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Man Pages


Manual Reference Pages  -  BIO::SEQIO::RAW (3)

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NAME

Bio::SeqIO::raw - raw sequence file input/output stream

CONTENTS

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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perl v5.20.3 BIO::SEQIO::RAW (3) 2016-04-05

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