[Bioperl-l] bioperl-db -- qualifier values

[Elia Stupka]

> Am I being overly optimistic to suggest having traps placed in the
> appropriate spots to capture EC numbers, like
> 
> /EC:*\s*(\d+\.\d+\.\d+\.\d+)/
> 
> and then spoon feed it as a tag value pair to the feature table code?

I think the issue here is that it is a perfectly sane thing for people to
do as their own local modifications that trap their own interest, but is
it an issue that bioperl should solve? We should stick to storing the
structure as originally intended, right? If we went off to solve these
problems (which are all related to either bad guidelines or misuse of
guidelines at submission), then we would be opening a can of worms, e.g.
genes in EMBL/Genbank files...

What do others think?

The nice thing to do would be of course to change our swiss parser to trap
these and store them *also* as features, but we cannot go to the extent of
trapping them as features and thus not storing them as description lines,
right? 

Ideally you want to go in and out of a parser and retain the exact same
file, though by altering the code you could be producing a "better" file.

Elia

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