dna attempt

Author: SamWilsn

rounds/3_dna/solution.py

@@ -5,13 +5,58 @@
 own faster implementation.
 """
 
-from .baseline import find_matches as _baseline
+from mmap import mmap, ACCESS_READ
+from concurrent.futures import ThreadPoolExecutor, wait
 
+def _subsearch(raw, record_id_start: int, data_start: int, data_end: int, pattern: bytes):
+    plen = len(pattern)
+    data = bytes(raw[data_start : data_end - 1]).replace(b"\n", b"")
+    locations = []
+    loc = data.find(pattern)
+    while loc != -1:
+        locations.append(loc)
+        loc = data.find(pattern, loc + plen)
+
+    if not locations:
+        return None
+
+    record_id = raw[record_id_start : data_start - 1].decode("ascii")
+    return (record_id, locations)
 
 def find_matches(fasta_path: str, pattern: bytes) -> list[tuple[str, list[int]]]:
     """Find every FASTA record whose sequence contains ``pattern``.
 
     Returns ``[(record_id, [positions...]), ...]`` in file order.
     """
-    # TODO: remove this delegation and write your own implementation here.
-    return _baseline(fasta_path, pattern)
+    source = open(fasta_path, "rb")
+    data = mmap(source.fileno(), 0, access=ACCESS_READ)
+
+    last = -1
+
+    data_end = len(data) - 1
+    while data[data_end] == b"\n":
+        data_end -= 1
+
+    with ThreadPoolExecutor(max_workers=16) as executor:
+        records = []
+        while data_end > 0:
+            gt_pos = data.rfind(b">", 0, data_end)
+            if gt_pos == -1:
+                raise Exception("expected greater than")
+
+            record_id_start = gt_pos + 1
+
+            nl_pos = data.find(b"\n", record_id_start)
+            if nl_pos == -1:
+                raise Exception("expected new line")
+
+            data_start = nl_pos + 1
+
+            records.append(
+                executor.submit(_subsearch, data, record_id_start, data_start, data_end, pattern)
+            )
+            data_end = gt_pos
+
+        results = [d.result() for d in records if d.result() is not None]
+        results.reverse()
+        return results