trevored-py performance improvements

README.md

@@ -91,3 +91,4 @@ scripts/
 ```
 
 Each round's `data/` directory is generated locally and gitignored.
+This is trevored-py's PR

rounds/3_dna/solution.py

@@ -5,13 +5,57 @@
 own faster implementation.
 """
 
-from .baseline import find_matches as _baseline
-
 
 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)
+
+    results = []
+
+    current_id = None
+    chunks = []
+
+    with open(fasta_path, "rb") as f:
+        for line in f:
+            line = line.rstrip(b"\n")
+
+            if line.startswith(b">"):
+                if current_id is not None:
+                    seq = b"".join(chunks)
+                    positions = find_all(seq, pattern)
+
+                    if positions:
+                        results.append((current_id, positions))
+
+                current_id = line[1:].decode("ascii")
+                chunks = []
+
+            else:
+                chunks.append(line)
+
+        if current_id is not None:
+            seq = b"".join(chunks)
+            positions = find_all(seq, pattern)
+
+            if positions:
+                results.append((current_id, positions))
+
+    return results
+
+
+def find_all(seq: bytes, pattern: bytes) -> list[int]:
+    positions = []
+    start = 0
+
+    while True:
+        pos = seq.find(pattern, start)
+
+        if pos == -1:
+            break
+
+        positions.append(pos)
+        start = pos + 1
+
+    return positions

rounds/3_dna/target_b.txt

@@ -0,0 +1 @@
+target = bytearray([65, 71, 84, 67, 67, 71, 84, 65])

rounds/3_dna/working_solution.py

@@ -0,0 +1,61 @@
+"""Your Round 3 solution — DNA sequence matcher.
+
+**Edit this file.** It currently delegates to ``baseline.py`` so everything
+passes out of the box. Replace the body of ``find_matches`` with your
+own faster implementation.
+"""
+
+
+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.
+    """
+
+    results = []
+
+    current_id = None
+    chunks = []
+
+    with open(fasta_path, "rb") as f:
+        for line in f:
+            line = line.rstrip(b"\n")
+
+            if line.startswith(b">"):
+                if current_id is not None:
+                    seq = b"".join(chunks)
+                    positions = find_all(seq, pattern)
+
+                    if positions:
+                        results.append((current_id, positions))
+
+                current_id = line[1:].decode("ascii")
+                chunks = []
+
+            else:
+                chunks.append(line)
+
+        if current_id is not None:
+            seq = b"".join(chunks)
+            positions = find_all(seq, pattern)
+
+            if positions:
+                results.append((current_id, positions))
+
+    return results
+
+
+def find_all(seq: bytes, pattern: bytes) -> list[int]:
+    positions = []
+    start = 0
+
+    while True:
+        pos = seq.find(pattern, start)
+
+        if pos == -1:
+            break
+
+        positions.append(pos)
+        start = pos + 1
+
+    return positions