smftools 0.2.1__py3-none-any.whl → 0.2.4__py3-none-any.whl

smftools-0.2.4.dist-info/RECORD

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smftools-0.2.4.dist-info/entry_points.txt

@@ -0,0 +1,2 @@
+[console_scripts]
+smftools = smftools.cli_entry:cli

smftools/cli.py

@@ -1,184 +0,0 @@
-import click
-import pandas as pd
-from pathlib import Path
-from typing import Dict, Optional
-
-from . import load_adata
-from .readwrite import merge_barcoded_anndatas_core, safe_read_h5ad, safe_write_h5ad
-
-@click.group()
-def cli():
-    """Command-line interface for smftools."""
-    pass
-
-####### Main processing workflow ###########
-@cli.command()
-@click.argument("config_path", type=click.Path(exists=True))
-def load(config_path):
-    """Load and process data from CONFIG_PATH."""
-    load_adata(config_path)
-##########################################
-
-
-####### Merging existing anndatas from an experiment that used two different demultiplexing rules #######
-REQUIRED_KEYS = ("adata_single_path", "adata_double_path")
-OPTIONAL_KEYS = (
-    "adata_single_backups_path",
-    "adata_double_backups_path",
-    "output_path",
-    "merged_filename",
-)
-
-def _read_config_csv(csv_path: Path) -> Dict[str, str]:
-    """
-    Read a multi-row, two-column CSV of key,value pairs into a dict.
-
-    Supported features:
-      - Optional header ("key,value") or none.
-      - Comments starting with '#' and blank lines are ignored.
-      - If duplicate keys occur, the last one wins.
-      - Keys are matched literally against REQUIRED_KEYS/OPTIONAL_KEYS.
-    """
-    try:
-        # Read as two columns regardless of header; comments ignored.
-        df = pd.read_csv(
-            csv_path,
-            dtype=str,
-            comment="#",
-            header=None,          # treat everything as rows; we'll normalize below
-            usecols=[0, 1],
-            names=["key", "value"]
-        )
-    except Exception as e:
-        raise click.ClickException(f"Failed to read CSV: {e}") from e
-
-    # Drop completely empty rows
-    df = df.fillna("").astype(str)
-    df["key"] = df["key"].str.strip()
-    df["value"] = df["value"].str.strip()
-    df = df[(df["key"] != "") & (df["key"].notna())]
-
-    if df.empty:
-        raise click.ClickException("Config CSV is empty after removing comments/blank lines.")
-
-    # Remove an optional header row if present
-    if df.iloc[0]["key"].lower() in {"key", "keys"}:
-        df = df.iloc[1:]
-        df = df[(df["key"] != "") & (df["key"].notna())]
-        if df.empty:
-            raise click.ClickException("Config CSV contains only a header row.")
-
-    # Build dict; last occurrence of a key wins
-    cfg = {}
-    for k, v in zip(df["key"], df["value"]):
-        cfg[k] = v
-
-    # Validate required keys
-    missing = [k for k in REQUIRED_KEYS if not cfg.get(k)]
-    if missing:
-        raise click.ClickException(
-            "Missing required keys in CSV: "
-            + ", ".join(missing)
-            + "\nExpected keys:\n  - "
-            + "\n  - ".join(REQUIRED_KEYS)
-            + "\nOptional keys:\n  - "
-            + "\n  - ".join(OPTIONAL_KEYS)
-        )
-
-    return cfg
-
-def _resolve_output_path(cfg: Dict[str, str], single_path: Path, double_path: Path) -> Path:
-    """Decide on the output .h5ad path based on CSV; create directories if needed."""
-    merged_filename = cfg.get("merged_filename") or f"merged_{single_path.stem}__{double_path.stem}.h5ad"
-    if not merged_filename.endswith(".h5ad"):
-        merged_filename += ".h5ad"
-
-    output_path_raw = cfg.get("output_path", "").strip()
-
-    if not output_path_raw:
-        out_dir = Path.cwd() / "merged_output"
-        out_dir.mkdir(parents=True, exist_ok=True)
