Pycashier
Tool for extracting and processing DNA barcode tags from Illumina sequencing.
Default parameters are designed for use by the Brock Lab to process data generated from ClonMapper lineage tracing experiments, but is extensible to other similarly designed tools.
Documentation
See the documentation for more in-depth installation and usage instructions.
Getting Started
Installation
Conda
You may use
conda,
mamba, or
micromamba
to install pycashier and it's runtime dependencies.
micromamba install bioconda::cutadapt bioconda::fastp bioconda::pysam bioconda::starcode conda-forge::pycashier
You can also use the included env.yml to create your environment and install everything you need.
wget https://raw.githubusercontent.com/brocklab/pycashier/main/conda/env.yml
micromamba create -f env.yml
micromamba activate cashierenv
Additionally, you may use pixi to install and use pycashier.
pixi init --channel conda-forge --channel bioconda myproject
cd myproject
pixi add pycashier starcode pysam cutadapt fastp
pixi shell
Docker
If you prefer to use use docker you can use the below command.
docker run --rm -it -v $PWD:/data -u $(id -u):$(id -g) ghcr.io/brocklab/pycashier
[!NOTE] You should specify a version tag with the image for better reproducibility for example,
ghrc.io/brocklab/pycashier:v2024.1001.
Usage
To extract barcodes from targeted sequencing data:
pycashier extract -i fastqs -o outs
To combine data from multiple samples and compute basic overlap metrics:
pycashier receipt -i outs -o combined.tsv
See pycashier --help and pycashier SUBCMD --help for additional subcommands and options.
Pycashier is open source and licensed under the MIT License.
1 maintainer
Release files for pycashier 2024.1007
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| pycashier-2024.1007.tar.gz | 268.2 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| pycashier-2024.1007-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 296.0 kB
Release files / pycashier-2024.1007.tar.gz
| Download URL | pycashier-2024.1007.tar.gz |
|---|---|
| Size | 268.2 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
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Release files / pycashier-2024.1007-py3-none-any.whl
| Download URL | pycashier-2024.1007-py3-none-any.whl |
|---|---|
| Size | 27.8 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
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Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
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