[Bioperl-l] Long /labels are wrapped, but can't be read

[Adam Sjøgren]

On Tue, 29 Sep 2009 22:54:04 -0500, Chris wrote:

> Not sure, but this could be a case of 'both'. Labels that are quoted
> and aren't are currently distinguished via a global hash lookup
> (%FTQUAL_NO_QUOTE) due to the way the parser works; there is some
> logic behind this, just can't quite recall at the moment why it is
> this way.

Yes, I saw that there is a number of qualifiers that aren't quoted
automatically.

The very easy "fix" for me would be to simply remove "label" from
%FTQUAL_NO_QUOTE, but I'm not really sure what the reason for not
quoting all values is, so I was hesitant to just propose that.

> You could set a hash key for the label in cases where it isn't quoted,
> that should work. You can also test out the Bio::SeqIO::embldriver
> version (-format => 'embldriver').

Ah, embldriver reads the wrapped qualifier when it isn't quoted without
problem. Nice! I hadn't noticed embldriver.

I wonder which one is correct in this case?

And should I switch to using embldriver to read, or does it make sense
to try and concoct a patch that changes embl?


  Thanks for the feedback!

     Adam

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                                                          Adam Sjøgren
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