/catch_and_kill

Simple utility to find and merge the metrics summary files from Cellranger for multiple samples

Primary LanguagePython

catch_and_kill

Utility script to gather and merge the CellRanger metrics summary files from cellranger-atac count or cellranger-multi count

CLI

Usage:

$ [OPTIONS] COMMAND [ARGS]...

Options:

  • --install-completion: Install completion for the current shell.
  • --show-completion: Show completion for the current shell, to copy it or customize the installation.
  • --help: Show this message and exit.

Commands:

  • atac-metrics: Find the 'summary.csv' files for the...
  • count-metrics: Find the 'metrics_summary.csv' files for...
  • find-and-rename: Find all of the web_summary files created...
  • version: Prints the version of the package.

atac-metrics

Find the 'summary.csv' files for the output from cellranger-atac for multiple samples that are organized under a single directory.

Usage:

$ atac-metrics [OPTIONS] ACCESS_FOLDER OUTPUT

Arguments:

  • ACCESS_FOLDER: Path to the parent folder under which the scATAC-seq count folder for each sample are [required]
  • OUTPUT: Path to where the compiled report should be written [required]

Options:

  • --version: Print version number.
  • --help: Show this message and exit.

count-metrics

Find the 'metrics_summary.csv' files for the output from cellranger-count and -multi for multiple samples that are organized under a single directory.

Usage:

$ count-metrics [OPTIONS] COUNT_FOLDER OUTPUT

Arguments:

  • COUNT_FOLDER: [required]
  • OUTPUT: [required]

Options:

  • --version: Print version number.
  • --help: Show this message and exit.

find-and-rename

Find all of the web_summary files created by cellranger count/multi or cellranger-atac count that are present in sample subdirectories organized under a single parent and then more and rename the files

Usage:

$ find-and-rename [OPTIONS]

Options:

  • --counts PATH: Parent directory containing sample cellranger output subdirectories [required]
  • --prefix TEXT: Prefix common among sample names. [required]
  • -p, --pattern TEXT: Regular expression to match the sample name/numbers after the sample_prefix [default: ([0-9]{2})]
  • --output PATH: Path to where files should be moved
  • -a, --type [scRNAseq|scATACseq]: Type of assay performed, either scRNAseq or scATACseq.
  • -d, --dry_run: Do not actually rename files but show what will be renamed
  • --version: Print version number.
  • --help: Show this message and exit.

version

Prints the version of the package.

Usage:

$ version [OPTIONS]

Options:

  • --value / --no-value: [default: value]
  • --help: Show this message and exit.