minimizers 0.1.0

A Python package for extracting minimizers from sequence data

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.