Metadata-Version: 2.1
Name: fastafurious
Version: 1.2.1
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
Platform: UNKNOWN

FASTAfurious
============

| |PyPI version|
| 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

Acknowledgments
===============

code for fastafurious subset was based on the python script originally
written by santiagosnchez
`here <https://github.com/santiagosnchez/faSomeRecords>`__

.. |PyPI version| image:: https://badge.fury.io/py/fastafurious.svg
   :target: https://badge.fury.io/py/fastafurious


