yamcot 1.0.0__cp312-cp312-win_amd64.whl

yamcot/execute.py

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+import logging
+import os
+import subprocess
+from io import StringIO
+
+import pandas as pd
+
+# Import the C++ extension
+from yamcot._core import run_motali_cpp
+
+
+def run_prosampler(foreground_path, background_path, output_dir, motif_length, number_of_motifs):
+    if not os.path.exists(output_dir):
+        os.makedirs(output_dir)
+    args = [
+        "ProSampler",
+        "-i",
+        foreground_path,
+        "-b",
+        background_path,
+        "-k",
+        f"{motif_length}",
+        "-l",
+        "0",
+        "-m",
+        f"{number_of_motifs}",
+        "-z",
+        "0",
+        "-t",
+        "4",
+        "-w",
+        "2",
+        "-o",
+        f"{output_dir}/motifs",
+    ]
+    logger = logging.getLogger(__name__)
+    logger.debug(" ".join(args))
+    stdout = subprocess.run(args, shell=False, capture_output=True)
+    logger.debug(stdout)
+    return 0
+
+
+def run_tomtom(motifs_1, motifs_2):
+    args = ["tomtom", motifs_1, motifs_2, "-thresh", "1", "-text"]
+
+    logger = logging.getLogger(__name__)
+    logger.debug(" ".join(args))
+
+    stdout = subprocess.run(args, shell=False, capture_output=True)
+
+    logger.debug(stdout)
+
+    table = pd.read_csv(StringIO(stdout.stdout.decode()), sep="\t", comment="#")
+    table = table[["Query_ID", "Target_ID", "p-value", "Overlap", "Orientation"]]
+    table.columns = ["query", "target", "p-value", "overlap", "orientation"]
+    table = table.reset_index(drop=True)
+
+    return table.iloc[0].to_dict()
+
+
+def run_motali(
+    fasta_path, motif_1, motif_2, type_1, type_2, dist_1, dist_2, overlap_path, all_path, prc_path, hist_path, sta_path
+):
+    """
+    Run motali comparison using either the C++ extension or subprocess fallback.
+    """
+    logger = logging.getLogger(__name__)
+
+    # Use the C++ extension directly
+    result = run_motali_cpp(
+        file_fasta=fasta_path,
+        type_model_1=type_1,
+        type_model_2=type_2,
+        file_model_1=motif_1,
+        file_model_2=motif_2,
+        file_table_1=dist_1,
+        file_table_2=dist_2,
+        shift=50,  # Default shift value
+        threshold=0.002,  # Default threshold
+        file_hist=hist_path,
+        yes_out_hist=1,
+        file_prc=prc_path,
+        yes_out_prc=1,
+        file_short_over=overlap_path,
+        file_short_all=all_path,
+        file_sta_long=sta_path,
+    )
+
+    if result != 0:
+        logger.error(f"C++ function returned error code: {result}")
+        raise RuntimeError(f"C++ function failed with error code: {result}")
+
+    # Read the result from the output file
+    with open(all_path) as file:
+        score = float(file.readline().strip())
+
+    return score