Bio::SeqIO::fasta 1.4

Bio::SeqIO::fasta is a Perl module with fasta sequence input/output stream.

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.

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Requirements:

· Perl