--- a/prepare_amplicon_info.py	Thu Mar 13 09:02:49 2025 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,63 +0,0 @@
-#!/usr/bin/env python
-
-# extends ivar trim's amplicon info parsing abilities
-# to include calculation of amplicon regions from
-# sets of nested (more than two) primers
-
-import sys
-
-
-# parse primers and their start positions from BED file
-primer_starts = {}
-with open(sys.argv[1]) as i:
-    for line in i:
-        line = line.strip()
-        if not line:
-            continue
-        f = line.split('\t')
-        try:
-            if f[5] == '+':
-                primer_starts[f[3]] = int(f[1])
-            elif f[5] == '-':
-                primer_starts[f[3]] = int(f[2]) - 1
-            else:
-                raise ValueError()
-        except (IndexError, ValueError):
-            sys.exit(
-                'Primer BED file needs to be TAB-separated with the '
-                'following columns: '
-                'chrom, chromStart, chromEnd, name, score, strand, '
-                'where "chromStart", "chromEnd" need to be integer values '
-                'and "strand" needs to be either "+" or "-".'
-            )
-
-# parse amplicon info and record outer primer names
-with open(sys.argv[2]) as i:
-    ret_lines = []
-    for line in i:
-        line = line.strip()
-        if not line:
-            continue
-        first = last = None
-        for pname in line.split('\t'):
-            try:
-                primer_start = primer_starts[pname]
-            except KeyError:
-                sys.exit(
-                    'Amplicon info with primer name not found in '
-                    f'primer BED file: "{pname}"'
-                )
-            if first is None or primer_start < primer_starts[first]:
-                first = pname
-            if last is None or primer_start > primer_starts[last]:
-                last = pname
-        if first == last:
-            sys.exit(
-                line
-                + 'is not a proper amplicon info line.'
-            )
-        ret_lines.append(f'{first}\t{last}\n')
-
-# write amended amplicon info
-with open(sys.argv[3], 'w') as o:
-    o.writelines(ret_lines)