Command-line tool for manipulating and displaying commonly used bioinformatic file formats.
Using virtualenv
First, create a new virtual environment in the desired location, e.g.:
python -m venv ~/venv/cats
Activate the virtual environment and install the required dependencies:
. ~/venv/cats/bin/activate
pip install biopython bcbio-gff
Next, clone and install cats:
git clone https://github.com/khughitt/cats
cd cats
pip install .
Using conda
No recipe for cats itself exists yet, but you can still use conda to easily isolate cats and install the necessary dependencies.
mamba is used in place of conda below, as it is usually faster when it comes to dependency resolution and downloads:
mamba create -n cats --file requirements.txt
mamba activate cats
git clone https://github.com/khughitt/cats
cd cats
pip install .
Basic usage:
cats <input file>
Some more examples:
cats --translate -translations-offset -1 sample.fasta
cats -t -n sample.fasta
cats -w 80 sample.fasta
cats --stop-codons 80 sample.fasta
You can also pipe the output into less to page through output:
cats sample.fasta | less
Or grep for an interesting feature and pipe the output into cats:
grep --color='always' "AAUAA" input.fastq | cats
Gzipped files are also supported, using zgrep:
zgrep --color='always' "AAAAA$" input.fastq.gz | cats
To run the tests included with cats, install pytest in the
environment you install cats in run pytest from within the cloned cats repo directory.