--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/write_amplicon_info_file.py	Thu Aug 05 12:44:05 2021 +0000
@@ -0,0 +1,50 @@
+#!/usr/bin/env python
+
+import argparse
+import re
+
+AMPLICON_NAME_RE = r'.*_(?P<num>\d+)_[^0-9]*(?P<name>L(?:EFT)?|R(?:IGHT)?)'
+
+
+def primer_info_to_position(name):
+    position = 0
+    re_match = re.match(AMPLICON_NAME_RE, name)
+    if re_match is None:
+        raise ValueError("{} does not match expected amplicon name format".format(name))
+    side = re_match.group('name')
+    num = re_match.group('num')
+    if side == 'RIGHT' or side == 'R':
+        position += 1000
+    if num is not None:
+        position += int(num)
+    return position
+
+
+def write_amplicon_info_file(bed_file, amplicon_info_file):
+    amplicon_sets = {}
+    amplicon_ids = set()
+    for line in bed_file:
+        fields = line.strip().split('\t')
+        name = fields[3]
+        re_match = re.match(AMPLICON_NAME_RE, name)
+        if re_match is None:
+            raise ValueError("{} does not match expected amplicon name format".format(name))
+        amplicon_id = int(re_match.group('num'))
+        amplicon_set = amplicon_sets.get(amplicon_id, [])
+        amplicon_set.append(name)
+        amplicon_sets[amplicon_id] = amplicon_set
+        amplicon_ids.add(amplicon_id)
+
+    for id in sorted(list(amplicon_ids)):
+        amplicon_info = '\t'.join([name for name in sorted(amplicon_sets[id], key=primer_info_to_position)]) + '\n'
+        amplicon_info_file.write(amplicon_info)
+    amplicon_info_file.close()
+
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser(description='Write an amplicon info file for iVar from a BED file describing primer positions')
+    parser.add_argument('bed_file', type=argparse.FileType(), help='Primer BED file')
+    parser.add_argument('amplicon_info_file', type=argparse.FileType('w'), help='Output file: amplicon info file in TSV format')
+    args = parser.parse_args()
+
+    write_amplicon_info_file(args.bed_file, args.amplicon_info_file)