LAST and LEAST UPDATE

Statistics_Calculation_DeepSignalPlant.py

@@ -14,6 +14,8 @@ import argparse
 import re
 from tkinter import *
 import tkinter as tk
+import glob
+import pandas as pd
 from matplotlib.backends.backend_tkagg import FigureCanvasTkAgg
 matplotlib.use('TkAgg')
 # Arguments
@@ -58,8 +60,8 @@ def CpG_context():
                 rows.append(row)
     rows_CG_df = pd.DataFrame(rows)
     rows_CG = rows_CG_df.sort_values("chromosome")
-    output_file = os.path.join(output_dir, filebasename + "_CG.csv")
-    rows_CG.to_csv(output_file, index=False, sep='\t')
+    #output_file = os.path.join(output_dir, filebasename + "_CG.csv")
+    #rows_CG.to_csv(output_file, index=False, sep='\t')
     #if not rows_CG.empty:
     #    for chromosome in rows_CG['chromosome'].unique():
     #        positions_par_chromosome[chromosome] = list(rows_CG.loc[rows_CG['chromosome'] == chromosome, ['strand', 'position']])
@@ -105,8 +107,8 @@ def CHG_context():
                 rows.append(row)
     rows_CHG_df = pd.DataFrame(rows)
     rows_CHG = rows_CHG_df.sort_values("chromosome")
-    #output_file = os.path.join(output_dir, filebasename + "_CHG.csv")
-    #rows_CHG.to_csv(output_file, index=False, sep='\t')
+    output_file = os.path.join(output_dir, filebasename + "_CHG.csv")
+    rows_CHG.to_csv(output_file, index=False, sep='\t')
     #if not rows_CHG.empty:
     #    for chromosome in rows_CHG['chromosome'].unique():
     #        positions_par_chromosome[chromosome] = list(rows_CHG.loc[rows_CHG['chromosome'] == chromosome, ['strand', 'position']])
@@ -156,8 +158,8 @@ def CHH_context():
                 rows.append(row)
     rows_CHH_df = pd.DataFrame(rows)
     rows_CHH = rows_CHH_df.sort_values("chromosome")
-    #output_file = os.path.join(output_dir, filebasename + "_CHH.csv")
-    #rows_CHH.to_csv(output_file, index=False, sep='\t')
+    output_file = os.path.join(output_dir, filebasename + "_CHH.csv")
+    rows_CHH.to_csv(output_file, index=False, sep='\t')
     #if not rows_CHH.empty:
     #    for chromosome in rows_CHH['chromosome'].unique():
     #        positions_par_chromosome[chromosome] = list(
@@ -285,3 +287,4 @@ for filename in glob.glob(files): # to select all files present in that path
     #CpG_context()
     #CHG_context()
     #CHH_context()
+    plotting()