[Bioperl-l] remoteblast doesn't save the Output File

[Torsten Seemann]

(Hubert - please send your emails to bioperl-l at bioperl.org so others
can help too)

> Sorry for the Misunderstanding, it was my fault. I have already read the 
> Module, and the Matrix is working well. But if I want to change the 
> Gapcost Parameter, I don't know
> how to format, because if I do it like that 'GAPCOSTS' = '9 1';  I will 
> get the following Message:
>
> MSG: Value 9 1 for PUT parameter GAPCOSTS does not match expression 
> -?\d+(\.\d+)\s+i-?\d+(\.\d+). Rejecting.
>
> if I do it like 'GAPCOSTS' = '9';  I will get the same Message like above.
> I have tried it with "" too, but there was no Impact on it, i got the 
> same Message:

The error is clear:
'9 1' fails because it does not match the regular expression 
/-?\d+(\.\d+)\s+i-?\d+(\.\d+)/

The $NUM='-?\d+(\.\d+)' parts are trying to match a floating point
number or integer, eg. "3.41" or "6" or "-78.1", which simplifies to
/$NUM\s+i$NUM/x which suggests it wants it in the form:

'GAPCOSTS' = '9 i1'

which looks unusual but would match the pattern?

The documentation says '9 1' should work?
http://www.ncbi.nlm.nih.gov/BLAST/Doc/node28.html

Perhaps a bug in NCBI's code, the 'i' might be a typo?

-- 
Torsten Seemann <torsten.seemann at infotech.monash.edu.au>
Victorian Bioinformatics Consortium