| Bio::Factory::SequenceStreamI(3pm) | User Contributed Perl Documentation | Bio::Factory::SequenceStreamI(3pm) |
Bio::Factory::SequenceStreamI - Interface describing the basics of a Sequence Stream.
# get a SequenceStreamI object somehow like with SeqIO
use Bio::SeqIO;
my $in = Bio::SeqIO->new(-file => '< fastafile');
while( my $seq = $in->next_seq ) {
}
This interface is for describing objects which produces Bio::PrimarySeqI objects or processes Bio::PrimarySeqI objects to a data stream.
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Please direct usage questions or support issues to the mailing list:
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rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : next_seq
Usage : $seq = stream->next_seq
Function: Reads the next sequence object from the stream and returns it.
Certain driver modules may encounter entries in the stream that
are either misformatted or that use syntax not yet understood
by the driver. If such an incident is recoverable, e.g., by
dismissing a feature of a feature table or some other non-mandatory
part of an entry, the driver will issue a warning. In the case
of a non-recoverable situation an exception will be thrown.
Do not assume that you can resume parsing the same stream after
catching the exception. Note that you can always turn recoverable
errors into exceptions by calling $stream->verbose(2).
Returns : a Bio::Seq sequence object
Args : none
See Bio::Root::RootI
Title : write_seq Usage : $stream->write_seq($seq) Function: writes the $seq object into the stream Returns : 1 for success and 0 for error Args : Bio::Seq object
Title : sequence_factory Usage : $seqio->sequence_factory($seqfactory) Function: Get the Bio::Factory::SequenceFactoryI Returns : Bio::Factory::SequenceFactoryI Args : none
| 2021-08-15 | perl v5.32.1 |