cpsnpic¶
This module implements the cpSNP-IC calculation pipeline, exposing both a Click CLI group and Python-callable wrappers.
CLI Commands¶
oddSNP cpsnpic¶
Usage
oddSNP cpsnpic [OPTIONS] COMMAND [ARGS]...
calculate-cpsnpic¶
- Calculate the cpSNP-IC for pairs of cells. Returns the name of the file
where the DataFrame with the cpSNP-IC counts per cell pair is stored.
Arguments:
- INPATH: Path to the folder containing pileup related files. The folder should
contain at least the following files:
cellSNP.samples.tsv,cellSNP.tag.AD/DPandOTHmatricesOUPATH: Path to the output folder where results will be saved.
Usage
oddSNP cpsnpic calculate-cpsnpic [OPTIONS] INPATH OUPATH
Options
- --nproc <nproc>¶
Number of parallel processes to use
- --batch_size <batch_size>¶
Number of cell pairs to process in each batch.
- --force¶
Override target file.
Arguments
- INPATH¶
Required argument
- OUPATH¶
Required argument
generate-histogram¶
Generate a histogram of cpSNP-IC values from a cpSNP-IC counts file. Returns the name of the file where the histogram DataFrame is stored.
Arguments:
CPFILE: Path to the cpSNP-IC counts file (pkl.gz) generated by calculate_cpsnpic.
OUPATH: Path to the folder where to store the histogram file.
Usage
oddSNP cpsnpic generate-histogram [OPTIONS] CPFILE OUPATH
Options
- --force¶
Override target file.
Arguments
- CPFILE¶
Required argument
- OUPATH¶
Required argument
run-all¶
Run all cpSNP-IC calculation steps.
Arguments:
- INPATH: Path to the folder containing pileup related files. The folder should
contain at least the following files: cellSNP.samples.tsv, cellSNP.tag.AD/DP and OTH matrices
OUPATH: Path to the output folder where results will be saved.
Usage
oddSNP cpsnpic run-all [OPTIONS] INPATH OUPATH
Options
- --nproc <nproc>¶
Number of parallel processes to use
- --batch_size <batch_size>¶
Number of cell pairs to process in each batch.
- --force¶
Override target files.
Arguments
- INPATH¶
Required argument
- OUPATH¶
Required argument
save-cpsnpic-plot¶
Save a cpSNP-IC histogram figure
Arguments:
HISTOFILE The file where histogram data is stored
OUTPUT The output file where to save the figure (with extension .html)
Usage
oddSNP cpsnpic save-cpsnpic-plot [OPTIONS] HISTOFILE OUTPUT
Options
- --force¶
Override target file.
Arguments
- HISTOFILE¶
Required argument
- OUTPUT¶
Required argument
Python API¶
- oddSNP.cpsnpic.call_calculate_cpsnpic(inpath, oupath, nproc, batch_size, force)[source]¶
Python API wrapper for
calculate_cpsnpic().- Parameters:
inpath – Path to the folder containing pileup related files. The folder should contain at least the following files:
cellSNP.samples.tsv,cellSNP.tag.AD/DPandOTHmatricesoupath – Path to the output folder where results will be saved.
nproc – Number of parallel processes to use
batch_size – Number of cell pairs to process in each batch.
force – If
True, override the target file.
- oddSNP.cpsnpic.call_generate_histogram(cpfile, oupath, force)[source]¶
Python API wrapper for
generate_histogram().- Parameters:
cpfile – Path to the cpSNP-IC counts file (pkl.gz)
oupath – Path to the folder where to store the histogram file
force – If
True, override the target file.
- oddSNP.cpsnpic.call_run_all(inpath, oupath, nproc, batch_size, force)[source]¶
Python API wrapper for
run_all().- Parameters:
inpath – Path to the folder containing pileup related files.
oupath – Path to the output folder where results will be saved.
nproc – Number of parallel processes to use.
batch_size – Number of cell pairs to process in each batch.
force – If
True, override target files.