Christopher Fields > BioPerl-1.6.901 > Bio::SeqIO::strider

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Module Version: 1.006901   Source   Latest Release: BioPerl-1.6.924

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://redmine.open-bio.org/projects/bioperl/

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
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