Command-line interface#
smftools#
Command-line interface for smftools.
.. program:: smftools .. rubric:: Usage
.. code-block:: shell
smftools [OPTIONS] COMMAND [ARGS]...
.. rubric:: Options
.. option:: --version
Show the version and exit.
.. option:: --log-file <log_file>
Optional file path to write smftools logs.
.. option:: --log-level <log_level>
Logging level for smftools output.
:default: ``'INFO'``
:options: CRITICAL | ERROR | WARNING | INFO | DEBUG
batch#
Run a TASK (load, preprocess, spatial, variant, hmm) on multiple CONFIG_PATHs listed in a CSV/TSV or plain TXT file.
Plain text format: one config path per line, no header.
.. program:: smftools batch .. rubric:: Usage
.. code-block:: shell
smftools batch [OPTIONS] {load|preprocess|spatial|variant|hmm} CONFIG_TABLE
.. rubric:: Options
.. option:: -c, --column
Column name containing config paths (ignored for plain TXT).
:default: ``'config_path'``
.. option:: --sep
Field separator: default auto-detect (.tsv -> '\t', .csv -> ',', others treated as TXT).
.. rubric:: Arguments
.. option:: TASK
Required argument
.. option:: CONFIG_TABLE
Required argument
chimeric#
Finding putative PCR chimeras
.. program:: smftools chimeric .. rubric:: Usage
.. code-block:: shell
smftools chimeric [OPTIONS] CONFIG_PATH
.. rubric:: Arguments
.. option:: CONFIG_PATH
Required argument
concatenate#
Concatenate multiple .h5ad files into a single output file.
Reads concatenation parameters from an experiment config CSV. Input source (directory or CSV of paths) is configured via concatenate_input_dir / concatenate_csv_path in the config, or overridden with --input-dir / --csv-path.
Output path is auto-detected from the pipeline stage of the input filenames (e.g. *_variant.h5ad → variant output directory). Use --output-path to override.
Example:
smftools concatenate experiment_config.csv
smftools concatenate experiment_config.csv --recompute-pp-vars
smftools concatenate experiment_config.csv --input-dir ./variant_h5ads/
.. program:: smftools concatenate .. rubric:: Usage
.. code-block:: shell
smftools concatenate [OPTIONS] CONFIG_PATH
.. rubric:: Options
.. option:: --recompute-pp-vars
Recompute calculate_coverage and append_base_context after concatenation.
.. option:: -d, --input-dir <input_dir>
Override concatenate_input_dir from config.
.. option:: -c, --csv-path <csv_path>
Override concatenate_csv_path from config.
.. option:: -o, --output-path <output_path>
Explicit output path (overrides stage auto-detection).
.. rubric:: Arguments
.. option:: CONFIG_PATH
Required argument
full#
Workflow: load preprocess spatial variant chimeric hmm latent
.. program:: smftools full .. rubric:: Usage
.. code-block:: shell
smftools full [OPTIONS] CONFIG_PATH
.. rubric:: Arguments
.. option:: CONFIG_PATH
Required argument
hmm#
HMM feature annotations and plotting
.. program:: smftools hmm .. rubric:: Usage
.. code-block:: shell
smftools hmm [OPTIONS] CONFIG_PATH
.. rubric:: Arguments
.. option:: CONFIG_PATH
Required argument
latent#
Latent representations of signal
.. program:: smftools latent .. rubric:: Usage
.. code-block:: shell
smftools latent [OPTIONS] CONFIG_PATH
.. rubric:: Arguments
.. option:: CONFIG_PATH
Required argument
load#
Load raw data into AnnData.
.. program:: smftools load .. rubric:: Usage
.. code-block:: shell
smftools load [OPTIONS] CONFIG_PATH
.. rubric:: Arguments
.. option:: CONFIG_PATH
Required argument
plot-current#
Plot nanopore current traces for specified reads.
.. program:: smftools plot-current .. rubric:: Usage
.. code-block:: shell
smftools plot-current [OPTIONS] CONFIG_PATH
.. rubric:: Arguments
.. option:: CONFIG_PATH
Required argument
preprocess#
Preprocessing.
.. program:: smftools preprocess .. rubric:: Usage
.. code-block:: shell
smftools preprocess [OPTIONS] CONFIG_PATH
.. rubric:: Arguments
.. option:: CONFIG_PATH
Required argument
spatial#
Spatial signal analysis
.. program:: smftools spatial .. rubric:: Usage
.. code-block:: shell
smftools spatial [OPTIONS] CONFIG_PATH
.. rubric:: Arguments
.. option:: CONFIG_PATH
Required argument
subsample-pod5#
Subsample POD5 file(s) by read ID list or random sampling.
.. program:: smftools subsample-pod5 .. rubric:: Usage
.. code-block:: shell
smftools subsample-pod5 [OPTIONS] POD5_PATH
.. rubric:: Options
.. option:: -r, --read-names <read_names>
Text file with one read_id per line.
.. option:: -n, --n-reads <n_reads>
Randomly subsample N reads.
.. option:: -o, --outdir
**Required** Output directory for subsampled POD5.
.. rubric:: Arguments
.. option:: POD5_PATH
Required argument
variant#
Sequence variation analyses
.. program:: smftools variant .. rubric:: Usage
.. code-block:: shell
smftools variant [OPTIONS] CONFIG_PATH
.. rubric:: Arguments
.. option:: CONFIG_PATH
Required argument