Module fasta

source code

FASTA format sequence I/O.

This module provides parsers and writers for sequences and alignments in FASTA format. The most basic usage is:

>>> parser = SequenceParser()
>>> parser.parse_file('sequences.fa')
<SequenceCollection>   # collection of L{AbstractSequence}s

This will load all sequences in memory. If you are parsing a huge file, then you could efficiently read the file sequence by sequence:

>>> for seq in parser.read('sequences.fa'):
        ...            # seq is an L{AbstractSequence}

BaseSequenceParser is the central class in this module, which defines a common infrastructure for all sequence readers. SequenceParser is a standard implementation, and PDBSequenceParser is specialized to read FASTA sequences with PDB headers.

For parsing alignments, have a look at SequenceAlignmentReader and StructureAlignmentFactory.

Finally, this module provides a number of OutputBuilders, which know how to write AbstractSequence and AbstractAlignment objects to FASTA files:

>>> with open('file.fa', 'w') as out:
        builder = OutputBuilder.create(AlignmentFormats.FASTA, out)
        builder.add_alignment(alignment)
        builder.add_sequence(sequence)
        ...

or you could instantiate any of the OutputBuilders directly.