NAME

Bio::Factory::SequenceStreamI - Interface describing the basics of a Sequence Stream.

SYNOPSIS

# get a SequenceStreamI object somehow like with SeqIO
use Bio::SeqIO;
my $in = Bio::SeqIO->new(-file => '< fastafile');
while( my $seq = $in->next_seq ) {
}

DESCRIPTION

This interface is for describing objects which produces Bio::PrimarySeqI objects or processes Bio::PrimarySeqI objects to a data stream.

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.

bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

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.

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:

https://github.com/bioperl/bioperl-live/issues

AUTHOR - Jason Stajich

Email jason@bioperl.org

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

next_seq

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

write_seq

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

sequence_factory

Title   : sequence_factory
Usage   : $seqio->sequence_factory($seqfactory)
Function: Get the Bio::Factory::SequenceFactoryI
Returns : Bio::Factory::SequenceFactoryI
Args    : none