Delete utils_dataset.py

utils_dataset.py

@@ -1,60 +0,0 @@
-import numpy as np
-import csv
-
-def load_GO_annot(filename):
-    # Load GO annotations
-    onts = ['mf', 'bp', 'cc']
-    prot2annot = {}
-    goterms = {ont: [] for ont in onts}
-    gonames = {ont: [] for ont in onts}
-    with open(filename, mode='r') as tsvfile:
-        reader = csv.reader(tsvfile, delimiter='\t')
-
-        # molecular function
-        next(reader, None)  # skip the headers
-        goterms[onts[0]] = next(reader)
-        next(reader, None)  # skip the headers
-        gonames[onts[0]] = next(reader)
-
-        # biological process
-        next(reader, None)  # skip the headers
-        goterms[onts[1]] = next(reader)
-        next(reader, None)  # skip the headers
-        gonames[onts[1]] = next(reader)
-
-        # cellular component
-        next(reader, None)  # skip the headers
-        goterms[onts[2]] = next(reader)
-        next(reader, None)  # skip the headers
-        gonames[onts[2]] = next(reader)
-
-        next(reader, None)  # skip the headers
-        counts = {ont: np.zeros(len(goterms[ont]), dtype=float) for ont in onts}
-        for row in reader:
-            prot, prot_goterms = row[0], row[1:]
-            prot2annot[prot] = {ont: [] for ont in onts}
-            for i in range(3):
-                goterm_indices = [goterms[onts[i]].index(goterm) for goterm in prot_goterms[i].split(',') if goterm != '']
-                prot2annot[prot][onts[i]] = np.zeros(len(goterms[onts[i]]))
-                prot2annot[prot][onts[i]][goterm_indices] = 1.0
-                counts[onts[i]][goterm_indices] += 1.0
-    return prot2annot, goterms, gonames, counts
-
-
-def load_EC_annot(filename):
-    # Load EC annotations """
-    prot2annot = {}
-    with open(filename, mode='r') as tsvfile:
-        reader = csv.reader(tsvfile, delimiter='\t')
-
-        # molecular function
-        next(reader, None)  # skip the headers
-        ec_numbers = {'ec': next(reader)}
-        next(reader, None)  # skip the headers
-        counts = {'ec': np.zeros(len(ec_numbers['ec']), dtype=float)}
-        for row in reader:
-            prot, prot_ec_numbers = row[0], row[1]
-            ec_indices = [ec_numbers['ec'].index(ec_num) for ec_num in prot_ec_numbers.split(',')]
-            prot2annot[prot] = {'ec': np.zeros(len(ec_numbers['ec']), dtype=np.int64)}
-            prot2annot[prot]['ec'][ec_indices] = 1.0
-            counts['ec'][ec_indices] += 1