Does Biopython Parse Blast -M8 Or -M9 (Aka Blasttable)?

I am getting the following error when I try -m9

  File "parseBlast.biopython.py", line 5, in ?
    blast_record = blast_parser.parse(result_handle)
  File "/src/biopython-1.52/build/lib.linux-x86_64-2.4/Bio/Blast/NCBIStandalone.py", line 763, in parse
    self._scanner.feed(handle, self._consumer)
  File "/src/biopython-1.52/build/lib.linux-x86_64-2.4/Bio/Blast/NCBIStandalone.py", line 96, in feed
    self._scan_header(uhandle, consumer)
  File "/src/biopython-1.52/build/lib.linux-x86_64-2.4/Bio/Blast/NCBIStandalone.py", line 213, in _scan_header
    raise ValueError("Invalid header?")
ValueError: Invalid header?

biopython python

• 5,096 views • link

updated 2.7 years ago by Ram

• written 16.3 years ago by Jeremy Leipzig

3 answers

Try with blast's XML output instead. As explained in biopython's FAQs (#17), the XML format is the only one that will be always supported.

• 3 views • link

updated 2.7 years ago by Ram

• written 16.3 years ago by Giovanni M Dall'Olio

uhhh no thanks xml is way too verbose. I have over 20M alignments.

• 0 views • link

written 16.3 years ago by Jeremy Leipzig

then either try the latest biopython's release or use another tool. Or write to the biopython's mailing list and explain your use case, maybe they will update the parser for you.

• 0 views • link

written 16.3 years ago by Giovanni M Dall'Olio

ParseBlastTable may do what you want, but it was designed for the output of blastpgp, not blastall. I can't get it to work with the BLASTN blasttable I have to hand.

• 4 views • link

updated 2.7 years ago by Ram

• written 16.3 years ago by Simon Cockell

Take a look at Biostar question: "How to convert BLAST results to GFF"

There is fairly easy Python solution for parsing blast column output.

• 4 views • link

written 16.3 years ago by Darked89