[Biopython] Fwd: Qblast : no hits

[Karthik Raja]

 Hello Peter,

As said i did try changing the parameters of qblast according to the set in
the web blast.
The parameters that I changed are
1. Martrix
2. Word size
3. Expect

There is a check box option in the web page that allows us to check it if we
want the web blast to adjust according short sequences. I am not sure how to
bring that option into the qblast.

*Below given are the code and the traceback. *
 >>> from Bio.Blast import NCBIWWW
>>> result_handle = NCBIWWW.qblast ("blastp", "nr", "SSRVQDGMGLYTARRVR",
auto_format=None, composition_based_statistics=None, db_genetic_code=None,
endpoints=None, entrez_query='(none)', expect=200000, filter=None,
gapcosts=None, genetic_code=None, hitlist_size=50, i_thresh=None,
layout=None, lcase_mask=None, matrix_name= 'PAM30', nucl_penalty=None,
nucl_reward=None, other_advanced=None, perc_ident=None, phi_pattern=None,
query_file=None, query_believe_defline=None, query_from=None, query_to=None,
searchsp_eff=None, service=None, threshold=None, ungapped_alignment=None,
word_size=2, alignments=500, alignment_view=None, descriptions=500,
entrez_links_new_window=None, expect_low=None, expect_high=None,
format_entrez_query=None, format_object=None, format_type='XML',
ncbi_gi=None, results_file=None, show_overview=None)

*Traceback (most recent call last):
*  File "<pyshell#2>", line 1, in <module>
    result_handle = NCBIWWW.qblast *("blastp", "nr",
"SSRVQDGMGLYTARRVR",*auto_format=None,
composition_based_statistics=None, db_genetic_code=None,
endpoints=None, entrez_query='(none)', *expect=200000*, filter=None,
gapcosts=None, genetic_code=None, hitlist_size=50, i_thresh=None,
layout=None, lcase_mask=None, *matrix_name= 'PAM30'*, nucl_penalty=None,
nucl_reward=None, other_advanced=None, perc_ident=None, phi_pattern=None,
query_file=None, query_believe_defline=None, query_from=None, query_to=None,
searchsp_eff=None, service=None, threshold=None, ungapped_alignment=None, *
word_size=2*, alignments=500, alignment_view=None, descriptions=500,
entrez_links_new_window=None, expect_low=None, expect_high=None,
format_entrez_query=None, format_object=None, format_type='XML',
ncbi_gi=None, results_file=None, show_overview=None)
  File "C:\Python26\lib\site-packages\Bio\Blast\NCBIWWW.py", line 117, in
qblast
    rid, rtoe = _parse_qblast_ref_page(handle)
  File "C:\Python26\lib\site-packages\Bio\Blast\NCBIWWW.py", line 203, in
_parse_qblast_ref_page
    raise ValueError("No RID and no RTOE found in the 'please wait' page."
ValueError: No RID and no RTOE found in the 'please wait' page. (there was
probably a problem with your request)

Here are a few examples of my MS sequences.


   1. *IMYTALPVIGKRHFRPSFTR *
   2. *RSSRGRGR *
   3. *AGPGPRRAKAAPYR *
   4. *ASRSYSSERRAR *
   5. *AASAAPPRAGRPDRGPLALAGR *
   6. *GSDGKSRGR *
   7. *TYGWRAEPR *
   8. *PPEPAREPRLSPRR *
   9. *GVLTALRR *
   10. *AGMRLPSRRQSFPAPVSR *

*Sincerely, *
*Karthikraja*

On Sat, Apr 24, 2010 at 5:19 PM, Peter <biopython at maubp.freeserve.co.uk>wrote:

> Hi all,
>
> Sorry for the blank email just now.
>
> On Sat, Apr 24, 2010 at 4:27 AM, Karthik Raja wrote:
> > Hello Peter,
> >
> > I did try changing the paramters according to the WWW BLAST
> > and its gives an error saying "no RID or no RTOE found". Its the
> > same error i was trying to tell you in the 1st post. Its the "request
> > time of execution". Is there any way to change this RTOE i.e. to
> > increase it? Any idea?
>
> Please show us an example with this problem (i.e. the python
> code and the traceback).
>
> What is meant to happen is we send the query to the NCBI, and
> they reply with reference details (RID and RTOE) which are
> used to fetch the results after BLAST has finished running.
>
> My guess for what is happening is your parameters are for
> some reason invalid, and the NCBI is giving an error page
> (so no RID and no RTOE). Biopython tries to spot any error
> message in this situation, but in your case could not.
>
> Peter
>