--- a/allele-counts.py	Tue Aug 23 02:30:56 2016 -0400
+++ b/allele-counts.py	Tue Mar 31 05:09:12 2020 -0400
@@ -1,4 +1,4 @@
-#!/usr/bin/python
+#!/usr/bin/python3
 """
 Run with -h option or see DESCRIPTION for description.
 This script's functionality is being obsoleted by the new, and much more sanely
@@ -11,7 +11,6 @@
 Naive Variant Caller variant count parsing one-liner:
 $ cat variants.vcf | grep -v '^#' | cut -f 10 | cut -d ':' -f 4 | tr ',=' '\t:'
 """
-from __future__ import division
 import os
 import sys
 import errno
@@ -49,6 +48,7 @@
 threshold (but not necessarily in the same order). If the site fails this test,
 the number of alleles is reported as 0."""
 
+
 def get_options(defaults, usage, description='', epilog=''):
   """Get options, print usage text."""
 
@@ -124,7 +124,6 @@
     if len(coords) > 2: print_sample = coords[2]
 
   # set infile_handle to either stdin or the input file
-  global infile_handle
   if infile == OPT_DEFAULTS.get('infile'):
     infile_handle = sys.stdin
     sys.stderr.write("Reading from standard input..\n")
@@ -135,7 +134,6 @@
       fail('Error: Input VCF file '+infile+' not found.')
 
   # set outfile_handle to either stdout or the output file
-  global outfile_handle
   if outfile == OPT_DEFAULTS.get('outfile'):
     outfile_handle = sys.stdout
   else:
@@ -186,23 +184,18 @@
           sys.stderr.write("Error: Sample '"+print_sample+"' not found.\n")
           sys.exit(1)
 
-
     site_summary = summarize_site(site_data, sample_names, CANONICAL_VARIANTS,
       freq_thres, covg_thres, stranded, debug=debug)
 
     if debug and site_summary[0]['print']:
-        print line.split('\t')[9].split(':')[-1]
+      print(line.split('\t')[9].split(':')[-1])
 
     try:
       print_site(outfile_handle, site_summary, COLUMNS)
     except IOError as ioe:
       if ioe.errno == errno.EPIPE:
-        cleanup()
         sys.exit(0)
 
-  # close any open filehandles
-  cleanup()
-
   # keeps Galaxy from giving an error if there were messages on stderr
   sys.exit(0)
 
@@ -341,7 +334,7 @@
         sample[strand+base_count[0]] = base_count[1]
       # fill in any zeros
       for base in canonical:
-        if not sample.has_key(strand+base):
+        if strand+base not in sample:
           sample[strand+base] = 0
 
     sample['alleles'] = count_alleles(variants, freq_thres, debug=debug)
@@ -354,7 +347,7 @@
         ranked_bases[1] = ranked_bases[2]
         ranked_bases[2] = tmp_base
 
-    if debug: print "ranked +-: "+str(ranked_bases)
+    if debug: print("ranked +-: "+str(ranked_bases))
 
     sample['coverage'] = coverage
     try:
@@ -399,7 +392,7 @@
     if strand in strands:
       summed_counts[base] = stranded_counts[variant] + summed_counts.get(base, 0)
 
-  return summed_counts.items()
+  return list(summed_counts.items())
 
 
 def process_read_counts(variant_counts, freq_thres=0, sort=False, debug=False):
@@ -426,10 +419,10 @@
     variant_counts.sort(reverse=True, key=lambda variant: variant[1])
 
   if debug:
-    print 'coverage: '+str(coverage)+', freq_thres: '+str(freq_thres)
+    print('coverage: '+str(coverage)+', freq_thres: '+str(freq_thres))
     for variant in variant_counts:
-      print (variant[0]+': '+str(variant[1])+'/'+str(float(coverage))+' = '+
-        str(variant[1]/coverage))
+      print((variant[0]+': '+str(variant[1])+'/'+str(float(coverage))+' = '+
+        str(variant[1]/coverage)))
 
   # remove bases below the frequency threshold
   if freq_thres > 0:
@@ -455,8 +448,8 @@
     sort=False, debug=debug)
 
   if debug:
-    print '+ '+str(alleles_plus)
-    print '- '+str(alleles_minus)
+    print('+ '+str(alleles_plus))
+    print('- '+str(alleles_minus))
 
   # Check if each strand reports the same set of alleles.
   # Sorting by base is to compare lists without regard to order (as sets).
@@ -495,17 +488,9 @@
 
 
 def fail(message):
-  cleanup()
   sys.stderr.write(message+'\n')
   sys.exit(1)
 
 
-def cleanup():
-  if isinstance(infile_handle, file):
-    infile_handle.close()
-  if isinstance(outfile_handle, file):
-    outfile_handle.close()
-
-
 if __name__ == "__main__":
   main()
\ No newline at end of file