Bio::SeqIO::strider - DNA strider sequence input/output stream
Do not use this module directly. Use it via the Bio::SeqIO class.
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).
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.
firstname.lastname@example.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Please direct usage questions or support issues to the mailing list:
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.
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:
Modelled after Bio::SeqIO::fasta by Ewan Birney <email@example.com> and
Lincoln Stein <firstname.lastname@example.org>
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: returns the next sequence in the stream
Returns : Bio::Seq object
Args : NONE
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