[Bioperl-l] patch to Bio::Location::Split - split locations whose strand is -1 don't print with complement when only one sublocation present

Hilmar Lapp hlapp at gmx.net
Fri Dec 9 13:22:41 EST 2005

On Dec 8, 2005, at 9:25 PM, Cook, Malcolm wrote:

> Also, while we're here, what do you understand the semantics of strand 
> in split sublocations to be?  Your logic of termporarily flipping the 
> sublocations strand seems to suggest that you expect that the strand 
> of the sublocation should in practice agree with that of the superiour 
> split location.  I'm building split locations 'by hand' and seem 
> forced to set the strand in both the parent and all subs.  Is this 
> what you expect?  thanks.

Setting the strand on the container location should propagate to all 
its sub-locations. I.e., you should only have to set a single strand, 
unless you want sub-locations on different strands. In that case, any 
manipulation of the container strand will override the manually set 
sub-location strands.

At least that's how it should be (i.e., was meant to be).

> As an aside but related issue, I've got a the bioperl source head cvs 
> checked out as anonymous with a bunch of edits (such as this) that I'd 
> like now to commit given that I now have privs (I'm user mcook).  Do 
> you now a way to edit my source tree to change them to be checked out 
> by mcook instead of anonymous.  Or do I have to recheck out a fresh 
> source tree and make my edits there for commit?  Thanks

It might be easiest to get a fresh checkout and then copy over your 
changed sources (just be careful to only copy .pm files, so as not to 
copy the CVS/* files used by cvs ...).

Actually, I'm going to retract this somewhat - it is really only a good 
idea if you're very sure that the repository wasn't updated from the 
time you made your changes. You can convince yourself whether a module 
was updated in the repository or not by comparing the revision IDs. If 
you have a series of modules you could skip that step, take a diff of 
your changed modules to the repository ('cvs diff') and apply the 
resulting patch(es) to your new checkout.


> Cheers,
> Malcolm Cook - mec at stowers-institute.org - 816-926-4449
> Database Applications Manager - Bioinformatics
> Stowers Institute for Medical Research - Kansas City, MO  USA
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> Bioperl-l mailing list
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757

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