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.
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.
email@example.com - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Please direct usage questions or support issues to the mailing list:
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.
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:
Email: firstname.lastname@example.org email@example.com
Jason Stajich, jason-at-bioperl.org
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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
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
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)
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 to easily indentify a position in a sequence by eye. Default : same value used for width. Returns : value of block Args : newvalue (optional)
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.