Created by
Dénes Türei
last modified
| #!/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"
)
|