Parasail¶

parasail is a SIMD C (C99) library containing implementations of the Smith-Waterman (local), Needleman-Wunsch (global), and various semi-global pairwise sequence alignment algorithms.

Note

From StdEnv/2023 onwards, the parasail-python extension is bundled in the parasail module. However, with StdEnv/2020, the parasail module needs to be loaded for the Python extension to be installed in a virtual environment.

Usage¶

Find the required versions using

module spider parasail

and load the library using

module load parasail/2.6.2

parasail_aligner Example¶

When using the binary parasail_aligner, it is important to set the number of threads according to the number of cores allocated in our job. We can set it with

parasail_aligner -t ${SLURM_CPUS_PER_TASK:-1} ...

Python extension¶

The module contains bindings for multiple Python versions. To discover which are the compatible Python versions, run

module spider parasail/1.3.4

Usage¶

Load the required modules.

module load parasail/2.6.2 python/3.11 scipy-stack/2023b

Import parasail 1.3.4.
```
python -c "import parasail"
```

If the command displays nothing, the import was successful.

Example¶

Run a quick local alignment score comparison between BioPython and parasail.

Write the Python script: ```python tab="parasail-sw.py" import parasail from Bio.Align import PairwiseAligner

A = "ACGT" * 1000

parasail¶

matrix = parasail.matrix_create("ACGT", 1, 0) parasail_score = parasail.sw(A, A, 1, 1, matrix).score

biopython¶

bio_score = PairwiseAligner().align(A, A)[0].score

print('parasail:', parasail_score) print('biopython:', bio_score)

2. Write the job submission script:

=== "Default StdEnv"

    ```bash tab="submit-parasail.sh"
    #!/bin/bash
    #SBATCH --account=def-someuser  # replace with your PI account
    #SBATCH --cpus-per-task=1
    #SBATCH --mem-per-cpu=3G      # increase as needed
    #SBATCH --time=1:00:00

    module load parasail/2.6.2 python/3.11 scipy-stack/2023b

    # Install any other requirements, such as Biopython
    virtualenv --no-download $SLURM_TMPDIR/env
    source $SLURM_TMPDIR/env/bin/activate
    pip install --no-index --upgrade pip
    pip install --no-index biopython==1.83

    python parasail-sw.py
    ```

=== "StdEnv/2020"

    2.1. Identify available wheels first :
    ```bash
    avail_wheel parasail
    ```

    ```text
    name      version    python    arch
    --------  ---------  --------  -------
    parasail  1.2.4      py2,py3   generic
    ```

    Install the desired version in your virtual environment:
    ```bash tab="submit-parasail.sh"
    #!/bin/bash
    #SBATCH --account=def-someuser  # replace with your PI account
    #SBATCH --cpus-per-task=1
    #SBATCH --mem-per-cpu=3G      # increase as needed
    #SBATCH --time=1:00:00

    module load StdEnv/2020 gcc parasail/2.5 python/3.10

    # Install any other requirements, such as Biopython:
    virtualenv --no-download $SLURM_TMPDIR/env
    source $SLURM_TMPDIR/env/bin/activate
    pip install --no-index --upgrade pip
    pip install --no-index parasail==1.2.4 biopython==1.83

    python parasail-sw.py
    ```

3. Submit the job with
```bash
sbatch submit-parasail.sh

When the job has run, the output will be in the Slurm output file:
```
less slurm-*.out
```

parasail: 4000
biopython: 4000.0

Available Python packages¶

Other Python packages that depend on parasail will have their requirement satisfied by loading the parasail module:

pip list | grep parasail

```text parasail 1.3.4