GetGeneIDs.py

#!/usr/bin/env python
#Brian Hanratty
#bhanratt@asu.edu
#Accepts a Gene Symbol from argument and produces a file to be read by logcollector.sh

import sys
data_table = {}

try:
    gene=sys.argv[1].upper()
except Exception:
    print("You need to specify a gene. e.g. \"python GetGeneIDs.py tp53\"")
    sys.exit(1)   
print("Using gene: "+gene)

#Import Gene Dictionary
try:
    f1=open('AllGeneIDs.txt')
    for line in f1:
        geneid = str.strip(line.split('|')[0])
        genesymbol = str.strip(line.split('|')[1])
        data_table.setdefault(genesymbol, set( )).add(geneid)

#Missing dictionary handling
except FileNotFoundError:
    print("Missing dependency: AllGeneIDs.txt")
    sys.exit(1)


#Do the thing
if gene in data_table:
    matchedids=list(data_table[gene])
    resultline= ' -e '.join(matchedids)
    fw=open('grepline.txt', 'w')
    fw.write('grep -e '+resultline+' $i.blr > $i.blr.tp53')
    fw.close()
else:
     print(gene+" not found in dictionary. Maybe a typo?")
     sys.exit(1)

print('Generated grepline file for '+gene)
f1.close()