Bio.Blast.NCBIXML

Package Bio :: Package Blast :: Module NCBIXML

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Module Bio.Blast.NCBIXML

This module provides code to work with the BLAST XML output
following the DTD available on the NCBI FTP
ftp://ftp.ncbi.nlm.nih.gov/blast/documents/xml/NCBI_BlastOutput.dtd

Classes:
BlastParser         Parses XML output from BLAST.
                    This (now) returns a list of Blast records.
                    Historically it returned a single Blast record.

_XMLParser          Generic SAX parser.

Functions:
parse               Incremental parser, this is an iterator that returns
                    Blast records.

Classes
`BlastParser`	Parse XML BLAST data into a Record.Blast object Methods: parse Parses BLAST XML data.
`_XMLparser`	Generic SAX Parser

Function Summary
	`parse(handle, debug)` Returns an iterator a Blast record for each query.

Function Details

parse(handle, debug=0)

Returns an iterator a Blast record for each query.

handle - file handle to and XML file to parse debug - integer, amount of debug information to print

This is a generator function that returns multiple Blast records objects - one for each query sequence given to blast. The file is read incrementally, returning complete records as they are read in.

Should cope with new BLAST 2.2.14+ which gives a single XML file for mutliple query records.

Should also cope with XML output from older versions BLAST which gave multiple XML files concatenated together (giving a single file which strictly speaking wasn't valid XML).

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