++ed by:
CJFIELDS FIBO ILUX PINGAN MAJENSEN

11 PAUSE users
14 non-PAUSE users.

Christopher Fields
and 1 contributors

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

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
 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.