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View dataframe_selection_done_right.py
import pandas as pd
data = {"colA": [1, 2 , 3, 4, 5, 6, 7 ,8],
"colB": ["one", "two", "one", "two", "one", "two", "one", "two"]}
df = pd.DataFrame(data)
# Always use the pattern
# df.loc[<selector>, column_to_change] = value
# selector is usually df['a_column'] == "something"
# the column can be one or more.
@mattions
mattions / INSTALL.md
Created Apr 17, 2018 — forked from vfdev-5/INSTALL.md
Jackal simulation in ROS kinetic
View INSTALL.md

Install dependencies :

This is manual way to install necessary packages :

sudo apt-get install ros-kinetic-robot-localization ros-kinetic-controller-manager ros-kinetic-joint-state-controller ros-kinetic-diff-drive-controller ros-kinetic-gazebo-ros ros-kinetic-gazebo-ros-control ros-kinetic-gazebo-plugins             ros-kinetic-lms1xx ros-kinetic-pointgrey-camera-description ros-kinetic-roslint ros-kinetic-amcl ros-kinetic-gmapping      ros-kinetic-map-server ros-kinetic-move-base ros-kinetic-urdf ros-kinetic-xacro ros-kinetic-message-runtime ros-kinetic-topic-tools ros-kinetic-teleop-twist-joy

If you want to use rosdep and install all dependencies (for example for doc generation etc), the skip this step.

Create a workspace and clone sources

@mattions
mattions / sbfs-privileged.sh
Created Apr 6, 2018
Seven Bridges Filesystem helper script
View sbfs-privileged.sh
# SBFS Privileged helper script
# Allow root to see projects. Needed if you want to use docker
#
# Note: export the $SBG_SBFS_MOUNT_POINT variable in your
# .bashrc
#
# For Example:
# export SBG_SBFS_MOUNT_POINT=~/sbfs_mount_point
# Make sure the `~/sbfs_mount_point` directory exists
#
@mattions
mattions / launch_st_viewer.sh
Last active May 4, 2018
SBG FS and ST Viewer helper scripts
View launch_st_viewer.sh
# Launch the docker container of the latest st_viewer
# Note: We are using the $SBG_SBFS_MOUNT_POINT variable
# You can replace that with the actual path if you do not
# want to use the env variable. Check the `sbfs-privileges.sh`
# file for details.
#
# The mounted projects will be found at `/STDatasets` mount point
# within the docker container
xhost +local:root
@mattions
mattions / setup.sh
Last active Oct 25, 2018 — forked from fracasula/setup.sh
How to install Bluejeans on Ubuntu
View setup.sh
sudo apt install alien -y
sudo alien bluejeans_1.28.9-2_amd64.rpm # or whatever is the file you downloaded from the bluejeans website
sudo dpkg -i bluejeans_1.28.9-2_amd64.deb
cd /lib/x86_64-linux-gnu
#sudo ln -s libudev.so libudev.so.0
sudo ln -s libudev.so.1 libudev.so.0
# now you can launch bluejeans
/opt/bluejeans/bluejeans-bin
View v2mom-template.md

Your Vision

What is a vision?

Your vision answers the question "What do I want?" A clear vision help you communicate why you're here and what impact you're going to have.

Your vision should be aligned with the company vision, with your manager's V2MOM, and it should be personal. It should be an honest reflection of your own vision for your own work.

If you manage a team, it should be reflective of the purpose of the team and your collective impact.

View upgrade_dependencies.sh
# Upgrade your requirements
# - Finds outdated package with pip
# - install latest stable version
# - Update the requirements with the latest
pip list --outdated | cut -d' ' -f1 | xargs pip install --upgrade
pip freeze > requirements.txt
View dockerfile
# blackkiwi - production app
FROM mattions/webber:1.0
MAINTAINER mattions "mattions@gmail.com"
ENV DEBIAN_FRONTEND noninteractive
ENV PYTHONUNBUFFERED 1
RUN apt-get update && apt-get -qy install\
python3 \
View benchmark_vcf_io.py
from pysam import VariantFile
import time
def count_oldvar_reg(vcffile_reg, labels=["OLDVARS", "OLDVARS_A", "OLDVARS_B"]):
t_start = time.time()
bcf_in = VariantFile(vcffile_reg)
total = 0
reg = 0
for rec in bcf_in:
View handycommands.md

Handy commands

Extract bam according to a bed file

bedtools intersect -abam path/to/input.bam -b path/to/regions.bed > out.bam

Extract region of a VCF

You can’t perform that action at this time.