[Bioperl-l] Thoughts on Bio::Tools::Glimmer

Torsten Seemann torsten.seemann at infotech.monash.edu.au
Wed Apr 11 20:33:02 EDT 2007


Andrew,

>                 # Glimmer 3.X prediction
>                 (/\w+(\d+)\s+       # orf (numeric portion)
> ...isn't picking up more than the last digit in the orf-number.  Not
> sure if that's intentional.  A sample of the feature output using -
>  >gff_string shows up as ...

I think that regexp should be \w+?(\d+)

ie. the \w+ should be non-greedy, otherwise it will swallow up all but
one of the following \d+ (as \d is a subset of \w)

I've CC:ed this to Mark Johnson who made the recent changes to this module.

Thanks for your feedback,

--Torsten Seemann


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