Bio::Factory::SequenceUseraContributed Perl DoBio::Factory::SequenceStreamI(3)NAMEBio::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:
http://bugzilla.open-bio.org/
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
perl v5.14.1 2011-07-22 Bio::Factory::SequenceStreamI(3)
