raonyguimaraes

Tabix command of htslib can query a locus to a remote s3 file using s3:// protocol.

$ aws s3 ls s3://your_bucket/
vcf.gz
vcf.gz.tbi

$ tabix -l s3://your_bucket/vcf.gz
chr1
chr2

raonyguimaraes

What I Wish I'd Known About Equity Before Joining A Unicorn

Disclaimer: This piece is written anonymously. The names of a few particular companies are mentioned, but as common examples only.

This is a short write-up on things that I wish I'd known and considered before joining a private company (aka startup, aka unicorn in some cases). I'm not trying to make the case that you should never join a private company, but the power imbalance between founder and employee is extreme, and that potential candidates would

raonyguimaraes

#arquivo media.py
class Movie():
    def __init__(self, movie_title, movie_storyline, poster_image, trailer_youtube):
        self.title = movie_title
        self.storyline = movie_storyline
        self.poster_image_url = poster_image
        self.trailer_youtube_url = trailer_youtube

#arquivo entertainment_center.py
import media

raonyguimaraes

"""
Disable registration/signup
"""
#models.py
from allauth.account.adapter import DefaultAccountAdapter

class MyAccountAdapter(DefaultAccountAdapter):    
    def is_open_for_signup(self, request):
        return False
        

raonyguimaraes

cd ~/webapps/app_name/
./apache2/bin/stop
rm -rf lib/python2.7/{D,d}jango* myproject*
PYTHONPATH=$PWD/lib/python2.7 easy_install-2.7 -s $PWD/bin -d $PWD/lib/python2.7 zc.buildout
wget https://pypi.python.org/packages/source/d/django-lfs/django-lfs-installer-0.7.7.tar.gz#md5=1e1c20a51e5bea9a26c2177a07c5de19 --no-check-certificate
tar zxf django-lfs-installer-0.7.7.tar.gz
cd lfs-installer/
python2.7 bootstrap.py
./bin/buildout -v # this will take a while to run and produce a lot of output, so be patient
#configure database now

raonyguimaraes

cd ~/webapps/app_name/
./apache2/bin/stop
rm -rf lib/python2.7/{D,d}jango* myproject*
PYTHONPATH=$PWD/lib/python2.7 easy_install-2.7 -s $PWD/bin -d $PWD/lib/python2.7 zc.buildout
wget http://pypi.python.org/packages/source/d/django-lfs/django-lfs-installer-0.6.0b5.tar.gz
tar zxf django-lfs-installer-0.6.0b5.tar.gz
cd lfs-installer/
python2.7 bootstrap.py
./bin/buildout -v # this will take a while to run and produce a lot of output, so be patient
sed -i "s/'ENGINE': 'django.db.backends.'/'ENGINE': 'django.db.backends.postgresql_psycopg2'/g" lfs_project/settings.py 

raonyguimaraes

#!/usr/bin/env python
"""
Given a file containing a table of genes and their coordinates (see "Inputs"), get their genotypes from 1000genomes.

This in reality is a wrapper to tabix. You need to have tabix installed in the .bin folder, and you also need to have a ./data/tabix_indexes folder on your file system.

Usage
=========

   $: python get_genotypes.py -l data/n-glycan.coords