A Python package for extracting minimizers from sequence data.
The package requires Python 3 and there are no constraints on the type of operating system.
It also requires the biopython package.
It can be installed with pip by typing the following command in your terminal:
pip install minimizers
Run minimizers --help for a list of available arguments:
usage: minimizers [-h] [-a] -i INPUT [-o OUTPUT] [-t {list,fasta}] -s SIZE -w
WINDOW [--report-counts] [--top-perc TOP_PERC]
[--top-num TOP_NUM] [-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)
-t {list,fasta}, --output-type {list,fasta}
The output can be formatted as a list of kmers or as a
fasta file (default: list)
-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)
--report-counts Report the frequencies of the minimizers. This is
compatible with "--output-type list" only (default:
False)
--top-perc TOP_PERC Report the top percentage of minimizers based on their
frequency (default: None)
--top-num TOP_NUM Report the top number of minimizers based on their
frequency (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.