Python matrix example cleanup

Add a proper __main__ entry point, and remove dead code.

Author: sampsyo

flatgfa-py/examples/matrix.py

@@ -1,61 +1,29 @@
 import pathlib
+import sys
 from itertools import islice
 
 import flatgfa
 
-
-def iter_bits_ones_dash(path, chunk_bytes: int = 64 * 1024):
-    ws = b" \t\r\n\v\f"
-    with open(path, "rb") as f:
-        while True:
-            chunk = f.read(chunk_bytes)
-            if not chunk:
-                break
-            for b in chunk:
-                if b in ws:
-                    continue
-                if b == ord("1"):
-                    yield True
-                elif b == ord("0"):
-                    yield False
-                else:
-                    raise ValueError(
-                        f"Invalid character in file: {chr(b)!r} (expected '1' or '0')"
-                    )
-
-
-def compare_row_to_file(row_bits, path) -> tuple[bool, int | None]:
-    n = len(row_bits)
-    i = 0
-    for fb in iter_bits_ones_dash(path):
-        if i >= n:
-            # file has extra bits
-            raise ValueError("File contains more bits than the row length.")
-        if fb != bool(row_bits[i]):
-            return False, i
-        i += 1
-
-    if i != n:
-        # file ended early
-        raise ValueError(f"File ended early: got {i} bits, expected {n}.")
-    return True, None
-
-
-TEST_DIR = pathlib.Path(__file__).parent
-TEST_GFA = TEST_DIR / "./matrix_gaf_folder/Chr3.gfa"
-GAF_DIR = (TEST_DIR / "./matrix_gaf_folder").resolve()
-# MASTER_TXT = TEST_DIR / "./matrix_gaf_folder/Chr3-pangenotype"
-
-graph = flatgfa.parse(str(TEST_GFA))
-gaf = [str(p) for p in GAF_DIR.glob("*.gaf")]
-pangenotype_matrix = graph.make_pangenotype_matrix(gaf)
-# assert len(pangenotype_matrix) == len(gaf)
-# first_row = list(pangenotype_matrix[0])
-# ok, where = compare_row_to_file(first_row, str(MASTER_TXT))
-# print("OK (all columns match)" if ok else f"Mismatch at column {where}")
 FIRST_N = 100
-for gaf_path, row in zip(gaf, pangenotype_matrix):
-    row01 = [int(b) for b in row]
-    # print(pathlib.Path(gaf_path).name, *row01)
-    first_bits = islice(row, FIRST_N)
-    print(pathlib.Path(gaf_path).name, *map(int, first_bits))
+
+
+def matrix_demo(gfa_path, gaf_dir):
+    # Construct a pangenotype matrix for the `gfa_path` graph and all the GAF
+    # files in `gaf_dir`.
+    graph = flatgfa.parse(gfa_path)
+    gaf = [str(p) for p in pathlib.Path(gaf_dir).glob("*.gaf")]
+    pangenotype_matrix = graph.make_pangenotype_matrix(gaf)
+
+    assert len(pangenotype_matrix) == len(gaf)
+
+    # Just print out a few entries from the matrix.
+    for gaf_path, row in zip(gaf, pangenotype_matrix):
+        first_bits = islice(row, FIRST_N)
+        print(pathlib.Path(gaf_path).name, *map(int, first_bits))
+
+
+if __name__ == "__main__":
+    if len(sys.argv) != 3:
+        print("usage: matrix.py <GFA file> <GAF directory>")
+        sys.exit(1)
+    matrix_demo(*sys.argv[1:])