60 lines
1.4 KiB
Org Mode
60 lines
1.4 KiB
Org Mode
* 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
|