🦍 kirill: Yet another bioinformatics toolbox

Kirill is a command-line interface (CLI) application that provides a collection of tools for bioinformatics. This repository contains the source code and documentation for the application. Kirill currently consists of two commands: fetchpdb and flipalleles.

Installation

To install Kirill, you can download the source code from this repository and build the binary using the Go compiler. Make sure you have Go installed on your system.

git clone https://github.com/kirilledition/kirill.git
cd kirill
make build

This will create an executable binary named kirill in the kirill/build directory.

Usage

fetchpdb

fetchpdb is a command-line tool to download protein structures from the Protein Data Bank (PDB). It accepts a list of PDB IDs or an input file containing PDB IDs, one per line.

Example usage:

Download structures for a list of PDB IDs:

kirill fetchpdb 1abc 2def 3ghi

Download structures from an input file (each PDB ID on a separate line):

kirill fetchpdb pdb_ids.txt

Download structures from an input file and save them to a specific output directory:

kirill fetchpdb pdb_ids.txt -o /path/to/output

flipalleles

flipalleles is a command-line tool designed to process and modify genetic summary statistics data by flipping alleles and their corresponding effects according to a reference summary statistics file. The primary use case for this program is to harmonize the data from two separate summary statistics files, ensuring consistency in allele representation and effects direction.

This tool was developed to address issues encountered when using the METAL meta-analysis program, which flips alleles in its summary statistics file.

Example usage:

kirill flipalleles \
	--sumstats test_data/wrong_alleles.tsv \
	--sumstats-effect-allele Allele1 \
	--sumstats-other-allele Allele2 \
	--sumstats-snp MarkerName \
	--sumstats-effect Zscore \
	--effect-type BETA \
	--reference test_data/reference.tsv \
	--reference-effect-allele A1 \
	--reference-other-allele A2 \
	--reference-snp SNP \
	--output test_data/flipped.tsv

Contributing

Contributions to Kirill are welcome! If you would like to add new features or improve existing ones, please create a fork of this repository and submit a pull request.

kirilledition / kirill