-        return out_dir / merged_filename
-
-    output_path = Path(output_path_raw)
-
-    if output_path.suffix.lower() == ".h5ad":
-        output_path.parent.mkdir(parents=True, exist_ok=True)
-        return output_path
-
-    # Treat as directory
-    output_path.mkdir(parents=True, exist_ok=True)
-    return output_path / merged_filename
-
-def _maybe_read_adata(label: str, primary: Path, backups: Optional[Path]):
-
-    if backups:
-        click.echo(f"Loading {label} from {primary} with backups at {backups} ...")
-        return safe_read_h5ad(primary, backups_path=backups, restore_backups=True)
-    else:
-        click.echo(f"Loading {label} from {primary} with backups disabled ...")
-        return safe_read_h5ad(primary, restore_backups=False)
-
-
-@cli.command()
-@click.argument("config_path", type=click.Path(exists=True, dir_okay=False, readable=True, path_type=Path))
-def merge_barcoded_anndatas(config_path: Path):
-    """
-    Merge two AnnData objects from the same experiment that were demultiplexed
-    under different end-barcoding requirements, using a 1-row CSV for config.
-
-    CSV must include:
-      - adata_single_path
-      - adata_double_path
-
-    Optional columns:
-      - adata_single_backups_path
-      - adata_double_backups_path
-      - output_path            (file or directory; default: ./merged_output/)
-      - merged_filename        (default: merged_<single>__<double>.h5ad)
-
-    Example CSV:
-
-        adata_single_path,adata_double_path,adata_single_backups_path,adata_double_backups_path,output_path,merged_filename
-        /path/single.h5ad,/path/double.h5ad,,,,merged_output,merged_run.h5ad
-    """
-    try:
-        cfg = _read_config_csv(config_path)
-
-        single_path = Path(cfg["adata_single_path"]).expanduser().resolve()
-        double_path = Path(cfg["adata_double_path"]).expanduser().resolve()
-
-        for p, label in [(single_path, "adata_single_path"), (double_path, "adata_double_path")]:
-            if not p.exists():
-                raise click.ClickException(f"{label} does not exist: {p}")
-
-        single_backups = Path(cfg["adata_single_backups_path"]).expanduser().resolve() if cfg.get("adata_single_backups_path") else None
-        double_backups = Path(cfg["adata_double_backups_path"]).expanduser().resolve() if cfg.get("adata_double_backups_path") else None
-
-        if single_backups and not single_backups.exists():
-            raise click.ClickException(f"adata_single_backups_path does not exist: {single_backups}")
-        if double_backups and not double_backups.exists():
-            raise click.ClickException(f"adata_double_backups_path does not exist: {double_backups}")
-
-        output_path = _resolve_output_path(cfg, single_path, double_path)
-
-        # Load
-        adata_single, read_report_single = _maybe_read_adata("single-barcoded AnnData", single_path, single_backups)
-        adata_double, read_report_double = _maybe_read_adata("double-barcoded AnnData", double_path, double_backups)
-
-        click.echo("Merging AnnDatas ...")
-        merged = merge_barcoded_anndatas_core(adata_single, adata_double)
-
-        click.echo(f"Writing merged AnnData to: {output_path}")
-        backup_dir = output_path.cwd() / "merged_backups"
-        safe_write_h5ad(merged, output_path, backup=True, backup_dir=backup_dir)
-
-        click.secho(f"Done. Merged AnnData saved to {output_path}", fg="green")
-
-    except click.ClickException:
-        raise
-    except Exception as e:
-        # Surface unexpected errors cleanly
-        raise click.ClickException(f"Unexpected error: {e}") from e
-
-################################################################################################################

