A Python package for extracting minimizers from sequence data
Project description
minimizers
A Python package for extracting minimizers from sequence data.
Requirements
The package requires Python 3 and there are no constraints on the type of operating system.
It also requires the biopython package.
Install
It can be installed with pip
by typing the following command in your terminal:
pip install minimizers
How to use it
Run minimizers --help
for a list of available arguments:
usage: minimizers [-h] [-a] -i INPUT [-o OUTPUT] -s SIZE -w WINDOW [-n NPROC] [--verbose] [-v]
Extract the set of minimizers from a sequence file
optional arguments:
-h, --help show this help message and exit
-a, --aggregate Aggregate record results (default: False)
-i INPUT, --input INPUT
Path to the input sequence file in fasta format. It can be Gzip compressed (default: None)
-o OUTPUT, --output OUTPUT
Path to the output file with minimizers. Results are printed on the stdout if no output is provided (default: None)
-s SIZE, --size SIZE Length of the minimizers (default: None)
-w WINDOW, --window WINDOW
Size of the sliding window. It must be greater than the minimizer size (default: None)
-n NPROC, --nproc NPROC
Make it parallel (default: 1)
--verbose Print messages on the stdout (default: False)
-v, --version Print the "minimizers" version and exit
Copyright © 2022 Fabio Cumbo. See LICENSE for additional details.
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