Bio::SeqIO::strider(3)User Contributed Perl DocumentatioBio::SeqIO::strider(3)NAMEBio::SeqIO::strider - DNA strider sequence input/output stream
SYNOPSIS
Do not use this module directly. Use it via the Bio::SeqIO class.
DESCRIPTION
This object can transform Bio::Seq objects to and from strider 'binary'
format, as documented in the strider manual, in which the first 112
bytes are a header, following by the sequence, followed by a sequence
description.
Note: it does NOT assign any sequence identifier, since they are not
contained in the byte stream of the file; the Strider application
simply displays the name of the file on disk as the name of the
sequence. The caller should set the id, probably based on the name of
the file (after possibly cleaning up whitespace, which ought not to be
used as the id in most applications).
Note: the strider 'comment' is mapped to the BioPerl 'description'
(since there is no other text field, and description maps to defline
text).
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 one
of the Bioperl mailing lists. 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
the bugs and their resolution. Bug reports can be submitted via the
web:
http://bugzilla.open-bio.org/
AUTHORS - Malcolm Cook
Email: mec@stowers-institute.org
CONTRIBUTORS
Modelled after Bio::SeqIO::fasta by Ewan Birney <birney@ebi.ac.uk> and
Lincoln Stein <lstein@cshl.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: returns the next sequence in the stream
Returns : Bio::Seq object
Args : NONE
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 : array of 1 to n Bio::PrimarySeqI objects
perl v5.14.1 2011-07-22 Bio::SeqIO::strider(3)
