smftools 0.2.4__py3-none-any.whl → 0.2.5__py3-none-any.whl

smftools/cli_entry.py

@@ -1,19 +1,38 @@
+import logging
+from pathlib import Path
+from typing import Sequence
+
 import click
 import pandas as pd
-from pathlib import Path
-from typing import Dict, Optional, Sequence
 
+from .cli.hmm_adata import hmm_adata
 from .cli.load_adata import load_adata
 from .cli.preprocess_adata import preprocess_adata
 from .cli.spatial_adata import spatial_adata
-from .cli.hmm_adata import hmm_adata
+from .informatics.pod5_functions import subsample_pod5
+from .logging_utils import setup_logging
+from .readwrite import concatenate_h5ads
 
-from .readwrite import safe_read_h5ad, safe_write_h5ad, concatenate_h5ads
 
 @click.group()
-def cli():
+@click.option(
+    "--log-file",
+    type=click.Path(dir_okay=False, writable=True, path_type=Path),
+    default=None,
+    help="Optional file path to write smftools logs.",
+)
+@click.option(
+    "--log-level",
+    type=click.Choice(["CRITICAL", "ERROR", "WARNING", "INFO", "DEBUG"], case_sensitive=False),
+    default="INFO",
+    show_default=True,
+    help="Logging level for smftools output.",
+)
+def cli(log_file: Path | None, log_level: str):
     """Command-line interface for smftools."""
-    pass
+    level = getattr(logging, log_level.upper(), logging.INFO)
+    setup_logging(level=level, log_file=log_file)
+
 
 ####### Load anndata from raw data ###########
 @cli.command()
@@ -21,32 +40,44 @@ def cli():
 def load(config_path):
     """Load and process data from CONFIG_PATH."""
     load_adata(config_path)
+
+
 ##########################################
 
+
 ####### Preprocessing ###########
 @cli.command()
 @click.argument("config_path", type=click.Path(exists=True))
 def preprocess(config_path):
     """Preprocess data from CONFIG_PATH."""
     preprocess_adata(config_path)
+
+
 ##########################################
 
+
 ####### Spatial ###########
 @cli.command()
 @click.argument("config_path", type=click.Path(exists=True))
 def spatial(config_path):
     """Process data from CONFIG_PATH."""
     spatial_adata(config_path)
+
+
 ##########################################
 
+
 ####### HMM ###########
 @cli.command()
 @click.argument("config_path", type=click.Path(exists=True))
 def hmm(config_path):
     """Process data from CONFIG_PATH."""
     hmm_adata(config_path)
+
+
 ##########################################
 
+
 ####### batch command ###########
 @cli.command()
 @click.argument(
@@ -125,7 +156,9 @@ def batch(task, config_table: Path, column: str, sep: str | None):
                     dtype=str,
                 )
             except Exception as e:
-                raise click.ClickException(f"Failed to read {config_table} as headerless list: {e}") from e
+                raise click.ClickException(
+                    f"Failed to read {config_table} as headerless list: {e}"
+                ) from e
 
             config_series = df[column]
         else:
@@ -136,12 +169,7 @@ def batch(task, config_table: Path, column: str, sep: str | None):
                 )
             config_series = df[column]
 
-        config_paths = (
-            config_series.dropna()
-            .map(str)
-            .map(lambda p: Path(p).expanduser())
-            .tolist()
-        )
+        config_paths = config_series.dropna().map(str).map(lambda p: Path(p).expanduser()).tolist()
 
     # ----------------------------
     # Validate config paths
@@ -162,9 +190,7 @@ def batch(task, config_table: Path, column: str, sep: str | None):
 
     func = task_funcs[task]
 
-    click.echo(
-        f"Running task '{task}' on {len(config_paths)} config paths from {config_table}"
-    )
+    click.echo(f"Running task '{task}' on {len(config_paths)} config paths from {config_table}")
 
