How to install bio

bio works on Linux and Mac computers and on Windows when using the Linux Subsystem.

Contact information

If you are reporting a bug please open an issue below:

If you have other questions/suggestions on how to use bio use the discussion board:

Installation

Installation:

pip install bio --upgrade

Some tasks (bio taxon, bio explain) need access to additional data. Install the required databases with:

bio --download

To execute a batch of tests run

bio test

Tests depend on the availability of a number of online services. Some test fail whenever the corresponding remote data service is unavailable. Connection problems are typically corrected within a short period of time.

Usage

Type bio followed by a task (fasta, gff, taxon) then followed by one or more flags or options.

bio fetch NC_045512 > genome.gb
bio fasta genome.gb
bio gff genome.gb --type CDS
bio taxon 2697049 --lineage

Getting help

You can get help on any command by just entering it

bio 
bio fasta
bio taxon

each line above will print a help on the task usage.

Use the discussion board for other questions:

Tasks

Tasks will have separate help pages that are shown when the command is run with no parameters (or using the -h flag)