[Biopython-dev] GSoC Python variant (penultimate) update

Lenna Peterson arklenna at gmail.com
Fri Aug 17 01:58:46 UTC 2012

Post: http://arklenna.tumblr.com/post/29592108099/

I have been considering how to handle gene strandedness. As long as
I'm correctly interpreting the following position, my coordinate
mapper should produce the correct coordinates with negative strand or
mixed strand features.

GenBank: join(complement(25..30), 36..40)
Biopython: FeatureLocation(24, 30, -1) + FeatureLocation(35, 40)

(please click through to post for monospaced font)

    23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40
       <----------------                ------------->
       5  4  3  2  1  0                 6  7  8  9  10

I have to admit that it wasn't until I read a BioStar
earlier this week that I fully understood the relationship between
plus/minus forward/reverse sense/antisense coding/template strands. So
please let me know as soon as possible if I've made a mistake in the
above code.

`c2g` yields the correct genome position, but not the strand. I still
need to integrate strand information into my `GenomePosition` object
and/or partially merge it with `ExactLocation`. This weekend I intend
to expand documentation and write a brief cookbook entry.



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