Package Bio :: Package SeqIO :: Module FastaIO
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Module FastaIO

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Bio.SeqIO support for the "fasta" (aka FastA or Pearson) file format.

You are expected to use this module via the Bio.SeqIO functions.

Classes [hide private]
  FastaWriter
Class to write Fasta format files.
Functions [hide private]
 
FastaIterator(handle, alphabet=SingleLetterAlphabet(), title2ids=None)
Generator function to iterate over Fasta records (as SeqRecord objects).
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Variables [hide private]
  __package__ = 'Bio.SeqIO'
Function Details [hide private]

FastaIterator(handle, alphabet=SingleLetterAlphabet(), title2ids=None)

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Generator function to iterate over Fasta records (as SeqRecord objects).

handle - input file alphabet - optional alphabet title2ids - A function that, when given the title of the FASTA file (without the beginning >), will return the id, name and description (in that order) for the record as a tuple of strings.

If this is not given, then the entire title line will be used as the description, and the first word as the id and name.

Note that use of title2ids matches that of Bio.Fasta.SequenceParser but the defaults are slightly different.