Parasail: Difference between revisions

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[https://github.com/jeffdaily/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.

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|Starting from StdEnv/2023, parasail python extension is now bundled in the module parasail. As for 2020, the module needs to be loaded in order for the python extension to be installed in a virtual environment.

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One can find the available version using  

{{Command|module spider parasail}}

and load the library using

{{Command|module load parasail/2.6.2}}

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

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The module contains bindings for multiple Python versions.  

To discover which are the compatible Python versions, run

{{Command|module spider parasail/1.3.4}}

1. Load the required modules.

{{Command|module load parasail/2.6.2 python/3.11 scipy-stack/2023b}}

2. Import parasail 1.3.4.

{{Command|python -c "import parasail"}}

If the command displays nothing, the import was successful.

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

1. Write the python script:

{{File

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. And the job submission script:

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#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

pip install --no-index biopython==1.83

python parasail-sw.py

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{{Command|avail_wheel parasail}}

Then install the desired version in your virtual environment:

{{File

#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

pip install --no-index parasail==1.2.4 biopython==1.83

python parasail-sw.py

}}

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3. Then submit the job with

{{Command

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4. The output will be in the slurm output file, once the job has run:

{{Command

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Other Python packages that depend on parasail will have their requirement satisfied with the module loaded:

{{Command