa('Bio::Location::SplitLocationI'));
my @sublocs = $location->sub_Location();
is(@sublocs, 29);

# version and primary ID - believe it or not, this wasn't working
is ($seq->version, 1);
is ($seq->seq_version, 1);
is ($seq->primary_id, "5734104");

# streaming and Bio::RichSeq creation
my $stream = Bio::SeqIO->new(-file => test_input_file("test.genbank"),
                                      -verbose => $verbose,
                             -format => 'gbdriver');
$stream->verbose($verbose);
my $seqnum = 0;
my $species;
my @cl;
my $lasts;
my @ids = qw(DDU63596 DDU63595 HUMBDNF);
my @tids = (44689, 44689, 9606);

t/SeqIO/Handler.t  view on Meta::CPAN

        @cl = $species->classification();
        is( $species->binomial(), $tnames[$seqnum],
             'species parsing incorrect for genbank');
        is( $cl[3] ne $species->genus(), 1,
             'genus duplicated in genbank parsing');
        is( $species->ncbi_taxid, $tids[$seqnum] );
    }
    $seqnum++;
    $lasts = $seq;
}
is($seqnum, 5,'streaming');
is $lasts->display_id(), "HUMBETGLOA";
my ($ref) = $lasts->annotation->get_Annotations('reference');
is($ref->medline, 94173918);
$stream->close();

$stream = Bio::SeqIO->new(-file => test_input_file("test.genbank.noseq"),
                                  -verbose => $verbose,
                                  -format => 'gbdriver' );
$seqnum = 0;
while($seq = $stream->next_seq()) {

t/SeqIO/genbank.t  view on Meta::CPAN

my $location = $features[1]->location;
ok($location->isa('Bio::Location::SplitLocationI'));
my @sublocs = $location->sub_Location;
is(@sublocs, 29);

# version and primary ID - believe it or not, this wasn't working
is ($seq->version, 1);
is ($seq->seq_version, 1);
is ($seq->primary_id, "5734104");

# streaming and Bio::RichSeq creation
my $stream = Bio::SeqIO->new(-file    => test_input_file('test.genbank'),
                             -verbose => $verbose,
                             -format  => 'genbank');
$stream->verbose($verbose);
my $seqnum = 0;
my $species;
my @cl;
my $lasts;
my @ids = qw(DDU63596 DDU63595 HUMBDNF);
my @tids = (44689, 44689, 9606);

t/SeqIO/genbank.t  view on Meta::CPAN

        @cl = $species->classification;
        is( $species->binomial, $tnames[$seqnum],
            'species parsing incorrect for genbank');
        is( $cl[3] ne $species->genus, 1,
            'genus duplicated in genbank parsing');
        is( $species->ncbi_taxid, $tids[$seqnum] );
    }
    $seqnum++;
    $lasts = $seq;
}
is($seqnum, 5,'streaming');
is $lasts->display_id, "HUMBETGLOA";
my ($ref) = $lasts->annotation->get_Annotations('reference');
is($ref->medline, 94173918);
$stream->close;

$stream = Bio::SeqIO->new(-file    => test_input_file('test.genbank.noseq'),
                          -verbose => $verbose,
                          -format  => 'genbank' );
$seqnum = 0;
while($seq = $stream->next_seq) {