treasureisland 1.0.0

Prediction of Genomic Islands

TREASUREISLAND

TreasureIsland python package is a machine learning-based Genomic Island prediction software, that uses an unsupervised representation of DNA for its prediction.

TreasureIsland was contructed from Benbow dataset.

Dependency :

Python >= 3.7

Installation:

Option1 - Use pip to install the package :

TreasureIsland can be installed by python package management system "pip" :

pip install treasureisland

Option2 - Locally install package:

git clone https://github.com/priyamayur/GenomicIslandPrediction.git
python -m pip install -e GenomicIslandPrediction

Usage:

The treasureisland package is used to find genomic island predictions which can be downloaded as csv, xlsx, txt files demonstrated in TreasureIsland package

Or, run script locally to get predicitons quickly:

Clone the github repository if not cloned before:

git clone https://github.com/priyamayur/GenomicIslandPrediction.git
cd GenomicIslandPrediction
python run_treasureisland.py <DNA file>     

Input file:

DNA sequence files in fasta format with a sequenceID.

example: >NC_002620.2 Chlamydia muridarum str. Nigg, complete sequence CACATAGCAAAACACTCAAAGTTTTTCAGCAAAAAAGCTTGTTGAAAAAATTGTTGACCGCCTGTTCACA....

Performance:

TreasureIsland takes 2-5 mins to run depending on the size of the input.

Output :

Can be downloaded in csv, xlsx, txt formats. The results are shown in the following format for each genomic island:

example : NC_002620.2 1.0 130000.0 0.95597

The sample outputs can be found in the repository - output_NC_002620.2.txt, output_NC_002620.2.csv, output_NC_002620.2.xlsx

Testing:

Repository contains some sample DNA files that can be used to test the TreasureIsland.

example :

cd GenomicIslandPrediction
python run_treasureisland.py genome/ecoli.fasta    

TreasureIsland package:

import the sequence class from treasureisland package:

from treasureisland.dna_sequence import sequence 

Instantiate the sequence with the DNA sequence file path as the argument. The DNA file used can be a fasta or genbank file.

seq = sequence("C:/Users/USER/GenomicIslandPrediction/genome/bsub.fasta") # enter local path for sequence file

Get prediction data frame from sequence by running the predict method.

pred = seq.predict()

The predictions can be downloaded in text, csv, excel formats.

seq.predictions_to_csv(pred)
seq.predictions_to_excel(pred)
seq.predictions_to_text(pred)

Contact:

Feel free to contact at [e-mail]