new

filter_solution_list.py

@@ -0,0 +1,47 @@
+#!/usr/bin/python
+# # -*- coding: utf-8 -*-
+
+"""
+@Authors Jerry Gao & Huy Bui
+TODO May offer more option to filter
+TODO Make the filter a common library and then reuse & rewrite some of the other programs
+"""
+
+import sys,os
+import pandas as pd
+
+def print_usage ():
+	print("usage: python filter_solution_list.py solutions_list minsize")
+	print("\tsolutions_list the revised csv file")
+	print("\tminsize minium size in amino acids")
+	print("eg: python filter_solution_list.py solutions_density1/fit_logs_revised.csv 100")
+	sys.exit()
+
+def filter_csv(fitcsv, minsize):
+	''' This function is similar load_tophits_in_chimerax.py. Can we merge it or make a common one to share'''
+	if os.path.exists(fitcsv):
+		df = pd.read_csv(fitcsv, header = 0)
+	else:
+		print("WARNING: {:s} does not exist. Check again!".format(fitcsv))
+		exit(0)
+
+	df = df.loc[df['NoRes'] > minsize]	
+	df_sub = df.reset_index(drop=True).copy()
+	#print(df_sub)
+	# Make index = 0 -> rank 1
+	return df_sub
+
+if __name__ == "__main__":
+	if len(sys.argv) < 3:
+		print_usage()
+
+	fitcsv = sys.argv[1]
+	minsize = int(sys.argv[2])
+
+	print("Filtering {:s} with a minumum size of {:d} amino acids".format(fitcsv, minsize))	
+	df = filter_csv(fitcsv, minsize)
+	print(df)
+	out_csv = fitcsv.replace('.csv', '_min{:d}.csv'.format(minsize))
+	df.to_csv(out_csv, index=False)
+	print("{:s} written!".format(out_csv))
+

load_tophits_in_chimerax.py

@@ -5,7 +5,6 @@
 @Authors Jerry Gao & Huy Bui
 """
 # Usage
-# python load_tophits_in_chimerax.py solutions_dir number_of_top_candidate_retained
 # Operate from the main folder
 # Load the top hits in ChimeraX
 
@@ -14,7 +13,7 @@
 
 def print_usage ():
 	print("usage: python load_tophits_in_chimerax.py density solutions_dir number_of_top_hit minsize")
-	print("eg: ppython load_tophits_in_chimerax.py density.mrc solutions_dir 5 60")
+	print("eg: python load_tophits_in_chimerax.py density.mrc solutions_dir 5 60")
 	sys.exit()
 
 def filter_csv(fitcsv, minsize):