smftools/informatics/fast5_to_pod5.py

@@ -1,24 +0,0 @@
-# fast5_to_pod5
-
-def fast5_to_pod5(fast5_dir, output_pod5='FAST5s_to_POD5.pod5'):
-    """
-    Convert Nanopore FAST5 files to POD5 file
-
-    Parameters:
-        fast5_dir (str): String representing the file path to a directory containing all FAST5 files to convert into a single POD5 output.
-        output_pod5 (str): The name of the output POD5.
-    
-    Returns:
-        None
-    
-    """
-    import subprocess
-    from pathlib import Path
-
-    if isinstance(fast5_dir, (list, tuple)):
-        cmd = ["pod5", "convert", "fast5"] + fast5_dir + ["--output", output_pod5]
-        subprocess.run(cmd)
-    elif Path(fast5_dir).is_file():
-        subprocess.run(["pod5", "convert", "fast5", fast5_dir, "--output", output_pod5])
-    elif Path(fast5_dir).is_dir():
-        subprocess.run(["pod5", "convert", "fast5", f".{fast5_dir}*.fast5", "--output", output_pod5])

smftools/informatics/helpers/__init__.py

@@ -1,73 +0,0 @@
-from .align_and_sort_BAM import align_and_sort_BAM
-from .aligned_BAM_to_bed import aligned_BAM_to_bed
-from .bam_qc import bam_qc
-from .bed_to_bigwig import bed_to_bigwig
-from .binarize_converted_base_identities import binarize_converted_base_identities
-from .canoncall import canoncall
-from .complement_base_list import complement_base_list
-from .converted_BAM_to_adata_II import converted_BAM_to_adata_II
-from .concatenate_fastqs_to_bam import concatenate_fastqs_to_bam
-from .count_aligned_reads import count_aligned_reads
-from .demux_and_index_BAM import demux_and_index_BAM
-from .discover_input_files import *
-from .extract_base_identities import extract_base_identities
-from .extract_mods import extract_mods
-from .extract_read_features_from_bam import extract_read_features_from_bam
-from .extract_read_lengths_from_bed import extract_read_lengths_from_bed
-from .extract_readnames_from_BAM import extract_readnames_from_BAM
-from .find_conversion_sites import find_conversion_sites
-from .generate_converted_FASTA import convert_FASTA_record, generate_converted_FASTA
-from .get_chromosome_lengths import get_chromosome_lengths
-from .get_native_references import get_native_references
-from .index_fasta import index_fasta
-from .make_dirs import make_dirs
-from .make_modbed import make_modbed
-from .modcall import modcall
-from .modkit_extract_to_adata import modkit_extract_to_adata
-from .modQC import modQC
-from .one_hot_encode import one_hot_encode
-from .ohe_batching import ohe_batching
-from .one_hot_decode import one_hot_decode
-from .ohe_layers_decode import ohe_layers_decode
-from .plot_bed_histograms import plot_bed_histograms
-from .run_multiqc import run_multiqc
-from .separate_bam_by_bc import separate_bam_by_bc
-from .split_and_index_BAM import split_and_index_BAM
-
-__all__ = [
-    "align_and_sort_BAM",
-    "aligned_BAM_to_bed",
-    "bam_qc",
-    "bed_to_bigwig",
-    "binarize_converted_base_identities",
-    "canoncall",
-    "complement_base_list",
-    "converted_BAM_to_adata_II",
-    "concatenate_fastqs_to_bam",
-    "count_aligned_reads",
-    "demux_and_index_BAM",
-    "extract_base_identities",
-    "extract_mods",
-    "extract_read_features_from_bam",
-    "extract_read_lengths_from_bed",
-    "extract_readnames_from_BAM",
-    "find_conversion_sites",
-    "convert_FASTA_record",
-    "generate_converted_FASTA",
-    "get_chromosome_lengths",
-    "get_native_references",
-    "index_fasta",
-    "make_dirs",
-    "make_modbed",
-    "modcall",
-    "modkit_extract_to_adata",
-    "modQC",
-    "one_hot_encode",
-    "ohe_batching",
-    "one_hot_decode",
-    "ohe_layers_decode",
-    "plot_bed_histograms",
-    "run_multiqc",
-    "separate_bam_by_bc",
-    "split_and_index_BAM"
-]

