biopython v1.71.0 Bio.Blast.NCBIXML
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
Link to this section Summary
Link to this section Functions
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).
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).