Skip to content

Instantly share code, notes, and snippets.

Created February 15, 2018 21:03
  • Star 6 You must be signed in to star a gist
  • Fork 4 You must be signed in to fork a gist
Star You must be signed in to star a gist
Save anonymous/cd8a0c460a419c2de351ccc48ecc1a3c to your computer and use it in GitHub Desktop.
# Get a list of all organisms
curl -s "" > 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
mkdir -p kgml
# Write a script that will download all the kgml files for all the organisms of interest
cat organisms-of-interest-codes.txt | while read code; do echo "curl '$code' | cut -f1 | while read path; do curl -o \"kgml/\${path}.xml\" \"\${path}/kgml\"; done "; done >
# Get in tmux and Run it
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment