--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tn93_cluster.py	Fri Apr 23 03:04:15 2021 +0000
@@ -0,0 +1,81 @@
+import argparse
+import json
+import os
+import shlex
+import shutil
+import subprocess
+import sys
+
+
+def cluster_to_fasta(json_file, fasta_file, reference_name=None):
+    with open(json_file, "r") as fh:
+        cluster_json = json.load(fh)
+        with open(fasta_file, "w") as fh2:
+            for c in cluster_json:
+                if reference_name is not None:
+                    if reference_name in c['members']:
+                        cc = c['centroid'].split('\n')
+                        cc[0] = ">" + reference_name
+                        print("\n".join(cc), file=fh2)
+                        continue
+                print(c['centroid'], file=fh2)
+
+    return(os.path.getmtime(fasta_file), len(cluster_json))
+
+
+def run_command(command):
+    proc = subprocess.Popen(shlex.split(command), stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+    stdout, stderr = proc.communicate()
+    result = proc.returncode
+    if result != 0:
+        print('Command `%s` failed with exit code %s\n' % (command, result), file=sys.stderr)
+        print('--------------------- STDOUT ---------------------')
+        print(stdout.decode().replace('\\n', '\n'))
+        print('------------------- END STDOUT -------------------')
+        print('--------------------- STDERR ---------------------', file=sys.stderr)
+        print(stderr.decode().replace('\\n', '\n'), file=sys.stderr)
+        print('------------------- END STDERR -------------------', file=sys.stderr)
+    return(int(result))
+
+
+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)
+        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:
+            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
+
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser(description='Combine alignments into a single file, adding a reference sequence as well')
+    parser.add_argument('--input', help='Input MSA', required=True, type=str)
+    parser.add_argument('--reference', help='Reference sequence', required=True, type=str)
+    parser.add_argument('--output', help='Input MSA', required=True, type=str)
+    parser.add_argument('--threshold', help='Threshold', required=True, type=float)
+    parser.add_argument('--ambigs', help='Handle ambigs', required=True, type=str)
+    parser.add_argument('--cluster-type', help='Cluster type', required=True, type=str)
+    parser.add_argument('--overlap', help='Overlap', required=True, type=int)
+    parser.add_argument('--fraction', help='Fraction', required=True, type=float)
+    parser.add_argument('--cluster-count', help='Max query', required=True, type=int)
+    parser.add_argument('--compressed', help='File to write compressed clusters to', required=True, type=str)
+    arguments = parser.parse_args()
+    exit(main(arguments))