     # ----------------------------
     # Loop over paths
@@ -177,13 +203,16 @@ def batch(task, config_table: Path, column: str, sep: str | None):
         click.echo(f"[{i}/{len(config_paths)}] {task} → {cfg}")
 
         try:
-            func(str(cfg))   # underlying functions take a string path
+            func(str(cfg))  # underlying functions take a string path
         except Exception as e:
             click.echo(f"  ERROR on {cfg}: {e}")
 
     click.echo("Batch processing complete.")
+
+
 ##########################################
 
+
 ####### concatenate command ###########
 @cli.command("concatenate")
 @click.argument(
@@ -269,166 +298,53 @@ def concatenate_cmd(
 
     except Exception as e:
         raise click.ClickException(str(e)) from e
+
+
 ##########################################
 
-####### 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
-################################################################################################################
+
+####### subsample pod5 command ###########
+@cli.command("subsample-pod5")
+@click.argument(
+    "pod5_path",
+    type=click.Path(exists=True, path_type=Path),
+)
+@click.option(
+    "--read-names",
+    "-r",
+    type=click.Path(exists=True, path_type=Path),
+    default=None,
+    help="Text file with one read_id per line.",
+)
+@click.option(
+    "--n-reads",
+    "-n",
+    type=int,
+    default=None,
+    help="Randomly subsample N reads.",
+)
+@click.option(
+    "--outdir",
+    "-o",
+    type=click.Path(path_type=Path, file_okay=False),
+    required=True,
+    help="Output directory for subsampled POD5.",
+)
+def subsample_pod5_cmd(pod5_path, read_names, n_reads, outdir):
+    """
+    Subsample POD5 file(s) by read ID list or random sampling.
+    """
+
+    # --- Validate mutually exclusive options ---
+    if (read_names is None and n_reads is None) or (read_names and n_reads):
+        raise click.UsageError("You must specify exactly ONE of --read-names or --n-reads.")
+
+    outdir.mkdir(parents=True, exist_ok=True)
+
+    subsample_arg = str(read_names) if read_names else n_reads
+
+    subsample_pod5(
+        pod5_path=str(pod5_path),
+        read_name_path=subsample_arg,
+        output_directory=str(outdir),
+    )

smftools/config/__init__.py

@@ -1 +1 @@
-from .experiment_config import LoadExperimentConfig, ExperimentConfig
+from .experiment_config import ExperimentConfig, LoadExperimentConfig

smftools/config/conversion.yaml

@@ -9,6 +9,10 @@ conversion_types:
 # Read QC Params
 read_mod_filtering_use_other_c_as_background: True
 
+# Spatial Analysis - Autocorr params
+autocorr_site_types:
+  - "GpC"
+
 # Spatial Analysis - Clustermap params
 layer_for_clustermap_plotting: 'nan0_0minus1'
 clustermap_cmap_c: "coolwarm"
@@ -42,4 +46,4 @@ hmm_feature_sets:
       cpg_patch: [0, inf]
 
 hmm_merge_layer_features:
-  - ["GpC_all_accessible_features", 80]
+  - ["all_accessible_features", 60]

smftools/config/deaminase.yaml

@@ -60,4 +60,4 @@ hmm_feature_sets:
       nucleosome_depleted_region: [110, inf]
 
 hmm_merge_layer_features:
-  - ["C_all_accessible_features", 80]
+  - ["all_accessible_features", 60]

smftools/config/default.yaml

@@ -1,7 +1,7 @@
 # General
 sample_sheet_path: null # path to sample_sheet to load metadata into anndata.
-sample_sheet_mapping_column: 'Barcode' # The column in the sample sheet and current anndata to use for mapping metadata.
-sample_name_col_for_plotting: 'Barcode'
+sample_sheet_mapping_column: 'Experiment_name_and_barcode' # The column in the sample sheet and current anndata to use for mapping metadata.
+sample_name_col_for_plotting: 'Experiment_name_and_barcode'
 
 # Compute params
 threads: 4
@@ -9,9 +9,7 @@ device: "auto"
 
 ######## smftools load params #########
 # Generic i/o
-bam_suffix: ".bam"
 recursive_input_search: True
-split_dir: "demultiplexed_BAMs"
 strands:
   - bottom
   - top
@@ -21,7 +19,7 @@ fastq_barcode_map: null # For FASTQ files, an optional map of file paths to barc
 fastq_auto_pairing: True # For FASTQ files, attempt to find read pair files automatically.
 input_already_demuxed: False # If the input files are already demultiplexed.
 delete_intermediate_hdfs: True # Whether to delete the intermediate hdfs from the conversion/deamination workflows.
-delete_intermediate_bams: False # Whether to delete intermediate BAM files.
+delete_intermediate_bams: True # Whether to delete intermediate BAM files.
 delete_intermediate_tsvs: True # Whether to delete intermediate TSV files.
 
