Feature Extraction Package for Biological Sequences Based on Mathematical Descriptors

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Preprocessing

Before executing any method in this package, it is necessary to run a pre-processing script, to eliminate any noise from the sequences (e.g., other letters as: N, K …,). To use this script, follow the example below:

Important: This package only accepts sequence files in Fasta format as input to the methods.

To run the tool (Example): $ python3.7 preprocessing/preprocessing.py -i input -o output


Where:

-h = help

-i = Input - Fasta format file, e.g., test.fasta

-o = output - Fasta format file, e.g., output.fasta

Running:

$ python3.7 preprocessing/preprocessing.py -i dataset.fasta -o preprocessing.fasta 

Fickett score

To use this model, follow the example below:

To run the code (Example): $ python3.7 methods/FickettScore.py -i input -o output -l label -seq type


Where:

-i = Input - Fasta format file, E.g., test.fasta

-o = Output - CSV format file, E.g., test.csv.

-l = label - lncRNA, circRNA...

-seq = type of sequence, e.g., 1 = DNA, 2 = RNA.

Running:

$ python3.7 methods/FickettScore.py -i sequences.fasta -o sequences.csv -l test -seq 1

Note Input sequences for feature extraction must be in fasta format.

Note This example will generate a csv file with the extracted features.