geneutils

This tool was originally inspired by the work here for dealing with nucleotide sequences and more tools will be added as needed. This toolbox requires python 3 and can be installed.

Table of contents

• Installation
• geneutils cli tools
  • blasthit

Installation

This assumes that you have native python 3 & pip installed in your system, you can test this by going to the terminal (or windows command prompt) and trying

python and then pip list

If you get no errors and you have python 3 or higher you should be good to go. To install geneutils you can install using two methods

pip install geneutils

or you can also try

pip install geneutils --user

or you can also try

git clone https://github.com/samapriya/geneutils.git
cd geneutils
python setup.py install

Installation is an optional step; the application can be also run directly by executing pydrop.py script. The advantage of having it installed is being able to execute porg as any command line tool. I recommend installation within virtual environment. If you don't want to install, browse into the geneutils folder and try python geneutils.py -h to get to the same result.

geneutils cli tools

This is a command line tool and it is designed to simply call the tools you need.

blasthit

This script is intended for taxonomic annotation of blast results (blastn, tblastn, blastp or blastx) saved in Hit Table CSV format where GenBank accession numbers are in the 4th column. It uses efetch function from Bio.Entrez package to get information about accessions from GenBank Nucleotide (Nuccore) or Protein databases. The output is an annotated CSV file "*_annotated.csv" with the following columns added:

• Record name
• Species name
• Full taxonomy
• Reference
• Date of update