Metadata-Version: 2.1
Name: minimizers
Version: 0.1.2
Summary: A Python package for extracting minimizers from sequence data
Home-page: http://github.com/cumbof/minimizers
Author: Fabio Cumbo
Author-email: fabio.cumbo@gmail.com
License: MIT
Download-URL: https://pypi.org/project/minimizers/
Project-URL: Issues, https://github.com/cumbof/minimizers/issues
Project-URL: Source, https://github.com/cumbof/minimizers
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](https://pypi.org/project/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] [-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](https://github.com/cumbof). See [LICENSE](https://github.com/cumbof/minimizers/blob/main/LICENSE) for additional details.
        
Keywords: bioinformatics,minimizers,sketches
Platform: UNKNOWN
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.6
Description-Content-Type: text/markdown
