[Biopython] Fwd: Qblast : no hits

[Karthik Raja]

Hello Peter,

I tried out what you suggested and it works perfectly. I checked the result
XML file and there was no problem at all.
But I still have one more small issue that I am sure you can help me with.
The main reason i wanted to use python was that I could put all the query
sequences in a file and blast it. So when I tried the above code to blast a
sequence that I have put in a fasta file, it gives an error. Same kinda
error. Below are the code and traceback.

>>> fasta_string = open("test.fasta").read()
>>> result_handle = NCBIWWW.qblast("blastp", "nr",
fasta_string,entrez_query='(none)', expect=200000, hitlist_size=50,
word_size=2, alignments=500, descriptions=500,format_type='XML')

*Traceback (most recent call last):
*  File "<pyshell#28>", line 2, in <module>
    word_size=2, alignments=500, descriptions=500,format_type='XML')
  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)

Please let me know if you could sense in the problem with the code.

Sincerely,
Karthik

On Sun, Apr 25, 2010 at 6:15 PM, Peter <biopython at maubp.freeserve.co.uk>wrote:

> On Sun, Apr 25, 2010 at 4:24 AM, Karthik Raja wrote:
>
> > *Below given are the code and the traceback. *
>
> Great - I can run that and get the same traceback.
>
> Here is a shorter version which does the same thing - removing all the
> parameters you don't actually set:
>
> from Bio.Blast import NCBIWWW
> result_handle = NCBIWWW.qblast("blastp", "nr", "SSRVQDGMGLYTARRVR",
> entrez_query='(none)', expect=200000, hitlist_size=50,
> matrix_name='PAM30', word_size=2, alignments=500, descriptions=500,
> format_type='XML')
>
> Getting shorter still:
>
> result_handle = NCBIWWW.qblast("blastp", "nr", "SSRVQDGMGLYTARRVR",
> matrix_name='PAM30')
>
> The problem is the matrix name - remove that and the error goes away.
> So progress :)
>
> Doing a little digging, this is the error message from the NCBI is:
>
> Message ID#35 Error: Cannot validate the Blast options:  Gap existence
> and extension values of 11 and 1 not supported for PAM30
> supported values are:
> 32767, 32767
> 7, 2
> 6, 2
> 5, 2
> 10, 1
> 9, 1
> 8, 1
>
> As I guessed earlier, Biopython needed a little update to recognise
> this error message and pass it to the user. I've done that.
>
> In your case, you need to pick gap parameters appropriate for PAM30.
>
> Peter
>