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
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
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
#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 |
""" | |
Disable registration/signup | |
""" | |
#models.py | |
from allauth.account.adapter import DefaultAccountAdapter | |
class MyAccountAdapter(DefaultAccountAdapter): | |
def is_open_for_signup(self, request): | |
return False | |
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 $PWD/lib/python2.7 zc.buildout | |
wget https://pypi.python.org/packages/source/d/django-lfs/django-lfs-installer-0.7.7.tar.gz#md5=1e1c20a51e5bea9a26c2177a07c5de19 --no-check-certificate | |
tar zxf django-lfs-installer-0.7.7.tar.gz | |
cd lfs-installer/ | |
python2.7 bootstrap.py | |
./bin/buildout -v # this will take a while to run and produce a lot of output, so be patient | |
#configure database now |
cd ~/webapps/app_name/ | |
./apache2/bin/stop | |
rm -rf lib/python2.7/{D,d}jango* myproject* | |
PYTHONPATH=$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 |
#!/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 |