RpGene

Documentation

RpGene : A soft-tool for automated gene extraction, gene sequencing analysis and dataset

The information on gene sequences is accessible in a variety of databases that are accessible online, like NCBI , DEG , OGEE and many more. The extraction of information on genes however, is a challenging task to extract from these databases. In the context of machine learning one of the most fundamental demands is the data to be well-organized and usable format. Converting information about gene sequences from sequences into datasets consisting of features derived from sequences in a proper format is a difficult task for researchers. In this study, we have created a soft tool called RpGene based on Python that can perform automatizing the extraction of sequence data of genes from the NCBI database, and analyzing the data using e-Path, and presenting the user with an optimally optimized dataset that can be utilized for dataset generation in context of machine learning and other statistical studies. Our soft tool vastly decreases the time and effort required for dataset generation from gene sequence information and automates the entire process. It finally calculates the sequence features from CodonW integration and outputs a read to go dataset for further studies.

1. Clone the reposatory

git clone https://github.com/KrisshRp/RpGene.git

2. Enter the folder

cd ./RpGene

3. Install the dependencies

sudo python3 install.py

4. start the server

sudo python3 main.py

5. Server is running

APP_PORT = 3000
INFO:     Started server process [4889]
INFO:     Waiting for application startup.
INFO:     Application startup complete.
INFO:     Uvicorn running on http://127.0.0.1:3000 (Press CTRL+C to quit)
INFO:     127.0.0.1:48506 - GET / HTTP/1.1 200 OK
INFO:     127.0.0.1:48506 - GET /stylesheets/main.css HTTP/1.1 200 OK
INFO:     127.0.0.1:48528 - GET /javascripts/main.js HTTP/1.1 200 OK
INFO:     127.0.0.1:48522 - GET /images/dna.png HTTP/1.1 200 OK
INFO:     127.0.0.1:33926 - GET /images/DNA-helix.mp4 HTTP/1.1 200 OK
INFO:     127.0.0.1:40292 - GET / HTTP/1.1 200 OK

6. visit the server by navigating

http://127.0.0.1:3000

or

http://localhost:3000

7. Provide Input Data

Fill all the inputs "organism name" , "NCBI accession id" and "ePath gene locus tags"

Then click the "Submit" button

After that click the "Run" to start the script

8. Output

If chrome driver is downloaded

Chrome Driver is up-to-dated

Else

Downloading Chrome Driver [108.0.5359.71]
100% [...................................] 6904173 / 6904173

In the Console the output showls like

https://www.ncbi.nlm.nih.gov/nuccore/CP005082.1
running script
--------------[Mycobacterium tuberculosis Beijing/NITR203]--------------
> [CP005082.1] :: sending request to server
> [CP005082.1] :: sending request to servere ->  3.24MB
> [CP005082.1] :: sending request to server
> [CP005082.1] :: sending request to servere ->  13.24MB
> [CP005082.1] :: 4155 -- J112_21090 -- [4410381, 4410525] [603]
> [CP005082.1] :: J112_12470 added 1057

In the Portal the output showls like

Lastly click the "download" button to download the sequence data in a zip format