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.\" ========================================================================
.\"
.IX Title "Bio::SeqIO::strider 3pm"
.TH Bio::SeqIO::strider 3pm "2014-07-13" "perl v5.18.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
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.SH "NAME"
Bio::SeqIO::strider \- DNA strider sequence input/output stream
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
Do not use this module directly.  Use it via the Bio::SeqIO class.
.SH "DESCRIPTION"
.IX Header "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.
.PP
Note: it does \s-1NOT\s0 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).
.PP
Note: the strider 'comment' is mapped to the BioPerl 'description'
(since there is no other text field, and description maps to defline
text).
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  https://github.com/bioperl/bioperl\-live/issues
.Ve
.SH "AUTHORS \- Malcolm Cook"
.IX Header "AUTHORS - Malcolm Cook"
Email: mec@stowers\-institute.org
.SH "CONTRIBUTORS"
.IX Header "CONTRIBUTORS"
Modelled after Bio::SeqIO::fasta by Ewan Birney <birney@ebi.ac.uk> and
Lincoln Stein <lstein@cshl.org>
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
.SS "next_seq"
.IX Subsection "next_seq"
.Vb 5
\& Title   : next_seq
\& Usage   : $seq = $stream\->next_seq()
\& Function: returns the next sequence in the stream
\& Returns : Bio::Seq object
\& Args    : NONE
.Ve
.SS "write_seq"
.IX Subsection "write_seq"
.Vb 5
\& 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
.Ve