Parasail/en

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

1. Load the required modules.

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

2. 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.

1. Write the Python script:

   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 StdEnvStdEnv/2020

   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
   

   2.1. Identify available wheels first:

   avail_wheel parasail
   

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

   Install the desired version in your virtual environment:

   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

   sbatch submit-parasail.sh
   

4. 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