A Snakemake workflow to get gene and protein information for different locus tags. This workflow produces a html report which displays different gene ID's, the gene description, the GC percentage and the sequence of the different genes.
These instructions will get you a copy of the project up and running on your local machine for development and testing purposes. See deployment for notes on how to deploy the project on a live system.
To run this workflow, this software needs to be installed:
If you don't use got Linux or MacOS X, you can setup a Linux virtual machine with Vagrant.
To install Vagrant:
> vagrant init hashicorp/precise64
> vagrant up
Install Miniconda 3
$ wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
$ bash Miniconda3-latest-Linux-x86_64.sh
After installing Miniconda 3 this git repository needs to be cloned.
$ git clone https://github.com/ALuesink/Workflow_Course11.git
Create a snakemake environment:
$ conda env create --name {name-environment} --file environment.yaml
$ source activate {name-environment}
$ source deactivate
To run the workflow:
$ snakemake report.html
The workflow exists of 8 rules. Below an overview of the workflow is shown.
| Rule | Description |
|---|---|
| open_file | opens a text file to retrieve all the locus tags |
| get_PMIDs | uses Biopython to retrieve PMIDs for the locus tags |
| gene_info | gets gene info from NCBI |
| seq_gc | gets the sequence and GC percentage of the gene |
| visualise | visualizes the GC percentage in a barplot |
| gen_ids | retrieves IDs of different databases of the genes |
| uniprot_info | gets Uniprot info of the genes |
| report | combines gene information in a html report |
| all | runs all rules |