--- a/RepEnrich_setup.py	Tue Apr 02 21:16:37 2024 +0000
+++ b/RepEnrich_setup.py	Sat Apr 20 12:13:52 2024 +0000
@@ -1,7 +1,6 @@
 #!/usr/bin/env python
 import argparse
 import csv
-import os
 import shlex
 import subprocess
 import sys
@@ -48,15 +47,6 @@
 genomefasta = args.genomefasta
 cpus = args.cpus
 
-# check that the programs we need are available
-try:
-    subprocess.call(shlex.split("bowtie --version"),
-                    stdout=open(os.devnull, 'wb'),
-                    stderr=open(os.devnull, 'wb'))
-except OSError:
-    print("Error: Bowtie not available in the path")
-    raise
-
 
 def starts_with_numerical(list):
     try:
@@ -115,7 +105,6 @@
     block = 3
     for i in range(0, len(rep_coords[repname]) - block + 1, block):
         batch = rep_coords[repname][i:i+block]
-        print(batch)
         chromosome = batch[0]
         start = max(int(batch[1]) - flankingl, 0)
         end = min(int(batch[2]) + flankingl,