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.

A method preferred_id_type() can be used to specify the type of ID we would like to parse from the fasta line. By default 'display' is used, which means it parses everything from the '>' to the first space and makes that the 'display_id' for the sequence.

Can be one of: - accession - accession.version - display - primary

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/MailList.shtml - 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.bioperl.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 to n 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.