[Bioperl-l] Long /labels are wrapped, but can't be read
Adam Sjøgren
adsj at novozymes.com
Wed Sep 30 09:50:36 UTC 2009
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
--
Adam Sjøgren
adsj at novozymes.com
More information about the Bioperl-l
mailing list