Bundled utilities for manipulating and integrating FASTA files
Project description
FASTAfurious
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
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