Bio::SeqIO::fasta.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

NAME

Bio::SeqIO::fasta - fasta 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 fasta 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 & Lincoln Stein

Email: birney@ebi.ac.uk
       lstein@cshl.org

CONTRIBUTORS

Jason Stajich, jason-at-bioperl.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, or nothing if no more available
  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 or more Bio::PrimarySeqI objects
 
 

width

  Title   : width
  Usage   : $obj->width($newval)
  Function: Get/Set the line width for FASTA output
  Returns : value of width
  Args    : newvalue (optional)
 
 

preferred_id_type

  Title   : preferred_id_type
  Usage   : $obj->preferred_id_type('accession')
  Function: Get/Set the preferred type of identifier to use in the ">ID" position
            for FASTA output.
  Returns : string, one of values defined in @Bio::SeqIO::fasta::SEQ_ID_TYPES.
            Default = $Bio::SeqIO::fasta::DEFAULT_SEQ_ID_TYPE ('display').
  Args    : string when setting. This must be one of values defined in 
            @Bio::SeqIO::fasta::SEQ_ID_TYPES. Allowable values:
            accession, accession.version, display, primary
  Throws  : fatal exception if the supplied id type is not in @SEQ_ID_TYPES.