--- a/tn93_cluster.py	Fri Apr 23 03:04:15 2021 +0000
+++ b/tn93_cluster.py	Wed Apr 20 17:00:11 2022 +0000
@@ -2,7 +2,6 @@
 import json
 import os
 import shlex
-import shutil
 import subprocess
 import sys
 
@@ -41,27 +40,22 @@
 def main(arguments):
     threshold = arguments.threshold
     step = threshold * 0.25
-    shutil.copy(arguments.input, os.path.join(os.getcwd(), 'reference_msa.fa'))
-    shutil.copy(arguments.input, os.path.join(os.getcwd(), 'reference_msa.fa.bak'))
     with open(arguments.reference) as fh:
         for line in fh:
             if line[0] == '>':
                 _ref_seq_name = line[1:].split(' ')[0].strip()
                 break
-    while True and threshold <= 1:
-        command = 'tn93-cluster -o clusters.json -t %g -a %s -c %s -m json -l %d -g %f reference_msa.fa' % (threshold, arguments.ambigs, arguments.cluster_type, arguments.overlap, arguments.fraction)
+    while threshold <= 1:
+        command = 'tn93-cluster -o clusters.json -t %g -a %s -c %s -m json -l %d -g %f %s' % (threshold, arguments.ambigs, arguments.cluster_type, arguments.overlap, arguments.fraction, arguments.input)
         return_code = run_command(command)
         if return_code != 0:
             return return_code
-        input_stamp, cluster_count = cluster_to_fasta('clusters.json', 'reference_msa.fa.bak', _ref_seq_name)
-        if cluster_count <= arguments.cluster_count or threshold == 1:
+        input_stamp, cluster_count = cluster_to_fasta('clusters.json', 'clusters.fa', _ref_seq_name)
+        if cluster_count <= arguments.cluster_count:
             break
         else:
             threshold += step
         print('Found %d clusters at threshold %f' % (cluster_count, threshold))
-    shutil.copy('reference_msa.fa.bak', arguments.compressed)
-    shutil.copy('clusters.json', arguments.output)
-    os.remove('reference_msa.fa.bak')
     return 0