[BioPython] blast output

[Edoardo Saccenti]

Dear all
I want to blast my sequence and get all possible results
If I run blast as in cookbook i get much more less results then
runnig blast manually and setting to 1000 the number of descriptions

How set the number of descrition NCBIWWW.qblast ???

Another question:
I run manually blast and saved my output page in html format using my browser.
Then I tried to parse but i get lot of errors:

=================================
Traceback (most recent call last):
  File "ParseBlastOutput.py", line 7, in ?
    b_record = b_parser.parse(blast_out)
  File "/usr/lib/python2.3/site-packages/Bio/Blast/NCBIWWW.py", line 47, in 
pars
e
    self._scanner.feed(handle, self._consumer)
  File "/usr/lib/python2.3/site-packages/Bio/Blast/NCBIWWW.py", line 100, in 
fee
d
    self._scan_header(uhandle, consumer)
  File "/usr/lib/python2.3/site-packages/Bio/Blast/NCBIWWW.py", line 167, in 
_sc
an_header
    self._scan_query_info(uhandle, consumer)
  File "/usr/lib/python2.3/site-packages/Bio/Blast/NCBIWWW.py", line 235, in 
_sc
an_query_info
    read_and_call_until(uhandle, consumer.query_info, blank=1)
  File "/usr/lib/python2.3/site-packages/Bio/ParserSupport.py", line 340, in 
rea
d_and_call_until
    method(line)
  File "/usr/lib/python2.3/site-packages/Bio/ParserSupport.py", line 136, in 
_ap
ply_clean_data
    self._prev_attr(clean)
  File "/usr/lib/python2.3/site-packages/Bio/Blast/NCBIStandalone.py", line 
651,
 in query_info
    "I could not find the number of letters in line\n%s" % line)
  File "/usr/lib/python2.3/site-packages/Bio/Blast/NCBIStandalone.py", line 
1618
, in _re_search
    raise SyntaxError, error_msg
SyntaxError: I could not find the number of letters in line
           27,711,076 sequences; 14,863,934,794 total letters
======================================================

I copied my alignments in a output file get from NCBIWWW.qblast using its 
header. This time I get a dfferent error:

=============
Traceback (most recent call last):
  File "ParseBlastOutput.py", line 7, in ?
    b_record = b_parser.parse(blast_out)
  File "/usr/lib/python2.3/site-packages/Bio/Blast/NCBIWWW.py", line 47, in 
parse
    self._scanner.feed(handle, self._consumer)
  File "/usr/lib/python2.3/site-packages/Bio/Blast/NCBIWWW.py", line 102, in 
feed
    self._scan_database_report(uhandle, consumer)
  File "/usr/lib/python2.3/site-packages/Bio/Blast/NCBIWWW.py", line 539, in 
_scan_database_report
    read_and_call(uhandle, consumer.noevent, blank=1)
  File "/usr/lib/python2.3/site-packages/Bio/ParserSupport.py", line 300, in 
read_and_call
    raise SyntaxError, errmsg
SyntaxError: Expected blank line, but got:
Gapped

Any Idea??

Thanks Edoardo


 
"Raffiniert ist der Herr Gott,
 aber boshaft ist Er nicht."

---
Dr. Edoardo Saccenti
CERM Nuclear Magnetic Resonance Research Center
Scientific Pole - University of Florence
Via Luigi Sacconi n° 6
50019 Sesto Fiorentino (FI)
tel: +39 055 4574193
fax: +39 055 4574253
saccenti at cerm.unifi.it
www.cerm.unifi.it