--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lcb_split.py	Mon Jun 05 02:54:34 2023 +0000
@@ -0,0 +1,94 @@
+#!/usr/bin/env python
+import argparse
+import copy
+import logging
+import xmfa
+from itertools import groupby
+
+logging.basicConfig(level=logging.INFO)
+log = logging.getLogger(__name__)
+
+
+def split_lcb(lcb, window_size=10, threshold=0.7):
+    # Transpose sequence
+    lines = []
+    max_align_num = len(lcb[0]["seq"])
+    for i in range(max_align_num):
+        lines.append([])
+        for j in range(len(lcb)):
+            c = lcb[j]["seq"][i]
+            if c != "-":
+                lines[i].append(j)
+
+    count_groups = []
+    for i in range(0, len(lines), window_size):
+        current_lines = lines[i : i + window_size]
+        flat_list = [a for b in current_lines for a in b]
+        counts = []
+        for i in range(len(lcb)):
+            value = float(flat_list.count(i)) / window_size
+            if value >= threshold:
+                counts.append(i)
+        count_groups.append(counts)
+
+    # groups = [(next(j), len(list(j)) + 1) for i, j in ]
+    # [([4], 2), ([2, 3, 4, 5, 6], 2), ([0, 1, 2, 3, 4, 5, 6], 14), ([0, 3], 1)]
+    # This says for 2 window sizes, we emit a new LCB with just [0:10] and
+    # [10:20] for lcb #4, then one with all but 0/1 for 2, then all for 14.
+    new_lcbs = []
+    position = 0
+    for i, j in groupby(count_groups):
+        tmp = list(j)
+        count = len(tmp)
+        members = tmp[0]
+        local_members = []
+        for member in members:
+            tmp_member = copy.deepcopy(lcb[member])
+            tmp_member["seq"] = tmp_member["seq"][
+                window_size * position : window_size * (position + count)
+            ]
+            tmp_member["start"] = tmp_member["start"] + (3 * window_size * position)
+            tmp_member["end"] = tmp_member["start"] + (3 * window_size * count)
+            local_members.append(tmp_member)
+        if len(local_members) > 0:
+            new_lcbs.append(local_members)
+
+        position += count
+    return new_lcbs
+
+
+def split_lcbs(lcbs, window_size=10, threshold=100):
+    new_lcbs = []
+    for lcb in lcbs:
+        new_lcbs.extend(split_lcb(lcb, window_size=window_size, threshold=threshold))
+    return new_lcbs
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(
+        description="Split XMFA alignments", prog="xmfa2smallerXmfa"
+    )
+    parser.add_argument("xmfa_file", type=argparse.FileType("r"), help="XMFA File")
+
+    parser.add_argument(
+        "--window_size", type=int, help="Window size for analysis", default=10
+    )
+    parser.add_argument(
+        "--threshold",
+        type=float,
+        help="All genomes must meet N percent similarity",
+        default=0.7,
+    )
+
+    args = parser.parse_args()
+
+    # Write
+    xmfa.to_xmfa(
+        # Split
+        split_lcbs(
+            # Parse
+            xmfa.parse_xmfa(args.xmfa_file),
+            window_size=args.window_size,
+            threshold=args.threshold,
+        )
+    )