/NCBI_TaxID_Counter

Couts and classifies the TaxIDs from result files from metagenomic taxonomy classification programs

Primary LanguagePython

NCBI TaxID Counter

This project is part of a collection of codes developed for my Undergraduate Thesis.

Dependencies

  • Biopython - Bio.Entrez package
  • Matplotlib - venn2, venn2_circle, pyplot
  • Modules - csv, os and sys
  • python 3.6+

Features

  • It takes the result files from Metagenome Taxonomy Classification Tools and sorts the TaxIDs between the taxonomy ranks (Superkingdom, Kingdom, Phylum, Class, Order, Family, Genus and Species) and the groups used by the programs (Bacteria, Archaea, Viruses, Fungi, Protozoa)

Usage

Arguments

It can handle as many files as need, each being processed individually.

Example:

./taxid_counter.py (-compare) krona_file metacache_file centrifuge_file [...]

Output

  • The output is a CSV file where the rows represent same rank and the columns same group. The name is the original file name + _sorted.csv"
  • It also outputs Venn diagrams in SVG format for Bacteria, Archaea, Viruses, Fungi and Protozoa with total TaxIds and only species.