Provided by: libbio-perl-perl_1.7.2-2_all
Bio::SeqIO::fasta - fasta sequence input/output stream
Do not use this module directly. Use it via the Bio::SeqIO class.
This object can transform Bio::Seq objects to and from fasta flat file databases.
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AUTHORS - Ewan Birney & Lincoln Stein
Email: email@example.com firstname.lastname@example.org
Jason Stajich, jason-at-bioperl.org
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 (not counting whitespace). Returns : value of width Args : newvalue (optional) block Title : block Usage : $obj->block($newval) Function: Get/Set the length of each block for FASTA output. Sequence blocks will be split with a space. Configuring block, to a value of 10 for example, allows one to easily identify a position in a sequence by eye. Default : same value used for width. Returns : value of block 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 : 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.