Christopher Fields > BioPerl > Bio::SeqIO::raw

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Module Version: 1.006924   Source  

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:

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

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
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