[BioPython] PSIBlastParser and blastpgp 2.2.18

[Miguel Ortiz-Lombardía]

Hi,

The PSIBlastParser (biopython 1.45) seems not to work with the latest
(2.2.18) version of NCBI blastpgp. Using the same script/inputs I can
successfully run it with blastpgp 2.2.15 but when using 2.2.18 I get this
error:

Traceback (most recent call last):
  File "./lpbl.py", line 23, in <module>
    b_record = b_parser.parse(blast_out)
  File "/home/mortiz/Progs//lib/python/Bio/Blast/NCBIStandalone.py", line
760, in parse
    self._scanner.feed(handle, self._consumer)
  File "/home/mortiz/Progs//lib/python/Bio/Blast/NCBIStandalone.py", line
98, in feed
    self._scan_header(uhandle, consumer)
  File "/home/mortiz/Progs//lib/python/Bio/Blast/NCBIStandalone.py", line
208, in _scan_header
    raise ValueError("Invalid header?")
ValueError: Invalid header?

In both cases I had setup align_view='0' so the psi-blast output is plain
text and not XML (This is because I don't think there is a PSI-Blast parser
working with XML, if there is one, please let me know how to invoke it)

Best regards,


Miguel

-- 
http://www.pangea.org/mol/spip.php?rubrique2
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Je suis de la mauvaise herbe,
Braves gens, braves gens,
Je pousse en liberté
Dans les jardins mal fréquentés!
Georges Brassens