Metadata-Version: 2.1
Name: fastafurious
Version: 1.2.5
Summary: Bundled utilities for manipulating and integrating FASTA files
Home-page: https://github.com/matt-sd-watson/FASTAfurious/
Author: Matthew Watson
Author-email: matthew.watson@uhn.ca
License: UNKNOWN
Project-URL: Issues, https://github.com/matt-sd-watson/FASTAfurious/issues
Project-URL: Source, https://github.com/matt-sd-watson/FASTAfurious
Description: # FASTAfurious
        [![PyPI version](https://badge.fury.io/py/fastafurious.svg)](https://badge.fury.io/py/fastafurious)
        ![example workflow](https://github.com/matt-sd-watson/FASTAfurious/actions/workflows/main.yml/badge.svg) \
        Bundled utilities for manipulation and integration of FASTA files
        
        FASTAfurious provides a set of utilities for the following routine FASTA modifications: 
        - creating a FASTA subset based on a list of sequence names (inclusion or exclusion)
        - printing statistics and filtering sequences based on genome completeness and length
        - renaming fasta headers based on a data sheet
        
        # Installation
        
        ```
        git clone https://github.com/matt-sd-watson/FASTAfurious.git && cd FASTAfurious
        conda env create -f environment.yml
        conda activate fastafurious
        pip install . 
        ```
        
        # Updating
        ```
        cd FASTAfurious && git pull
        pip install . 
        ```
        
        # Usage
        
        ```
        fastafurious -h
        usage: fastafurious [-h] {filter,composition,subset,rename,compare} ...
        
        fastafurious: Bundled utilities for manipulating and integrating FASTA files
        
        optional arguments:
          -h, --help            show this help message and exit
        
        subcommands:
          fastafurious provides a series of bundled functions to 
          easily manipulate and integrate FASTA FILES into routine 
          bioinformatics workflows
        
          {filter,composition,subset,rename,compare}
            filter              filter sequences in FASTA based on completeness and length
            composition         Print the composition statistics of FASTA sequences (completeness/length)
            subset              Create a FASTA subset based on a txt list or bash record input
            rename              Rename the headers of a fasta file based on the columns of a CSV file
            compare             Compare the header entries of two FASTA input files
            version             Print the current FASTAfurious version then exit.
        ```
        
        # Acknowledgments
        
        code for fastafurious subset was based on the python script originally written by santiagosnchez [here](https://github.com/santiagosnchez/faSomeRecords)
        
Platform: UNKNOWN
Description-Content-Type: text/markdown
