Bioperl: Bio::Species.pm: fixed bug #226

[Ewan Birney]

On 7 May 2000, Keith James wrote:

> 
> I was responsible for a number of fixes on the main branch (which
> didn't make it into the 0.6 release) which were similar to Hilmar's in
> their aim:
> 
>  Handling rarer locations (123^124) for reading and writing
>  Handling badly wrapped "" within qualifiers
>  Handling locations with < and > for reading and writing
>  Fixed rejection of 1 bp long features on the complement
>  Subspecies handling for EMBL format fixed (to a degree)
> 
> I was concentrating on getting EMBL parsing to work for us as quickly
> as possible, so I neglected Genbank support due to lack of
> time. Likewise, I've had no time to move the fixes to the 0.6
> release. (I'm not familiar with CVS, especially on multiple branches).
> 
> Anyway, I'll be happy to help merge the two sets.

My suggestion is that Keith looks at the fixes that Hilmar has made on 
the branch, propagates them over to the main trunk with perhaps some
additional changes to the genbank parsing and then Hilmar reviews keith's
changes. One of you two then post about the entire suite and raise any
discussion points about the object model (for example, weird location
lines).


Hilmar and Keith - feel free to ignore this advice if it does not suit
you.



To check out a branch, use the normal command with additional -r and 
possibly -d tags

  cvs -d <blah-blah> co -r branch-06 -d bioperl-06 bioperl-live

builds a bioperl-06 directory on the branch-06 tag.



> 
> Keith
> 
> -- 
> 
> Keith James  --  kdj@sanger.ac.uk  --  http://www.sanger.ac.uk/Users/kdj
> The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SA
> 
> =========== Bioperl Project Mailing List Message Footer =======
> Project URL: http://bio.perl.org/
> For info about how to (un)subscribe, where messages are archived, etc:
> http://www.techfak.uni-bielefeld.de/bcd/Perl/Bio/vsns-bcd-perl.html
> ====================================================================
> 

-----------------------------------------------------------------
Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
<birney@ebi.ac.uk>. 
-----------------------------------------------------------------

=========== Bioperl Project Mailing List Message Footer =======
Project URL: http://bio.perl.org/
For info about how to (un)subscribe, where messages are archived, etc:
http://www.techfak.uni-bielefeld.de/bcd/Perl/Bio/vsns-bcd-perl.html
====================================================================