diff amino2consensus.py @ 0:023064145bea draft

"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/amino2consensus.py	Mon Jan 06 19:10:15 2020 -0500
@@ -0,0 +1,64 @@
+#!/usr/bin/env python
+
+from __future__ import print_function
+
+import argparse
+import csv
+
+
+AMINO_ACIDS = ['A', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'K', 'L', 'M', 'N', 'P', 'Q', 'R', 'S', 'T', 'V', 'W', 'Y', '*']
+
+
+def determine_amino(amino_counts, threshold):
+    amino = ""
+    total_count = sum(amino_counts.values())
+    amino_with_max_counts = sorted(amino_counts, key=amino_counts.get, reverse=True)[0]
+    if total_count == 0:
+        amino = "#"
+    elif (amino_counts[amino_with_max_counts] / float(total_count)) > threshold:
+        amino = amino_with_max_counts
+    else:
+        amino = "@"
+    return amino
+
+
+def determine_first_region(amino_file):
+    with open(amino_file) as f:
+        reader = csv.DictReader(f)
+        row = next(reader)
+        region = row['region']
+    return region
+
+
+def main(args):
+    current_region = determine_first_region(args.amino)
+    seq = []
+    with open(args.amino) as f:
+        reader = csv.DictReader(f)
+        for row in reader:
+            if row['region'] == current_region:
+                amino_counts = {}
+                for amino_acid in AMINO_ACIDS:
+                    amino_counts[amino_acid] = int(row[amino_acid])
+                amino = determine_amino(amino_counts, args.threshold)
+                seq.append(amino)
+            else:
+                print(">" + current_region)
+                print(''.join(seq))
+                current_region = row['region']
+                seq = []
+                amino_counts = {}
+                for amino_acid in AMINO_ACIDS:
+                    amino_counts[amino_acid] = int(row[amino_acid])
+                amino = determine_amino(amino_counts, args.threshold)
+                seq.append(amino)
+        print(">" + current_region)
+        print(''.join(seq))
+
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser()
+    parser.add_argument("amino", help="MiCall amino.csv output file")
+    parser.add_argument("--threshold", default=0.15, type=float, help="Threshold for calling")
+    args = parser.parse_args()
+    main(args)