 # Sequencing modality and general experiment params
@@ -53,7 +51,6 @@ aligner_args:
       - '-y'
       - '-N'
       - '5'
-      - '--secondary=no' 
     pacbio:
       - '-a'
       - '-x'
@@ -63,7 +60,6 @@ aligner_args:
       - '-y'
       - '-N'
       - '5'
-      - '--secondary=no' 
     illumina:
       - '-a'
       - '-x'
@@ -73,7 +69,6 @@ aligner_args:
       - '-y'
       - '-N'
       - '5'
-      - '--secondary=no'     
   dorado:
     ont:
       - "--mm2-opts"
@@ -88,9 +83,9 @@ barcode_both_ends: False # dorado demultiplexing
 trim: False # dorado adapter and barcode removal during demultiplexing
 
 # Anndata structure
-mapping_threshold: 0.01 # Minimum proportion of mapped reads that need to fall within a region to include in the final AnnData.
+mapping_threshold: 0.10 # Minimum proportion of mapped reads that need to fall within a region to include in the final AnnData.
 reference_column: 'Reference_strand'
-sample_column: 'Barcode'
+sample_column: 'Experiment_name_and_barcode'
 
 ######## smftools preprocess params #########
 # Read length, quality, and mapping filtering params
@@ -101,7 +96,7 @@ read_len_filter_thresholds:
   - 100
   - null
 read_len_to_ref_ratio_filter_thresholds:
-  - 0.5
+  - null
   - null
 read_quality_filter_thresholds:
   - 15
@@ -179,13 +174,12 @@ umap_layers_to_plot:
   - "Raw_modification_signal"
 
 # Spatial Analysis - Spatial Autocorrelation params
+autocorr_normalization_method: "pearson" # options are pearson or sum
 rows_per_qc_autocorr_grid: 6
 autocorr_rolling_window_size: 25
 autocorr_max_lag: 800
 autocorr_site_types:
   - "GpC"
-  - "CpG"
-  - "C"
 
 # Spatial Analysis - Correlation Matrix params
 correlation_matrix_types:
@@ -210,10 +204,19 @@ hmm_init_start_probs:
   - 0.5
   - 0.5
 hmm_eps: 1e-8
+# Fitting strategy
+hmm_fit_strategy: "per_group"      # "per_group" | "shared_transitions"
+hmm_shared_scope: ["reference", "methbase"]
+hmm_groupby: ["sample", "reference", "methbase"]
+# If hmm_fit_strategy == shared_transitions
+hmm_adapt_emissions: true
+hmm_adapt_startprobs: true
+hmm_emission_adapt_iters: 5
+hmm_emission_adapt_tol: 1.0e-4
 hmm_dtype: "float64"
-hmm_annotation_threshold: 0.5
-hmm_batch_size: 1024
-hmm_use_viterbi: False
+hmm_annotation_threshold: 0.5 # The minimum probability threshold of a feature interval to accept it for layer annotation.
+hmm_batch_size: 1024 # hmm batch size
+hmm_use_viterbi: False # Whether to use viterbi decoding. If False, uses forward-backward gammas. Viterbi is smoother, but less sensitive.
 footprints: True # whether to use the default HMM footprint params
 accessible_patches: True # whether to use the default HMM accessible patch params
 cpg: False # whether to use the default HMM endogenous CpG patch params
@@ -238,7 +241,7 @@ hmm_feature_sets:
       large_accessible_patch: [40, 110]
       nucleosome_depleted_region: [110, inf]
 hmm_merge_layer_features:
-  - [null, 80]
+  - ["all_accessible_features", 60]
 clustermap_cmap_hmm: "coolwarm"
 hmm_clustermap_feature_layers:
   - all_accessible_features
@@ -246,7 +249,9 @@ hmm_clustermap_feature_layers:
   - small_accessible_patch
   - mid_accessible_patch
   - large_accessible_patch
+  - large_accessible_patch_merged
   - nucleosome_depleted_region
+  - nucleosome_depleted_region_merged
   - small_bound_stretch
   - medium_bound_stretch
   - putative_nucleosome

