mol2tar.sh

#!/bin/bash

# This script will get a list of targets related to a compound.
# Each compound, identified by its chembl id will be read from
# the CSV file specified as the first argument.

# This script assumes that you have a 'jq' command line tool installed.
# Installation instructions can be found here: 
# https://stedolan.github.io/jq/download/

# Some constants first: we need to know the root URL of the ChEMBL API.
# We will also use a tool called "resty" and we first need to download it
# from the Internet so we need to know its adress.
DEFAULT_INPUT=${1-"./compounds_list_lite.csv"}
DEFAULT_OUTPUT=${2-"./bash_out.csv"}
RESTY_LOCATION="https://raw.githubusercontent.com/micha/resty/master/resty"
URL_ROOT="https://www.ebi.ac.uk/chembl/api/data"

# Here, we download "resty", a tiny but useful wrapper for curl to make 
# out task easier
curl -L $RESTY_LOCATION > resty

# A dot (.) means "sourcing" the "resty" script we've just downloaded
# To "source" means more or less to activate the script so we can use it
# in the following lines 
. resty

# Once the "resty" tool is sourced we need to configure it. The only configuration is
# specifying the API root URL
resty $URL_ROOT

# Once we have "resty" loaded and configured we can loop through the CSV file
# line by line
cat $DEFAULT_INPUT|while read line
  do
  	# For each line we extract the first column and store it in the "chembl_id" variable
    read -d, chembl_id < <(echo $line)

    # Just prinint the id here to see if reading from CSV works...
    echo "Targets for: $chembl_id"

    # For each chembl_id extracted from the file we make a single API call to retrive 
    # information about compound bioactivities, extract target ids using 'jq', sort them
    # and making resulting target ids unique.
    targets=$(GET "/activity.json" -q "molecule_chembl_id=$chembl_id" | jq '.activities[].target_chembl_id' | tr -d '"' | sort | uniq | tr "\n" "," )
    GET "/activity.json" -q "molecule_chembl_id=$chembl_id" | jq '.activities[].target_chembl_id'
    echo "$chembl_id,$targets" >> $DEFAULT_OUTPUT
  done