treasureisland 0.2b3

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.

Dependency :

Python >= 3.7

Installation and Usage:

Use pip to install the package :

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

pip install treasureisland --pre 

The treasureisland package can be used to find predictions and downloaded as csv, xlsx, txt files demonstrated in TreasureIsland package

Option1 - Locally install package and use it:

git clone https://github.com/priyamayur/GenomicIslandPrediction.git
python -m pip install -e GenomicIslandPrediction
cd GenomicIslandPrediction
python test_ti <DNA file> 

Option2 - 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(seqfile)

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)

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