[BioPython] blast output
Edoardo Saccenti
saccenti at cerm.unifi.it
Fri Jul 1 05:38:34 EDT 2005
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
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