snpic¶

This module implements the SNP-IC calculation pipeline, exposing both a Click CLI group and Python-callable wrappers.

CLI Commands¶

oddSNP snpic¶

Usage

oddSNP snpic [OPTIONS] COMMAND [ARGS]...

calculate-snpic¶

Computes the SNP Information Content (SNP-IC) for each cell based on the pileup output of cellSNP and saves the per-cell counts to a compressed pickle file. Results are stored in snpic_counts.pkl.gz under OUPATH.

Arguments:

INPATH: Path to the folder containing cellSNP output files. Must contain cellSNP.samples.tsv, cellSNP.tag.AD.mtx, cellSNP.tag.DP.mtx, and cellSNP.tag.OTH.mtx.

OUPATH: Path where the SNP-IC counts will be saved

Usage

oddSNP snpic calculate-snpic [OPTIONS] INPATH OUPATH

Options

--force¶: Override target file.

Arguments

INPATH¶: Required argument

OUPATH¶: Required argument

estimate-donor-assignment¶

Estimate donor assignment for each barcode based on SNP-IC values.

Arguments:

BARCODES: Path to the list of barcodes to be assigned

AGFILE: Path to the SNP-IC counts file (pkl.gz) generated by calculate_snpic.

OUPATH: Path to the folder where to store the resulting bars file

N: Number of donors (ex: 5) or List of probabilities (ex: [0.1,0.3,0.4,0.2] - no spaces).

Usage

oddSNP snpic estimate-donor-assignment [OPTIONS] BARFILE AGFILE OUPATH N

Options

--seed <seed>¶: Seed used for reproducible results.

--force¶: Override target files

Arguments

BARFILE¶: Required argument

AGFILE¶: Required argument

OUPATH¶: Required argument

N¶: Required argument

generate-histogram¶

Generate a histogram of SNP-IC values from a SNP-IC counts file. Returns the name of the file where the histogram DataFrame is stored.

Arguments:

AGFILE: Path to the SNP-IC counts file (pkl.gz) generated by calculate_snpic.

OUPATH: Path to the folder where to store the histogram file.

Usage

oddSNP snpic generate-histogram [OPTIONS] AGFILE OUPATH

Options

--force¶: Override target file.

Arguments

AGFILE¶: Required argument

OUPATH¶: Required argument

run-all¶

Full SNP-IC calculation pipeline.

Arguments:

INPATH: Path to the folder containing cellSNP output files. The folder
should contain at least the following files: cellSNP.samples.tsv, cellSNP.tag.AD.mtx, cellSNP.tag.DP.mtx, and cellSNP.tag.OTH.mtx.

OUPATH: Path to the output folder where all results will be stored.

Usage

oddSNP snpic run-all [OPTIONS] INPATH OUPATH

Options

--force¶: Override target files.

Arguments

INPATH¶: Required argument

OUPATH¶: Required argument

save-donor-estimation-plot¶

Save a donor estimation plot

Arguments:

BARFILE: Path to the bar definitions file (pkl) generated by the
estimate_donor_assignment function

OUTPUT: Path to the output file where to save the figure

Usage

oddSNP snpic save-donor-estimation-plot [OPTIONS] BARFILE OUTPUT

Options

--force¶: Override target file.

Arguments

BARFILE¶: Required argument

OUTPUT¶: Required argument

save-snpic-plot¶

Save a SNP-IC histogram plot.

Arguments:

HISTOFILE: Path to the SNP-IC histogram file (pkl) generated by generate_histogram.

OUTPUT: Path to the output file where to save the figure (should end with .html).

Usage

oddSNP snpic save-snpic-plot [OPTIONS] HISTOFILE OUTPUT

Options

--force¶: Override target file.

Arguments

HISTOFILE¶: Required argument

OUTPUT¶: Required argument

Python API¶

oddSNP.snpic.call_calculate_snpic(inpath, oupath, force)[source]¶

Python API wrapper for calculate_snpic().

Parameters:

inpath – Path to the folder containing cellSNP output files. Must contain cellSNP.samples.tsv, cellSNP.tag.AD.mtx, cellSNP.tag.DP.mtx, and cellSNP.tag.OTH.mtx.
oupath – Path where the SNP-IC counts will be saved.
force – If True, overrides any existing output file.

Returns:

Path to snpic_counts.pkl.gz.

Return type:

pathlib.Path

oddSNP.snpic.call_estimate_donor_assignment(barfile, agfile, oupath, n, seed=None, force=False)[source]¶

Python API wrapper for estimate_donor_assignment()

Parameters:

barfile (str) – Path to the list of barcodes to be assigned
agfile (str) – Path to the SNP-IC counts file (pkl.gz) generated by calculate_snpic
oupath (str) – Path to the folder where to store the resulting bars file
n (int or list) – Number of donors or list of probabilities
seed (int, optional) – Seed used for reproducible results
force (bool) – Override target files

Returns:

Path to the generated bars file

Return type:

Path

oddSNP.snpic.call_generate_histogram(agfile, oupath, force)[source]¶

Python API wrapper for generate_histogram().

Parameters:

agfile – Path to the SNP-IC counts file (pkl.gz) generated by calculate_snpic.
oupath – Path to the folder where to store the histogram file.
force – If True, overrides any existing output file.

Returns:

Path to the generated histogram file.

Return type:

pathlib.Path

oddSNP.snpic.call_run_all(inpath, oupath, force)[source]¶

Python API wrapper for run_all().

Parameters:

inpath – Path to the folder containing cellSNP output files. The folder should contain at least the following files: cellSNP.samples.tsv, cellSNP.tag.AD.mtx, cellSNP.tag.DP.mtx, and cellSNP.tag.OTH.mtx.
oupath – Path to the output folder where all results will be stored.
force – If True, overrides any existing output files.

oddSNP.snpic.call_save_donor_estimation_plot(barfile, output, force)[source]¶

Python API wrapper for save_donor_estimation_plot()

Parameters:

barfile (str) – Path to the bar definitions file (pkl) generated by the estimate_donor_assignment function
output (str) – Path to the output file where to save the figure
force (bool) – Override target file

oddSNP.snpic.call_save_snpic_plot(histofile, output, force)[source]¶

Python API wrapper for save_snpic_plot().

Parameters:

histofile – Path to the SNP-IC histogram file (pkl) generated by generate_histogram.
output – Path to the output file where to save the figure (should end with .html).
force – If True, overrides any existing output file.

Returns:

Path to the generated figure file.

Return type:

pathlib.Path