#!/bin/bash

# Turei Denes 2018
# turei.denes@gmail.com
# Query OmniPath webservice by list of gene symbols

curl -o enzyme_substrate.tsv \
    $(printf '%s' \
        "http://omnipathdb.org/ptms/?substrates=" \
        "`sed 's/^M/\n/g' samplesRNAseq.txt | \
          tail -n +2 |
          awk 'BEGIN{FS="\t";ORS=","}{print $1}' |
          sed 's/,$//'`" \
        "&fields=sources,references" \
        "&genesymbols=yes"
    )

curl -o interactions.tsv \
    $(printf '%s' \
        "http://omnipathdb.org/interactions/?partners=" \
        "`sed 's/^M/\n/g' samplesRNAseq.txt | \
          tail -n +2 |
          awk 'BEGIN{FS="\t";ORS=","}{print $1}' |
          sed 's/,$//'`" \
        "&fields=sources,references" \
        "&datasets=omnipath,kinaseextra" \
        "&genesymbols=yes"
    )