--- a/windowSplitter.py	Fri Oct 09 15:50:53 2015 -0400
+++ b/windowSplitter.py	Wed Jun 03 09:45:06 2020 -0400
@@ -1,39 +1,46 @@
 #!/usr/bin/env python
-
 """
 Split into windows.
 
 usage: %prog input size out_file
    -l, --cols=N,N,N,N: Columns for chrom, start, end, strand in file
 """
+from __future__ import print_function
 
 import sys
 
-from galaxy import eggs
-import pkg_resources
-pkg_resources.require( "bx-python" )
 from bx.cookbook import doc_optparse
-from galaxy.tools.util.galaxyops import *
+
+
+# Default chrom, start, end, strand cols for a bed file
+BED_DEFAULT_COLS = 0, 1, 2, 5
+
 
-def stop_err( msg ):
-    sys.stderr.write( msg )
-    sys.exit()
+def parse_cols_arg(cols):
+    """Parse a columns command line argument into a four-tuple"""
+    if cols:
+        # Handle case where no strand column included - in this case, cols
+        # looks something like 1,2,3,
+        if cols.endswith(','):
+            cols += '0'
+        col_list = [int(x) - 1 for x in cols.split(",")]
+        return col_list
+    else:
+        return BED_DEFAULT_COLS
 
 
 def main():
     # Parsing Command Line here
-    options, args = doc_optparse.parse( __doc__ )
-    
+    options, args = doc_optparse.parse(__doc__)
+
     try:
-        chr_col_1, start_col_1, end_col_1, strand_col_1 = parse_cols_arg( options.cols )
+        chr_col_1, start_col_1, end_col_1, strand_col_1 = parse_cols_arg(options.cols)
         inp_file, winsize, out_file, makesliding, offset = args
         winsize = int(winsize)
         offset = int(offset)
         makesliding = int(makesliding)
-    except:
-        stop_err( "Data issue, click the pencil icon in the history item to correct the metadata attributes of the input dataset." )
-    
-    fo = open(out_file,'w')
+    except Exception:
+        sys.exit("Data issue, click the pencil icon in the history item to correct the metadata attributes of the input dataset.")
 
     skipped_lines = 0
     first_invalid_line = 0
@@ -41,43 +48,42 @@
     if offset == 0:
         makesliding = 0
 
-    for i, line in enumerate( file( inp_file ) ):
-        line = line.strip()
-        if line and line[0:1] != "#":
-            try:
-                elems = line.split('\t')
-                start = int(elems[start_col_1])
-                end = int(elems[end_col_1])
-                if makesliding == 0:
-                    numwin = (end - start)/winsize
-                else:
-                    numwin = (end - start)/offset
-                if numwin > 0:
-                    for win in range(numwin):
-                        elems_1 = elems
-                        elems_1[start_col_1] = str(start)
-                        elems_1[end_col_1] = str(start + winsize)
-                        fo.write( "%s\n" % '\t'.join( elems_1 ) )
-                        if makesliding == 0:
-                            start = start + winsize
-                        else:
-                            start = start + offset
-                            if start+winsize > end:
-                                break
-            except:
-                skipped_lines += 1
-                if not invalid_line:
-                    first_invalid_line = i + 1
-                    invalid_line = line
-    
-    fo.close()
+    with open(out_file, 'w') as fo, open(inp_file) as fi:
+        for i, line in enumerate(fi):
+            line = line.strip()
+            if line and line[0:1] != "#":
+                try:
+                    elems = line.split('\t')
+                    start = int(elems[start_col_1])
+                    end = int(elems[end_col_1])
+                    if makesliding == 0:
+                        numwin = (end - start) // winsize
+                    else:
+                        numwin = (end - start) // offset
+                    if numwin > 0:
+                        for _ in range(numwin):
+                            elems_1 = elems
+                            elems_1[start_col_1] = str(start)
+                            elems_1[end_col_1] = str(start + winsize)
+                            fo.write("%s\n" % '\t'.join(elems_1))
+                            if makesliding == 0:
+                                start = start + winsize
+                            else:
+                                start = start + offset
+                                if start + winsize > end:
+                                    break
+                except Exception:
+                    skipped_lines += 1
+                    if not invalid_line:
+                        first_invalid_line = i + 1
+                        invalid_line = line
 
     if makesliding == 1:
-        print 'Window size=%d, Sliding=Yes, Offset=%d' % ( winsize, offset )
+        print('Window size=%d, Sliding=Yes, Offset=%d' % (winsize, offset))
     else:
-        print 'Window size=%d, Sliding=No' % (winsize)
+        print('Window size=%d, Sliding=No' % (winsize))
     if skipped_lines > 0:
-        print 'Skipped %d invalid lines starting with #%d: "%s"' % ( skipped_lines, first_invalid_line, invalid_line )
+        print('Skipped %d invalid lines starting with #%d: "%s"' % (skipped_lines, first_invalid_line, invalid_line))
 
 
 if __name__ == "__main__":