Feature Extraction Package for Biological Sequences Based on Mathematical Descriptors

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Complex Networks

This method generates features based on complex networks, see our pipeline in this article. To use this model, follow the example below:

To run the tool (Example): $ python3.7 methods/ComplexNetworksClass.py -i input -o output -l label -k kmer -t threshold


Where:

-h = help

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

-o = output - CSV format file, e.g., test.csv

-l = Label - Dataset Label, e.g., lncRNA, mRNA, sncRNA

-k = k size, e.g., 2, 3 (default = 3 (codon)), 4

-t = threshold size, e.g., 2, 3 (default = 10).

Running:

$ python3.7 methods/ComplexNetworksClass.py -i sequences.fasta -o sequences.csv -l mRNA -k 3 -t 10

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

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