60 lines
1.3 KiB
Org Mode
60 lines
1.3 KiB
Org Mode
* Adapter parser
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This tool parses fastqc reports to extract the adapter sequences, from the *Overrepresented sequences*, and then outputs them to a text file.
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** Technologies
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- Pandas
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** Installation
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This project uses [Nix](https://nixos.org/) to ensure reproducible
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builds.
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1. Install Nix (compatible with MacOS, Linux and
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[WSL](https://docs.microsoft.com/en-us/windows/wsl/about)):
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#+begin_src bash
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curl -L https://nixos.org/nix/install | sh
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#+end_src
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2. Clone the repository:
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#+begin_src bash
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git clone https://git.coolneng.duckdns.org/coolneng/adapter-parser
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#+end_src
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3. Change the working directory to the project:
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#+begin_src bash
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cd adapter-parser
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#+end_src
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4. Enter the nix-shell:
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#+begin_src bash
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nix-shell
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#+end_src
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After running these commands, you will find yourself in a shell that
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contains all the needed dependencies.
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** Usage
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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.
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#+begin_src bash
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python src/parser.py <input> <output>
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#+end_src
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#+RESULTS:
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:
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: usage: parser.py [-h] input output
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:
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: positional arguments:
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: input directory containing the fastqc reports
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: output file where to export the sequences
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:
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: optional arguments:
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: -h, --help show this help message and exit
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