[BioPython] Blast parser error (blast output format changed?)

Sagar Damle sagar@caltech.edu
Thu, 7 Feb 2002 11:39:28 -0800


Hello all,
 I'm new to BioPython (and relatively new to Python), and am having trouble getting past this error.  It appears that the format has changed slightly, and the parser is broken.  Is there a quick fix I can apply?  (problem exists on latest CVS version as well as latest stable version of BioPython

---------------------------------------python stack---------------------------------------
Traceback (most recent call last):
  File "<stdin>", line 1, in ?
  File "/usr/software/python/2.1/lib/python2.1/site-packages/Bio/Blast/NCBIWWW.py", line 47, in parse
    self._scanner.feed(handle, self._consumer)
  File "/usr/software/python/2.1/lib/python2.1/site-packages/Bio/Blast/NCBIWWW.py", line 98, in feed
    self._scan_header(uhandle, consumer)
  File "/usr/software/python/2.1/lib/python2.1/site-packages/Bio/Blast/NCBIWWW.py", line 161, in _scan_header
    self._scan_database_info(uhandle, consumer)
  File "/usr/software/python/2.1/lib/python2.1/site-packages/Bio/Blast/NCBIWWW.py", line 171, in _scan_database_info
    read_and_call(uhandle, consumer.noevent, blank=1)
  File "/usr/software/python/2.1/lib/python2.1/site-packages/Bio/ParserSupport.py", line 331, in read_and_call
    raise SyntaxError, errmsg
SyntaxError: Expected blank line, but got:
           1,140,404 sequences; 4,812,034,933 total letters

------------------------------------blast record lines------------------------------------
'<b>Query=</b> |gb|AB012851|AB012851.1| Homo sapiens mRNA for Musashi,\n',
 'complete cds.\n',
 '         (1940 letters)\n',
 '\n',
 '<p>\n',
 '<b>Database:</b> All GenBank+EMBL+DDBJ+PDB sequences (but no EST, STS,\n',
 'GSS, or phase 0, 1 or 2 HTGS sequences) \n',
 '           1,140,404 sequences; 4,812,034,933 total letters\n',
 '\n',
 '<p> <p>If you have any problems or questions with the results of this search <br>please refer to the <b><a href=http://www.ncbi.nlm.nih.gov/blast/blast_FAQs.html>BLAST FAQs</a></b><br><p>\n',
 '<a href="Blast.cgi?CMD=Get&RID=1013109987-11472-9246&FORMAT_OBJECT=TaxBlast" TARGET="Taxonomy BLAST Results for 1013109987-11472-9246">Taxonomy reports</a>\n'