[Bioperl-l] additional methods for Bio::SeqUtils for in-silico cloning

Fields, Christopher J cjfields at illinois.edu
Thu Jan 19 10:29:32 EST 2012


On Jan 19, 2012, at 5:04 AM, Peter Cock wrote:

> On Wed, Jan 18, 2012 at 6:11 PM, Fields, Christopher J
> <cjfields at illinois.edu> wrote:
>> You could probably change "<1" to "<" if the start isn't meant to be defined;
>> the former seems to imply the feature location is '1 or before the start', the
>> latter is simply 'before the start'.  Either version should work within bioperl
>> AFAIK, though I'm not sure whether the feature table definition covers '<N'
>> as a location type.
>> 
>> Just thinking aloud, but such behavior might be something that needs to
>> be defined more specifically in the Bio::RangeI implementation, via trunc().
>> 
>> chris
> 
> Using '<1' or in general '<N' for an integer N should be fine for GenBank/EMBL
> feature tables - not sure about '<' though, can say I recall ever seeing that.
> 
> There are some similar issues with UniProt/SwissProt files and features.
> There I've seen '<1' used for before start (a partial peptide), but they also
> have '?' for unknown which has no analogue in the GenBank/EMBL feature
> table.
> 
> Peter

Yes, after you posted this and  re-reviewing the FT again I realized my mistake.  Thanks for correcting.  Helps to have a proper coffee before responding :P

chris


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