variation-number 0.1.6

A package for computing variation numbers

variation_number

A package for calculating the variation number of nucleotide/protein sequence using sequence orthologs.

This package can be found on GitHub.

Features

• Download orthologs
• Build phylogenetic trees
• Generate variation numbers

Usage

import variation_number as vn
import os
gene = 'BRCA1'
seqtype =' protein'
outputDir = '{}/output'.format(os.getcwd())

# Download orthologs from NCBI orthologs database
acc = vn.getFasta(gene, outputDir,seqtype,refseqID=None)

# Calculate variation numbers
vn.processVN(gene, outputDir, acc, seqtype)