Just bytes

Author: Alopalao

rounds/3_dna/solution.py

@@ -6,12 +6,47 @@
 """
 
 from .baseline import find_matches as _baseline
+from threading import Thread
+import numpy as np
 
 
 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)
+    # Step 1: read the whole FASTA file as text and decode the pattern so the
+    # search below can use a single ``str`` API.
+    pattern_str = pattern.decode("ascii")
+    with open(fasta_path, "rb") as f:
+        text = f.read()
+    matches: list[tuple[str, list[int]]] = []
+
+    # Step 2: split the file on '>' to peel off one record at a time. The
+    # first element is the chunk before any header (empty for well-formed
+    # files) and is skipped by the ``.strip()`` guard below.
+    for record in text.split(b">"):
+        if not record.strip():
+            continue
+
+        # Step 3: a record looks like ``"<id>\n<seq line 1>\n<seq line 2>\n..."``.
+        # The id is the first line; the remaining lines are joined back into a
+        # single contiguous sequence string.
+        lines = record.split(b"\n")
+        record_id = lines[0].strip().decode("ascii")
+        sequence = b"".join(lines[1:]).replace(b" ", b"").decode("ascii")
+
+        # Step 4: walk the sequence with ``str.find()``, advancing one byte
+        # past each hit so overlapping matches are reported too.
+        positions: list[int] = []
+        start = 0
+        while True:
+            pos = sequence.find(pattern_str, start)
+            if pos == -1:
+                break
+            positions.append(pos)
+            start = pos + 1
+
+        if positions:
+            matches.append((record_id, positions))
+    return matches