FASTAfurious

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