A package for computing variation numbers
Project description
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, email='')
# Calculate variation numbers
vn.processVN(gene, outputDir, acc, seqtype)
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