Linux Certif

Toute la documentation sur la certification Linux LPI

Bio::SeqIO::raw.3pm

NAME

Bio::SeqIO::raw - raw sequence file 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 raw flat file databases.

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

   Ewan Birney   E<lt>birney@ebi.ac.ukE<gt>
   Lincoln Stein E<lt>lstein@cshl.orgE<gt>
 
 

CONTRIBUTORS

   Jason Stajich E<lt>jason@bioperl.org<gt>
 
 

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    :
 
 

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 Bio::PrimarySeqI objects
 
 

write_qual

  Title   : write_qual
  Usage   : $stream->write_qual($seq)
  Function: writes the $seq object into the stream
  Returns : 1 for success and 0 for error
  Args    : Bio::Seq::Quality object
 
 

variant

  Title   : variant
  Usage   : $format  = $obj->variant();
  Function: Get and set method for the sequence variant.  For raw sequence, this
            indicates whether to treat the input as multiple sequences (the
            default) or as a single sequence.
 
            Current values accepted are:
 
             'single'    single sequence
             'multiple'  multiple sequences (default)
  Returns : string
  Args    : new value, string