--- a/maf2bed.py	Sun Dec 15 23:47:40 2024 +0000
+++ b/maf2bed.py	Thu Oct 02 10:20:29 2025 +0000
@@ -1,44 +1,58 @@
 #!/usr/bin/env python
-# painfully converted from b0rken perl from
+
+# adapted from https://github.com/bgruening/galaxytools/blob/f96142ca5acea989b828d6c92940172355b7f125/tools/jbrowse2/maf2bed.py
+# which was "painfully converted from b0rken perl from:"
 # https://unpkg.com/browse/jbrowse-plugin-mafviewer@1.0.6/dist/
-# license is Apache2_license.txt included here
 
+import argparse
 import sys
 
-id = 0
-buffer = ''
-start = 0
-end = 0
-score = 0
-chrom = ''
 
-db = "%s." % sys.argv[1]
-# Read input from stdin
-for line in sys.stdin:
-    line = line.strip()
-    if not line:
-        continue
+def maf2bed(assembly_name, input, output):
+    id = 0
+    buffer = ''
+    start = 0
+    end = 0
+    score = 0
+    chrom = ''
+
+    db = "%s." % assembly_name
+    # Read input from stdin
+    for line in input:
+        line = line.strip()
+        if not line:
+            continue
 
-    line = line.split()
-    if line[0] == 's' and line[1].startswith(db):
-        chrom = line[1]
-        chrom = chrom.replace(db, '')
-        start = int(line[2])
-        end = int(line[2]) + int(line[3])
-        line = line[1:]
-        line = ':'.join(line)
-        temp = line
-        buffer = temp if buffer == '' else f"{buffer},{temp}"
-    elif line[0] == 'a':
-        score = int(line[1].split('=')[1])
-        if id > 0:
-            sys.stdout.write('\t'.join([chrom, '%d' % start, '%d' % end, f"{sys.argv[1]}_{id}", '%d' % score, buffer]) + '\n')
-        id += 1
-        buffer = ''
-    elif line[0] == 's':
-        line = line[1:]
-        line = ':'.join(line)
-        temp = line
-        buffer = temp if buffer == '' else f"{buffer},{temp}"
+        line = line.split()
+        if line[0] == 's' and line[1].startswith(db):
+            chrom = line[1]
+            chrom = chrom.replace(db, '')
+            start = int(line[2])
+            end = int(line[2]) + int(line[3])
+            line = line[1:]
+            line = ':'.join(line)
+            temp = line
+            buffer = temp if buffer == '' else f"{buffer},{temp}"
+        elif line[0] == 'a':
+            score = int(line[1].split('=')[1])
+            if id > 0:
+                output.write('\t'.join([chrom, '%d' % start, '%d' % end, f"{assembly_name}_{id}", '%d' % score, buffer]) + '\n')
+            id += 1
+            buffer = ''
+        elif line[0] == 's':
+            line = line[1:]
+            line = ':'.join(line)
+            temp = line
+            buffer = temp if buffer == '' else f"{buffer},{temp}"
 
-sys.stdout.write('\t'.join([chrom, '%d' % start, '%d' % end, f"{sys.argv[1]}_{id}", '%d' % score, buffer]) + '\n')
+    output.write('\t'.join([chrom, '%d' % start, '%d' % end, f"{assembly_name}_{id}", '%d' % score, buffer]) + '\n')
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description="", epilog="")
+    parser.add_argument("assembly_name", help="Assembly name")
+    parser.add_argument('input', nargs='?', type=argparse.FileType('r'), default=sys.stdin)
+    parser.add_argument('output', nargs='?', type=argparse.FileType('w'), default=sys.stdout)
+    args = parser.parse_args()
+
+    maf2bed(args.assembly_name, args.input, args.output)