bionic (3) Bio::SeqIO::strider.3pm.gz

NAME

       Bio::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:

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

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