Counts to CSV

Writes the counts matrix in an AnnData file to a CSV file. The file must be an H5 or H5AD file, and it must have the CSR formatted counts matrix in /X/data.

Install as a Python package

Installation

You must have Rust installed. Instructions to install Rust are here: https://www.rust-lang.org/tools/install

You must have setuptools-rust. Install this package using pip install setuptools-rust.

Clone the repository by running git clone https://github.com/swemeshy/counts_to_csv.git in your terminal.

Then in the repository, run pip install -e . to install the Python package.

Arguments

This package has only one function, counts_to_csv, which has the following parameters:

adata: the AnnData object.

delimiter: delimiter for the CSV file. Possible options: comma, tab, colon, pipe, semicolon. Default is comma.

column_orient: orient the CSV file with var-names as column names or obs-names as column names. Possible options: var-names, obs-names. Default is var-names.

outfile: file path of the output CSV file. Default is out.csv.

Example Usage

>>> import scanpy as sc
>>> import counts_to_csv as ctc
>>> adata = sc.read('anndata.h5ad')
>>> ctc.counts_to_csv(adata, "comma", "obs-names", "anndata.csv")

Compile and use Rust binary

Installation

You must have Rust installed. Instructions to install Rust are here: https://www.rust-lang.org/tools/install

Clone the repository by running git clone https://github.com/swemeshy/counts_to_csv.git in your terminal.

Then in the repository, run cargo build --release. The compiled binary will be located here: target/release/counts_to_csv

For ease of running the binary, you can either

• Add the path to the binary to your PATH
• Move the binary to a folder on your PATH
• Create a bash alias in your startup file. For example, for UNIX users, you can add this to .bashrc:

alias counts_to_csv="/path/to/repo/target/release/counts_to_csv"

Make sure to reload your startup file!

Arguments

-f, --h5-file <h5-file>

file path of H5 file that must be readable as an AnnData, and must have the counts matrix in CSR format

-c, --column-orient <column-orient>

orient the CSV file with var-names as column names or obs-names as column names

-d, --delimiter <delimiter>

delimiter for the CSV file

-o, --outfile <outfile>

file path of the output CSV file