MitoToolPy

Copyright © 2014 MitoTool & DomeTree Team
Author: Long Fan (mitotool@gmail.com)
Project on GitHub: https://github.com/kizcas/MitoToolPy


This page was last updated on 26 Oct 2014

Contents

Introduction

MitoToolPy-Seq

MitoToolPy-Var

Download


Introduction

MitoToolPy written in python and running on various operation systems (e.g. Windows, Linux, Mac), is designed for data analysis of mitochondrial DNA of eight domestic animals, including cattle, chicken, dog, horse, goat, pig, sheep and yak. It utilizes dometree (www.dometree.org) as the reference, and its analysis for mtDNA sequences include (1) outputting variants scored relative to the reference sequences; (2) classifying haplogroup status (haplogrouping); and (3) checking potential errors. MitoToolPy can also handle partial mtDNA genome (e.g. control region) sequences and can serve as a convenient "barcoding tool" for strains or breeds of domestic animals.

The tool is licensed under GPLv3.

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mitotoolpy-seq.py

Description:

This script is used for classifying haplogroup according to input sequence(s), outputting variants scored relative to the reference sequences, listing potential missing variants and private variants.

Usage:

i) python mitotoolpy-seq.py -s [species] -r [region] -i [input] -o [output]

where
  [species] = an animal selected from 'cattle', 'chicken', 'dog', 'horse', 'goat', 'pig', 'sheep' and 'yak'.
  [region] = a region selected from 'dloop', 'nondloop', 'whole' and '[begin_position]:[end_position]'; Default: 'whole'.
  [input] = input fasta file.
  [output] = output file or 'stdout'; Default: 'stdout' (i.e., the interface of command line prompt)
.

ii) python mitotoolpy-seq.py -v , which displays current version number.

iii) python mitotoolpy-seq.py -h , which displays help document.

Notes:

(1) Input file would be a single fasta file, which could store single record or multiple records.

(2) Output file would be a tab-delimited text file with five columns:

  Column 1)  Sample name
  Column 2)  Recommended Haplogroup
  Column 3)  Missing variants of recommended haplogroup
  Column 4)  Private variants of recommended haplogroup
  Column 5)  Variants of selected region                   

(3) Time cost for analysing each whole mtDNA sequence is approximate 50 seconds.

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mitotoolpy-var.py

Description:

This script is used for classifying haplogroup according to input variants, listing potential missing variants and private variants. Given candidate haplogroup(s) is/are provided by users, it could also detect missing variants of claimed haplogroup.

Usage:

i) python mitotoolpy-var.py -s [species] -r [region] -i [input] -o [output]

where
  [species] = an animal selected from 'cattle', 'chicken', 'dog', 'horse', 'goat', 'pig', 'sheep' and 'yak'.
  [region] = a region selected from 'dloop', 'nondloop', 'whole' and '[begin_position]:[end_position]'; Default: 'whole'.
  [input] = input text file, see following notes for details.
  [output] = output file or 'stdout'; Default: 'stdout' (i.e., the interface of command line prompt)
.

ii) python mitotoolpy-var.py -v , which displays current version number.

iii) python mitotoolpy-var.py -h , which displays help document.

Notes:

(1) Input file should be a tab-delimited text file with two or three columns:

  Column 1)  Sample name
  Column 2)  Variants
  Column 3 (optional))  Candidate haplogroup(s) claimed by user. Multiple haplogroups seperated by comma, colon or semicolon could be given together.

(2) Output file would be a tab-delimited text file with five columns:

  Column 1)  Sample name
  Column 2)  Recommended Haplogroup
  Column 3)  Missing variants of recommended haplogroup
  Column 4)  Private variants of recommended haplogroup
  Column 5)  Missing variants of haplogroup(s) claimed by user.
  Column 6)  Variants of selected region                   

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Download

MitoToolPy is licensed under GPLv3. Its preinstallation includes Python and Biopython. Meanwhile, ClulstalW 2 will be downloaded together for pairwise alignment between reference sequence and query sequence. Therefore, after the download, please make sure that ClustalW (in 'bin' directory) has right to execute on your system. Supposed your system is not mentioned below, please download one of below versions and replace original ClustalW (in 'bin' directory) with compiled ClustalW of your system.

Operation System Version
Windows (XP/Vista/7/8) MitoToolPy_Win
Linux MitoToolPy_Linux
Mac MitoToolPy_Mac

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Citation
Peng MS, Fan L, Shi NN, Ning T, Yao YG, Murphy RW, Wang WZ, Zhang YP. DomeTree: a Canonical Toolkit for Mitochondrial DNA Analyses in Domesticated Animals. Molecular Ecology Resources. doi: 10.1111/1755-0998.12386
[Link]