download_kegg.sh

# Get a list of all organisms
curl -s  "http://rest.kegg.jp/list/organism"  > organisms-all.txt

# Get just a few of interest
cat organisms-all.txt | awk '$2~/^(hsa|mmu|rno|cfa|bta|gga|xla|xtr|dre|dme|cel|ath|ehi|tgo|eco|sau|mtu|mav|cje|ccol)$/' > organisms-of-interest.txt

# Get the accession codes for each
cut -f1 organisms-of-interest.txt > organisms-of-interest-codes.txt

# Make a directory to put all the kgml files downloaded

jarutis

## install Catalyst proprietary
sudo ntfsfix /dev/sda2
sudo cp /etc/X11/xorg.conf /etc/X11/xorg.conf.BAK
sudo apt-get remove --purge fglrx*
sudo apt-get install linux-headers-generic
sudo apt-get install fglrx xvba-va-driver libva-glx1 libva-egl1 vainfo 
sudo amdconfig --initial

## install build essentials
sudo apt-get install cmake

bsweger

Useful Pandas Snippets

A personal diary of DataFrame munging over the years.

Data Types and Conversion

Convert Series datatype to numeric (will error if column has non-numeric values)
(h/t @makmanalp)