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

Torsten Seemann torsten.seemann at infotech.monash.edu.au
Tue Dec 6 19:08:47 EST 2005

> >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?

> Thanks, I have tried your Example:
> 'GAPCOSTS' = '9 i1'    ...... it wasn't working, but if you took float 
> instead of integer the gap existence will work but not the Gap extend, 
> like 'GAPCOSTS' = '9.0 i1.0'
> It never minds, if I take 'GAPCOSTS' = '9.0 i1.0' or 'GAPCOSTS' = '9.0 
> i-1.0' or instead of 1.0 any other float value, I always get the same 
> Message:
> Gap existence and extension values of 10 and 0 not supported for BLOSUM80
> it always sets the extension Value to 0.

If I was awake when I wrote this I would have realised that it
was $NUM='-?\d+(\.\d+)' which means you MUST have the number with
a decimal point and a zero after it. i.e. integers are NOT accepted.
They would be accepted if it was $NUM='-?\d+(\.\d+)?' - the fact that
they have bracketed it suggests they forgot to put the ? after it, other
wise their isn't much point to bracketing it.

So you are right that "9.0 i1.0" matches the expression.

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

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