smftools 0.1.6__py3-none-any.whl → 0.2.1__py3-none-any.whl

smftools/informatics/helpers/modcall.py

@@ -0,0 +1,36 @@
+## modcall
+
+# Direct methylation specific
+def modcall(model_dir, model, pod5_dir, barcode_kit, mod_list, bam, bam_suffix, barcode_both_ends=True, trim=False, device='auto'):
+    """
+    Wrapper function for dorado modified base calling.
+
+    Parameters:
+        model_dir (str): a string representing the file path to the dorado basecalling model directory.
+        model (str): a string representing the the dorado basecalling model.
+        pod5_dir (str): a string representing the file path to the experiment directory containing the POD5 files.
+        barcode_kit (str): A string representing the barcoding kit used in the experiment.
+        mod_list (list): A list of modification types to use in the analysis.
+        bam (str): File path to the BAM file to output.
+        bam_suffix (str): The suffix to use for the BAM file.
+        barcode_both_ends (bool): Whether to require a barcode detection on both ends for demultiplexing.
+        trim (bool): Whether to trim barcodes, adapters, and primers from read ends
+        device (str): Device to use for basecalling. auto, metal, cpu, cuda.
+    
+    Returns:
+        None
+            Outputs a BAM file holding the modified base calls output by the dorado basecaller.
+    """
+    import subprocess
+    output = bam + bam_suffix
+    command = ["dorado", "basecaller", "--models-directory", model_dir, "--kit-name", barcode_kit, "--modified-bases"]
+    command += mod_list
+    command += ["--device", device, "--batchsize", "0"]
+    if barcode_both_ends:
+        command.append("--barcode-both-ends")
+    if not trim:
+        command.append("--no-trim")
+    command += [model, pod5_dir]
+    print(f'Running: {" ".join(command)}')
+    with open(output, "w") as outfile:
+        subprocess.run(command, stdout=outfile)