Map human gene symbols to ensembl gene ids, using the ensembl REST api, curl and jq

gene2ensembl.sh

#!/usr/bin/env bash

# USAGE:
# 0. install jq from https://stedolan.github.io/jq/ if not already present
# 1. make this script executable
#     chmod u+x gene2ensembl.sh
# 2. then run it on a gene list with one gene ID per line
      ./gene2ensembl.sh genesymbollist.txt > ensembl_list.txt

# NOTE: this command does not run in parallel on purpose
# so that ordering of the gene IDs remains constant

while read gene; do  
  curl -X GET http://rest.ensembl.org/xrefs/symbol/homo_sapiens/$gene?content-type=application/json 2>/dev/null | jq -r '.[0].id'
done < "${1:-/dev/stdin}"  
#The substitution ${1:-...} takes $1 if defined otherwise the file name
# of the standard input of the own process is used.