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
  • init
  • 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

To upgrade to a new version from old you can try

pip install geneutils --upgrade

or

pip install geneutils --user --upgrade

or you can also try

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

Though there is a conda installer for linux/mac for geneutils

conda install -c samapriya geneutils

The recommended way would be to use the conda environment/terminal and then do a pip install geneutils

Installation is an optional step; the application can be also run directly by executing geneutils.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.

init

Turns out there are benefits of registering for a NCBI account and to use your email address and your API key. Apart from NCBI having a way of contacting you, the API key raises the rate limit imposed on your queries. This is a recommended step and a user should not skip thought it is possible to use the blashit tool without the API key. From the NCBI account page you can find this information

E-utils users are allowed 3 requests/second without an API key. Create an API key to increase your e-utils limit to 10 requests/second......Only one API Key per user. Replacing or deleting will inactivate the current key. Use this key by passing it with api_key=API_KEY parameter.

Generate your API Key

The init tool saves your email address and API key to be saved in your local machine which can be used instead of typing out your email over and over again. The API key is a clear entry meaning you cannot see when you type in or paste your API key for safety.

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

arguments	description
path	Pathway to csv-formatted Hit Table file with blastn results. Positional argument
db	For the output of nucleotide blast or tblastn, use n. For the output of protein blast or blastx, use p. Positional argument
email	Your NCBI email. Optional argument
-h, --help	Show help message and exit. Optional argument

Changelog

0.0.6

• Dedupes accession ids & remove empty rows
• Subset handling is cleaner and better error handling with try except blocks
• general code improvements to run style and functionality
• performance improvements to overall runtime

0.0.5

• Fixed issue with empty rows
• Includes version check
• general code cleanup

0.0.4

• Fixed issue with path basename

0.0.3

• Fixed issue with repeating email id for accession blocks
• Updated ReadMe to include geneutils init as first step.
• Fixed CSV write issue outside loop

0.0.2

• Added credential tool to save NCBI email and API Key
• Minor fixes to overall functionality.