Package Bio :: Package Blast :: Module NCBIXML
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Module NCBIXML

source code

Code to work with the BLAST XML output.

The BLAST XML DTD file is on the NCBI FTP site at: ftp://ftp.ncbi.nlm.nih.gov/blast/documents/xml/NCBI_BlastOutput.dtd

Classes [hide private]
  _XMLparser
Generic SAX Parser (PRIVATE).
  BlastParser
Parse XML BLAST data into a Record.Blast object.
Functions [hide private]
 
read(handle, debug=0)
Returns a single Blast record (assumes just one query).
source code
 
parse(handle, debug=0)
Returns an iterator a Blast record for each query.
source code
Variables [hide private]
  __package__ = 'Bio.Blast'
Function Details [hide private]

read(handle, debug=0)

source code 

Returns a single Blast record (assumes just one query).

Uses the BlastParser internally.

This function is for use when there is one and only one BLAST result in your XML file.

Use the Bio.Blast.NCBIXML.parse() function if you expect more than one BLAST record (i.e. if you have more than one query sequence).

parse(handle, debug=0)

source code 

Returns an iterator a Blast record for each query.

Incremental parser, this is an iterator that returns Blast records. It uses the BlastParser internally.

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 multiple 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).