Package Bio :: Package AlignIO :: Module FastaIO
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Module FastaIO

source code

Bio.AlignIO support for "fasta-m10" output from Bill Pearson's FASTA tools.

You are expected to use this module via the Bio.AlignIO functions (or the
Bio.SeqIO functions if you want to work directly with the gapped sequences).

This module contains a parser for the pairwise alignments produced by Bill
Pearson's FASTA tools, for use from the Bio.AlignIO interface where it is
refered to as the "fasta-m10" file format (as we only support the machine
readable output format selected with the -m 10 command line option).

This module does NOT cover the generic "fasta" file format originally
developed as an input format to the FASTA tools.  The Bio.AlignIO and
Bio.SeqIO both use the Bio.SeqIO.FastaIO module to deal with these files,
which can also be used to store a multiple sequence alignments.

Functions [hide private]
 
_extract_alignment_region(alignment_seq_with_flanking, annotation)
Helper function for the main parsing code (PRIVATE).
source code
 
FastaM10Iterator(handle, alphabet=SingleLetterAlphabet())
Alignment iterator for the FASTA tool's pairwise alignment output.
source code
Variables [hide private]
  __package__ = 'Bio.AlignIO'
Function Details [hide private]

_extract_alignment_region(alignment_seq_with_flanking, annotation)

source code 
Helper function for the main parsing code (PRIVATE).

To get the actual pairwise alignment sequences, we must first
translate the un-gapped sequence based coordinates into positions
in the gapped sequence (which may have a flanking region shown
using leading - characters).  To date, I have never seen any
trailing flanking region shown in the m10 file, but the
following code should also cope with that.

Note that this code seems to work fine even when the "sq_offset"
entries are prsent as a result of using the -X command line option.

FastaM10Iterator(handle, alphabet=SingleLetterAlphabet())

source code 
Alignment iterator for the FASTA tool's pairwise alignment output.

This is for reading the pairwise alignments output by Bill Pearson's
FASTA program when called with the -m 10 command line option for machine
readable output.  For more details about the FASTA tools, see the website
http://fasta.bioch.virginia.edu/ and the paper:

     W.R. Pearson & D.J. Lipman PNAS (1988) 85:2444-2448

This class is intended to be used via the Bio.AlignIO.parse() function
by specifying the format as "fasta-m10" as shown in the following code:

    from Bio import AlignIO
    handle = ...
    for a in AlignIO.parse(handle, "fasta-m10"):
        assert len(a) == 2, "Should be pairwise!"
        print("Alignment length %i" % a.get_alignment_length())
        for record in a:
            print("%s %s %s" % (record.seq, record.name, record.id))

Note that this is not a full blown parser for all the information
in the FASTA output - for example, most of the header and all of the
footer is ignored.  Also, the alignments are not batched according to
the input queries.

Also note that there can be up to about 30 letters of flanking region
included in the raw FASTA output as contextual information.  This is NOT
part of the alignment itself, and is not included in the resulting
MultipleSeqAlignment objects returned.