Bio.Blast.NCBIXML

Module 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

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_XMLparser
Generic SAX Parser

BlastParser
Parse XML BLAST data into a Record.Blast object

Functions

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parse(handle, debug=0)
Returns an iterator a Blast record for each query.

source code

Function Details

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parse(handle, debug=0)

source code

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).