smftools/config/direct.yaml

@@ -27,10 +27,10 @@ delete_batch_hdfs: True # Whether to delete intermediate barcode level hdfs afte
 
 ######## smftools preprocess params ########
 fit_position_methylation_thresholds: False # Whether to use Youden J-stat to determine position by positions thresholds for modification binarization.
-binarize_on_fixed_methlyation_threshold: 0.7 # The threshold used to binarize the anndata using a fixed value if fitting parameter above is False.
+binarize_on_fixed_methlyation_threshold: 0.5 # The threshold used to binarize the anndata using a fixed value if fitting parameter above is False.
 positive_control_sample_methylation_fitting: null # A positive control Sample_name to use for fully modified template data
 negative_control_sample_methylation_fitting: null # A negative control Sample_name to use for fully unmodified template data
-infer_on_percentile_sample_methylation_fitting: 10 # If a positive/negative control are not provided and fitting the data is requested, use the indicated percentile windows from the top and bottom of the dataset.
+infer_on_percentile_sample_methylation_fitting: 5 # If a positive/negative control are not provided and fitting the data is requested, use the indicated percentile windows from the top and bottom of the dataset.
 inference_variable_sample_methylation_fitting: "Raw_modification_signal" # The obs column value used for the percentile metric above.
 fit_j_threshold: 0.5 # The J-statistic threhold to use for determining which positions pass qc for mod detection thresholding
 output_binary_layer_name: "binarized_methylation" # The layer to store the binarized methylation data in
@@ -39,6 +39,11 @@ output_binary_layer_name: "binarized_methylation" # The layer to store the binar
 autocorr_site_types:
   - "A"
 
+spatial_clustermap_sortby: "a"
+
 ######## smftools hmm params #########
 hmm_methbases:
-  - "A"
+  - "A"
+
+hmm_merge_layer_features:
+  - ["A_all_accessible_features", 60]

smftools/config/discover_input_files.py

@@ -1,11 +1,14 @@
 from __future__ import annotations
 
 from pathlib import Path
-from typing import Dict, List, Any, Iterable, Union
+from typing import Any, Dict, List, Union
+
+from smftools.constants import BAM_SUFFIX
+
 
 def discover_input_files(
     input_data_path: Union[str, Path],
-    bam_suffix: str = ".bam",
+    bam_suffix: str = BAM_SUFFIX,
     recursive: bool = False,
     follow_symlinks: bool = False,
 ) -> Dict[str, Any]:
@@ -30,10 +33,21 @@ def discover_input_files(
     bam_suffix = bam_suffix.lower()
 
     # Sets of canonical extension keys we’ll compare against
-    pod5_exts  = {".pod5", ".p5"}
+    pod5_exts = {".pod5", ".p5"}
     fast5_exts = {".fast5", ".f5"}
-    fastq_exts = {".fastq", ".fq", ".fastq.gz", ".fq.gz", ".fastq.bz2", ".fq.bz2", ".fastq.xz", ".fq.xz", ".fastq.zst", ".fq.zst"}
-    h5ad_exts  = {".h5ad", ".h5"}
+    fastq_exts = {
+        ".fastq",
+        ".fq",
+        ".fastq.gz",
+        ".fq.gz",
+        ".fastq.bz2",
+        ".fq.bz2",
+        ".fastq.xz",
+        ".fq.xz",
+        ".fastq.zst",
+        ".fq.zst",
+    }
+    h5ad_exts = {".h5ad", ".h5"}
     compressed_exts = {".gz", ".bz2", ".xz", ".zst"}
 
     def ext_key(pp: Path) -> str: