
Show HN: PyGeno, a Python Package for Precision Medicine - daoudat
https://github.com/tariqdaouda/pyGeno
======
theophrastus
Apologies for a trivial objection: but the serpentine icon associated with
this, likely otherwise fine, package embodies an odd little annoyance to all
us structural biochemists: It depicts the DNA helix as left-handed. This is a
rare form of DNA at best, most likely an unlucky graphical choice, and causes
many nerdy folk to suspect that you don't know what you're doing. If you think
i'm nuts (and hey maybe...) there are entire websites devoted to this error,
because for some reason it's a common error and makes our eyes bleed [wink]:
[http://users.fred.net/tds/leftdna/](http://users.fred.net/tds/leftdna/)

~~~
mrestko
Other nerdy folks will be happy to grant that an icon is merely that and not
intended to be a perfect embodiment of a molecule.

~~~
lvs
Those folks lack expertise in the domain. Sequences are simply abstract
representations of real molecules, and knowledge of sequence means very little
without exercising effort and rigor to understand structure and function.

------
gh02t
Damn, that's a really cool logo they came up with. Looks to me like combining
the snake from the Rod of Asclepius, plus Python, plus the DNA double helix
and the mouse snake head (which I'm guessing is supposed to stand represent
using computers for medicine). Whoever made it, that's pretty awesome.

Oh yeah, the actual package is pretty cool too ;)

~~~
nickpsecurity
That logo is awesome. :)

~~~
daoudat
100% the work of:
[http://www.sawssankaddoura.com/](http://www.sawssankaddoura.com/)

------
adenadel
Just FYI, I found multiple spelling errors in the documentation and readme.

specically -> specifically

Therefor -> therefore

Instanciating -> Instantiating

aned -> and

Also the first sentence in the readme isn't grammatically correct. This is a
cool library, but I think it's important to have these sorts of things cleaned
up :)

~~~
jhull
contribute a pull request?

~~~
daoudat
Many thanks to the persons who submitted pull requests.

------
searine
As far as I can tell, this is just a python wrapper for common bioinformatics
tools?

I feel like this might not be sophisticated enough for bioinformaticians, but
too complex for the casual user or clinician. Unfortunately, proper
bioinformatics requires a heafty dose of background knowledge. If you don't
understand what you are aligning and filtering, and why, then the results will
always just be a shot in the dark.

~~~
daoudat
Actually it's not. It has been written from scratch including the ORM that
runs in the background
([https://github.com/tariqdaouda/rabaDB](https://github.com/tariqdaouda/rabaDB)).
The goal was to have a powerful optimized tool with 0 dependencies that can be
easily deployed on any platform. It was designed to be flexible and powerful
enough to be appealing to both bioinformaticians and casual users, and it used
daily here at the Institute for Research in Immunology and Cancer
(www.iric.ca) by professional bioinformaticians, as well as biologists who
have learned to program using it.

PyGeno was already used for two peer reviewed articles:

-Impact of genomic polymorphisms on the repertoire of human MHC class I-associated peptides. Granados, Sriranganadane, Daouda et al. 2014, Nat. Comm

-MHC I-associated peptides preferentially derive from transcripts bearing miRNA response elements. Granados et al. 2012, Blood

And four others are on the way.

------
brudgers
Documentation: [http://pygeno.iric.ca/](http://pygeno.iric.ca/)

~~~
daoudat
Thank you ;)

~~~
brudgers
You're welcome. It's an interesting project.

------
Abundnce10
It's times like these that I wish I had a better understanding of
biology/chemistry/genetics. I fancy myself a Python/data person, does anyone
have any advice on what to read to begin understanding how to utilize a
package like this?

~~~
cing
Why not take an online course?
[https://www.coursera.org/courses?query=bioinformatics](https://www.coursera.org/courses?query=bioinformatics)

