smftools 0.1.3__py3-none-any.whl → 0.1.6__py3-none-any.whl

smftools/informatics/helpers/get_native_references.py

@@ -1,28 +0,0 @@
-## get_native_references
-
-# Direct methylation specific
-def get_native_references(fasta_file):
-    """
-    Makes a dictionary keyed by record id which points to the record length and record sequence.
-
-    Paramaters:
-        fasta_file (str): A string representing the path to the FASTA file for the experiment.
-
-    Returns: 
-        None
-    """
-    from .. import readwrite
-    from Bio import SeqIO
-    from Bio.SeqRecord import SeqRecord
-    from Bio.Seq import Seq
-    record_dict = {}
-    print('{0}: Opening FASTA file {1}'.format(readwrite.time_string(), fasta_file))
-    # Open the FASTA record as read only
-    with open(fasta_file, "r") as f:
-        # Iterate over records in the FASTA
-        for record in SeqIO.parse(f, "fasta"):
-            # Extract the sequence string of the record
-            sequence = str(record.seq).upper()
-            sequence_length = len(sequence) 
-            record_dict[record.id] = [sequence_length, sequence]
-    return record_dict

smftools/informatics/helpers/index_fasta.py

@@ -1,12 +0,0 @@
-# index_fasta
-
-def index_fasta(fasta):
-    """
-    Generate a FASTA index file for an input fasta.
-
-    Parameters:
-        fasta (str): Path to the input fasta to make an index file for.
-    """
-    import subprocess
-
-    subprocess.run(["samtools", "faidx", fasta])

smftools/informatics/helpers/make_dirs.py

@@ -1,21 +0,0 @@
-## make_dirs
-
-# General
-def make_dirs(directories):
-    """
-    Takes a list of file paths and makes new directories if the directory does not already exist.
-
-    Parameters:
-        directories (list): A list of directories to make
-    
-    Returns:
-        None
-    """
-    import os
-
-    for directory in directories:
-        if not os.path.isdir(directory):
-            os.mkdir(directory)
-            print(f"Directory '{directory}' created successfully.")
-        else:
-            print(f"Directory '{directory}' already exists.")

smftools/informatics/helpers/make_modbed.py

@@ -1,27 +0,0 @@
-## make_modbed
-
-# Direct SMF
-def make_modbed(aligned_sorted_output, thresholds, mod_bed_dir):
-    """
-    Generating position methylation summaries for each barcoded sample starting from the overall BAM file that was direct output of dorado aligner.
-    Parameters:
-        aligned_sorted_output (str): A string representing the file path to the aligned_sorted non-split BAM file.
-    
-    Returns:
-        None
-    """
-    import os
-    import subprocess
-    
-    os.chdir(mod_bed_dir)
-    filter_threshold, m6A_threshold, m5C_threshold, hm5C_threshold = thresholds
-    command = [
-        "modkit", "pileup", aligned_sorted_output, mod_bed_dir,
-        "--partition-tag", "BC",
-        "--only-tabs",
-        "--filter-threshold", f'{filter_threshold}',
-        "--mod-thresholds", f"m:{m5C_threshold}",
-        "--mod-thresholds", f"a:{m6A_threshold}",
-        "--mod-thresholds", f"h:{hm5C_threshold}"
-    ]
-    subprocess.run(command)

smftools/informatics/helpers/modQC.py

@@ -1,27 +0,0 @@
-## modQC
-
-# Direct SMF
-def modQC(aligned_sorted_output, thresholds):
-    """
-    Output the percentile of bases falling at a call threshold (threshold is a probability between 0-1) for the overall BAM file.
-    It is generally good to look at these parameters on positive and negative controls.
-
-    Parameters:
-        aligned_sorted_output (str): A string representing the file path of the aligned_sorted non-split BAM file output by the dorado aligned.
-        thresholds (list): A list of floats to pass for call thresholds.
-
-    Returns:
-        None
-    """
-    import subprocess
-
-    filter_threshold, m6A_threshold, m5C_threshold, hm5C_threshold = thresholds
-    subprocess.run(["modkit", "sample-probs", aligned_sorted_output])
-    command = [
-        "modkit", "summary", aligned_sorted_output,
-        "--filter-threshold", f"{filter_threshold}",
-        "--mod-thresholds", f"m:{m5C_threshold}",
-        "--mod-thresholds", f"a:{m6A_threshold}",
-        "--mod-thresholds", f"h:{hm5C_threshold}"
-    ]
-    subprocess.run(command)

smftools/informatics/helpers/modcall.py

@@ -1,28 +0,0 @@
-## modcall
-
-# Direct methylation specific
-def modcall(model, pod5_dir, barcode_kit, mod_list, bam, bam_suffix):
-    """
-    Wrapper function for dorado modified base calling.
-
-    Parameters:
-        model (str): a string representing the file path to 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.
-    
-    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", model, pod5_dir, "--kit-name", barcode_kit, "-Y",
-    "--modified-bases"]
-    command += mod_list
-    print(f'Running: {" ".join(command)}')
-    with open(output, "w") as outfile:
-        subprocess.run(command, stdout=outfile)