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Bio::AlignIO::FastaIO::FastaM10Iterator Class Reference

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List of all members.

Public Member Functions

def next

Private Member Functions

def _extract_alignment_region
def _parse_query_header
def _parse_tag_section
def _skip_file_header

Private Attributes

 _header
 _query_descr
 _query_header_annotation

Detailed Description

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.get_all_seqs()) == 2, "Should be pairwise!"
        print "Alignment length %i" % a.get_alignment_length()
        for record in a :
            print 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
Alignment objects returned.

Definition at line 29 of file FastaIO.py.


The documentation for this class was generated from the following file:

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