smftools/informatics/helpers/align_and_sort_BAM.py

@@ -1,86 +0,0 @@
-## align_and_sort_BAM
-
-def align_and_sort_BAM(fasta, 
-                       input, 
-                       bam_suffix='.bam', 
-                       output_directory='aligned_outputs', 
-                       make_bigwigs=False, 
-                       threads=None, 
-                       aligner='minimap2',
-                       aligner_args=['-a', '-x', 'map-ont', '--MD', '-Y', '-y', '-N', '5', '--secondary=no']):
-    """
-    A wrapper for running dorado aligner and samtools functions
-    
-    Parameters:
-        fasta (str): File path to the reference genome to align to.
-        input (str): File path to the basecalled file to align. Works for .bam and .fastq files
-        bam_suffix (str): The suffix to use for the BAM file.
-        output_directory (str): A file path to the directory to output all the analyses.
-        make_bigwigs (bool): Whether to make bigwigs
-        threads (int): Number of additional threads to use
-        aligner (str): Aligner to use. minimap2 and dorado options
-        aligner_args (list): list of optional parameters to use for the alignment
-
-    Returns:
-        None
-            The function writes out files for: 1) An aligned BAM, 2) and aligned_sorted BAM, 3) an index file for the aligned_sorted BAM, 4) A bed file for the aligned_sorted BAM, 5) A text file containing read names in the aligned_sorted BAM
-    """
-    import subprocess
-    import os
-
-    input_basename = os.path.basename(input)
-    input_suffix = '.' + input_basename.split('.')[1]
-    input_as_fastq = input_basename.split('.')[0] + '.fastq'
-
-    output_path_minus_suffix = os.path.join(output_directory, input_basename.split(input_suffix)[0])
-    
-    aligned_BAM=f"{output_path_minus_suffix}_aligned"
-    aligned_sorted_BAM=f"{aligned_BAM}_sorted"
-    aligned_output = aligned_BAM + bam_suffix
-    aligned_sorted_output = aligned_sorted_BAM + bam_suffix
-
-    if threads:
-        threads = str(threads)
-    else:
-        pass
-    
-    if aligner == 'minimap2':
-        print(f"Converting BAM to FASTQ: {input}")
-        bam_to_fastq_command = ['samtools', 'fastq', input]
-        subprocess.run(bam_to_fastq_command, stdout=open(input_as_fastq, "w"))
-        print(f"Aligning FASTQ to Reference: {input_as_fastq}")
-        if threads:
-            minimap_command = ['minimap2'] + aligner_args + ['-t', threads, fasta, input_as_fastq]
-        else:
-            minimap_command = ['minimap2'] + aligner_args + [fasta, input_as_fastq]
-        subprocess.run(minimap_command, stdout=open(aligned_output, "w"))
-        os.remove(input_as_fastq)
-
-    elif aligner == 'dorado':
-        # Run dorado aligner
-        print(f"Aligning BAM to Reference: {input}")
-        if threads:
-            alignment_command = ["dorado", "aligner", "-t", threads] + aligner_args + [fasta, input]
-        else:
-            alignment_command = ["dorado", "aligner"] + aligner_args + [fasta, input]
-        subprocess.run(alignment_command, stdout=open(aligned_output, "w"))
-
-    else:
-        print(f'Aligner not recognized: {aligner}. Choose from minimap2 and dorado')
-        return
-
-    # Sort the BAM on positional coordinates
-    print(f"Sorting BAM: {aligned_output}")
-    if threads:
-        sort_command = ["samtools", "sort", "-@", threads, "-o", aligned_sorted_output, aligned_output]
-    else:
-        sort_command = ["samtools", "sort", "-o", aligned_sorted_output, aligned_output]
-    subprocess.run(sort_command)
-
-    # Create a BAM index file
-    print(f"Indexing BAM: {aligned_sorted_output}")
-    if threads:
-        index_command = ["samtools", "index", "-@", threads, aligned_sorted_output]
-    else:
-        index_command = ["samtools", "index", aligned_sorted_output]
-    subprocess.run(index_command)

smftools/informatics/helpers/bam_qc.py

@@ -1,66 +0,0 @@
-## bam_qc
-
-def bam_qc(bam_files, bam_qc_dir, threads, modality, stats=True, flagstats=True, idxstats=True):
-    """
-    Performs QC on BAM files by running samtools stats, flagstat, and idxstats.
-    
-    Parameters:
-    - bam_files: List of BAM file paths.
-    - bam_qc_dir: Directory to save QC reports.
-    - threads: Number threads to use.
-    - modality: 'conversion' or 'direct' (affects processing mode).
-    - stats: Run `samtools stats` if True.
-    - flagstats: Run `samtools flagstat` if True.
-    - idxstats: Run `samtools idxstats` if True.
-    """
-    import os
-    import subprocess
-    
-    # Ensure the QC output directory exists
-    os.makedirs(bam_qc_dir, exist_ok=True)
-
-    if threads:
-        threads = str(threads)
-    else:
-        pass
-
-    for bam in bam_files:
-        bam_name = os.path.basename(bam).replace(".bam", "")  # Extract filename without extension
-
-        # Run samtools QC commands based on selected options
-        if stats:
-            stats_out = os.path.join(bam_qc_dir, f"{bam_name}_stats.txt")
-            if threads:
-                command = ["samtools", "stats", "-@", threads, bam]
-            else: 
-                command = ["samtools", "stats", bam]
-            print(f"Running: {' '.join(command)} > {stats_out}")
-            with open(stats_out, "w") as out_file:
-                subprocess.run(command, stdout=out_file)
-
-        if flagstats:
-            flagstats_out = os.path.join(bam_qc_dir, f"{bam_name}_flagstat.txt")
-            if threads:
-                command = ["samtools", "flagstat", "-@", threads, bam]
-            else:
-                command = ["samtools", "flagstat", bam]
-            print(f"Running: {' '.join(command)} > {flagstats_out}")
-            with open(flagstats_out, "w") as out_file:
-                subprocess.run(command, stdout=out_file)
-
-        if idxstats:
-            idxstats_out = os.path.join(bam_qc_dir, f"{bam_name}_idxstats.txt")
-            if threads:
-                command = ["samtools", "idxstats", "-@", threads, bam]
-            else:
-                command = ["samtools", "idxstats", bam]
-            print(f"Running: {' '.join(command)} > {idxstats_out}")
-            with open(idxstats_out, "w") as out_file:
-                subprocess.run(command, stdout=out_file)
-
-        if modality == 'conversion':
-            pass
-        elif modality == 'direct':
-            pass
-
-    print("QC processing completed.")