deleting of unused imports and explaining why the other imports are n…

…eeded

call_peaks.py

@@ -5,24 +5,16 @@
 @contact: anastasiia.petrova(at)mpi-bn.mpg.de
 """
 
-import argparse
-import sys
-import os
-import re
-import time
-import multiprocessing
-import logging
-import subprocess
-from Bio import SeqIO
-import Bio.SeqIO.FastaIO as bio
-import numpy as np
-from collections import defaultdict
-from scipy import stats
-import pyBigWig
-from statsmodels.sandbox.stats.multicomp import multipletests #for bonfferoni
-import matplotlib.pyplot as plt
-import random
-import textwrap
+import argparse #for parsing the parameters
+import sys #for example to exit if a problem occured
+import os #for example to check the existing path of a file
+import re #for example to split a string
+import time #to calculate time needed to proceed the data
+import logging #to write informaiton about the programm run
+import numpy as np #to calculate mean for example
+from collections import defaultdict #to create nested dictionaries
+import pyBigWig #to work with bigWig files
+import textwrap #to print the help message nice
 
 logger = logging.getLogger('call_peaks')
 logger.setLevel(logging.INFO)
@@ -329,16 +321,6 @@ def main():
 
 	start = time.time()
 
-	#peaks_bed_file = "./small_peaks.bed"
-	#peaks_bed_file = "./control_peaks.bed"
-	#peaks_bed_file = "./one_peak.bed"
-	#find_window(peaks_bed_file)
-
-	#bw_file = "./control_footprints.bw"
-
-	#window_length = 200
-	#step = 100
-
 	args = parse_args()
 
 	check_existing_input_files(args)