coolneng
/
adapter-parser
1
0
Fork 0
Code Issues Pull Requests Projects Releases Wiki Activity
12 Commits 1 Branch 0 Tags 66 KiB
Python 84.2%
Nix 15.8%
Go to file
coolneng e59683b925
Correct extract_adapters type hint 		2021-11-13 18:46:37 +01:00
.gitignore Add gitignore 2021-11-13 12:52:17 +01:00
LICENSE.md Initial commit 2021-11-13 12:46:53 +01:00
README.org Update README 2021-11-13 18:43:33 +01:00
flake.lock Add dependencies 2021-11-13 12:50:20 +01:00
flake.nix Initial commit 2021-11-13 12:46:53 +01:00
parser.py Correct extract_adapters type hint 2021-11-13 18:46:37 +01:00
shell.nix Implement HTML parsing and output to a file 2021-11-13 14:21:24 +01:00

README.org

Adapter parser

This tool parses fastqc reports to extract the adapter sequences, from the Overrepresented sequences, and then outputs them to a text file. It also outputs the mean and standard deviation of the sequences length.

Technologies

  • Pandas

Installation

This project uses Nix to ensure reproducible builds.

  1. Install Nix (compatible with MacOS, Linux and WSL):
curl -L https://nixos.org/nix/install | sh
  1. Clone the repository:
git clone https://git.coolneng.duckdns.org/coolneng/adapter-parser
  1. Change the working directory to the project:
cd adapter-parser
  1. Enter the nix-shell:
nix-shell

After running these commands, you will find yourself in a shell that contains all the needed dependencies.

Usage

The program expects a folder containing the fastqc reports as an input and an output file where to store the sequences in the FASTA format.

python src/parser.py <input> <output>

usage: parser.py [-h] input output

positional arguments:
  input       directory containing the fastqc reports
  output      file where to export the sequences

optional arguments:
  -h, --help  show this help message and exit