[Bioperl-l] LocatableSeq NSE format - suggested changes

[Chris Fields]

I think option 1 is cleaner as well; very easily added, so committed to main trunk as I consider this a bug, as one can potentially lose strand information when round-tripping data (original data with a -1 strand would be converted to +1).  

I'll work out the test fails on trunk along the way (ensure they're due to erroneous test data and not something else).

chris

On Dec 16, 2009, at 6:51 AM, Mark A. Jensen wrote:

> I'm with Dave; option 1 is cleaner. The only problem might be the automatic interpretation of older output as always plus strand, but presumably these would have had to record the strandedness explicitly elsewhere, so they would be updatable. I'm definitely for making strandedness part of the spec in some way. cheers MAJ
> ----- Original Message ----- From: "Chris Fields" <cjfields at illinois.edu>
> To: "BioPerl List" <bioperl-l at lists.open-bio.org>
> Sent: Monday, December 14, 2009 8:23 PM
> Subject: [Bioperl-l] LocatableSeq NSE format - suggested changes
> 
> 
>> All,
>> 
>> The current output for NSE format (Name/Start-End) via Bio::LocatableSeq::get_nse() currently doesn't allow for strandedness.  I have seen two variations of NSE that incorporate strandedness:
>> 
>> 1) Stockholm Rfam reverses start and end if the strand == -1
>> 
>>  chrY/598-1
>> 
>> 2) Sheldon McKay's Gbrowse_syn uses Name(strand)/start-end
>> 
>>  rice-3(+)/16598648-16600199
>> 
>> The former breaks fewer things within BioPerl, but the latter seems more explicit.  Any preferences?  Do we want a new method that creates this, and deprecate out simple non-stranded NSE?
>> 
>> chris
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