adapter-parser/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 [[https://nixos.org][Nix]] to ensure reproducible
builds.

1.  Install Nix (compatible with MacOS, Linux and
    [[https://docs.microsoft.com/en-us/windows/wsl/about][WSL]]):

#+begin_src bash
curl -L https://nixos.org/nix/install | sh
#+end_src

2.  Clone the repository:

#+begin_src bash
git clone https://git.coolneng.duckdns.org/coolneng/adapter-parser
#+end_src

3.  Change the working directory to the project:

#+begin_src bash
cd adapter-parser
#+end_src

4.  Enter the nix-shell:

#+begin_src bash
nix-shell
#+end_src

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.

#+begin_src bash
python src/parser.py <input> <output>
#+end_src

#+RESULTS:
:
: 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