def main():
'''
Get a GAF, Convert, Calculate, and output.
'''
# Use the assessment configuration file to grab the OBO file.
obo_path, gaf_path = read_config()
print "Read the config"
ICHelper.setupGraphs(obo_path)
print "Graphs are done"
gaf = GOA._gaf20iterator(open(gaf_path))
print "I have made the GAF generator"
data = GAFtoDICT(gaf)
print "I have made the dictionary"
WyattClarkIC(data)
print("IC values created")
#!/usr/bin/python
import unittest
import os
from Bio.UniProt import GOA
from gothresher import gothresher
input_file = os.getcwd(
) + os.sep + ".." + os.sep + "example_data" + os.sep + "goa_exampleYeast.gaf"
# print(input_file)
# Convert from GAF to required format
gaf_output = GOA._gaf20iterator(open(input_file, "r"))
data = gothresher.convert_from_gaf_to_required_format(gaf_output)
gaf_output.close()
prot_list = []
for key in data.keys():
prot_list.append(data[key]["DB_Object_Symbol"])
# Choose proteins based on publications
new_data = gothresher.choose_proteins_based_on_publications(data, 50, None)
new_prot_list = []
for key in new_data.keys():
new_prot_list.append(new_data[key]["DB_Object_Symbol"])
# Count proteins
prot_count = gothresher.count_proteins(data)
# GO terms frequency
go_freq = gothresher.freq_go_term(data)