tool-make-aligned-dataset

This repository provides a Python script for creating a dataset with aligned sequences from a dataset with unaligned sequences. Alignment is performed using mafft.

Prerequisites

1. Install conda or mamba. If using mamba, replace instances of conda below with mamba.

Instructions

1. Create a conda environment with the necessary dependencies.

   a. If you are using Linux or a non-Apple Silicon based Mac, run

   conda env create -n tool-make-aligned-dataset -f environment.yml
   

   Proceed to Step 2.

   b. Otherwise (e.g. using Windows without WSL or an Apple Silicon based Mac), run

   conda env create -n tool-make-aligned-dataset -f environment-no-mafft.yml
   

   Next, install mafft. For Apple Silicon, you can simply run brew install mafft. For Windows, follow the instructions on the mafft website.

   Proceed to Step 2.

2. Activate the conda environment

   conda activate tool-make-aligned-dataset
   

3. Run the make_aligned_dataset.py script on your dataset:

   python make_aligned_dataset.py \
       --dataset <path-to-dataset> \
       --sequence_column_name <name-of-column-with-sequences>
   

   The dataset must be in csv format. Remember to replace the values in angle brackets <>!

   The script will output a file with the aligned dataset and the name of the file will be the name of the input file with _aligned appended to it. The file will be located in the same directory as the input file.

Example

1. The file example_dataset.csv contains an example dataset of unaligned sequences (the data is made up). The name of the column containing sequences is sequence, and the dataset contains three sequences and measurements for three properties. We run the following command to create an aligned version of this dataset:

    python make_aligned_dataset.py \
        --dataset example_dataset.csv \
        --sequence_column_name sequence
   

2. This should create a file called example_dataset_aligned.csv which contains the aligned dataset i.e. everything the same as the original dataset file except that the sequences in the sequence column are now aligned sequences.