c0.15.30

pep_mod.py

@@ -44,31 +44,29 @@ class BAlaS:
 		return df_ddg
 
 
-	def replot_filter(self, threshold):
+	def replot_filter(self, mutation_lock=[], lower_threshold=0, upper_threshold=1):
 		"""Filter out based on ddG thresholds"""
+		# Remove mutation_lock positions.
 		df = self.df_ddg
-		# ddg_pos = df[df['ddGs'] > 0]
-		# print("Positive DDG values:\n", ddg_pos.sort_values('ddGs', ascending=False))
+		drop_positions = [int(x)-1 for x in mutation_lock if True]
+		df = df.drop(drop_positions)
 
-		# ddg_neg = df[df['ddGs'] < 0]
-		# print("Negative DDG values:\n", ddg_neg.sort_values('ddGs', ascending=True))
-
-		# print("Ascending DDG values:\n", df.sort_values('ddGs', ascending=True))
-
-		df = df[df['ddGs'] > 0]
-		ddg_threshold = df[df['ddGs'] < threshold]
-		print("DDG values for less than threshold", threshold, "kCal/mol:\n",
+		df = df[df['ddGs'] > lower_threshold]
+		ddg_threshold = df[df['ddGs'] < upper_threshold]
+		print("DDG values for between", lower_threshold, 
+			"and", upper_threshold, "kCal/mol:\n",
 			ddg_threshold.sort_values('ddGs', ascending=True))
 
 		self.ddg_threshold = ddg_threshold
 		return ddg_threshold
 
 
-	def replot_get_positions(self, count=5, mutation_lock=[]):
+	def replot_get_positions(self, count=5):
 		"""Get positions from filtered ddG thresholds"""
 		ddg_threshold_sorted = self.ddg_threshold.sort_values('ddGs', ascending=True)
 		df_ResNumber = ddg_threshold_sorted[['ResNumber']]
 		df_ResNumber_clipped = df_ResNumber.head(count)
+		df_ResNumber_clipped.reset_index()
 
 		positions = []
 		for index, ResNumber in df_ResNumber_clipped.iterrows():
@@ -420,8 +418,8 @@ def main():
 	if args.alaninescan:
 		bude = BAlaS()
 		df_ddg = bude.replot_read(args.alaninescan)
-		ddg_preferences = bude.replot_filter(1)
-		positions = bude.replot_get_positions(args.mutation_count, mutations_obj.mutation_lock)
+		ddg_preferences = bude.replot_filter(mutation_lock, 0, 1)
+		positions = bude.replot_get_positions(args.mutation_count)
 
 		muts = to_mut_obj(sequence, positions)
 		mutations_obj = mutater(sequence=sequence, mutations=muts, mutation_lock=[])