/OldBarcodeFinder

Bioinformatics competition

Primary LanguagePythonGNU General Public License v3.0GPL-3.0

BarcodeFinder

What is BarcodeFinder?

BarcodeFinder is a BLAST based program written by python3, which could find single-copy barcode sequence of given data in reasonable time.

The main features of BarcodeFinder were listed below.

  1. Output barcode sequence of given data. Till now, it could find out barcode of given multiple genome sequences of two bacteria organism. Notice that the program was designed for higher taxonomic class and bigger organism number, which would be available in followed version after more test.

  2. Only generate single-copy barcode. A nice barcode should be single-copy among genome. Herein, BarcodeFinder could automatically drop multi-copy candidate barcodes which lead to less result (but more accurate).

  3. Appropriate resolution of barcode. With given barcode, species come from different higher taxonomy grade could be neatly divided while remain same group in lower level. However, among lower grade, subgroups are possible if the barcode has enough mutation to cause distinguishable distinction which has no effect on higher level.

  4. Reasonable resource consumption. Most of CPU time, memory and hard disk space were used by BLAST while the number is unexpectedly small. For instance, with less than half minutes, ~500mb memory and twice hard disk usage for given data size, 4 barcodes were successfully generated from ~700mb input data.

Requirements

Hardware

It depends on input data. If less than 1gb, the program could normally run on mainstream PC with less than 1 minute. Bigger data need more memory (not test).

Software

  1. python3

Be sure to install python3 rather than python 2.7. Besides, to use subprocess.run, you would better install python 3.5 or above

  1. biopython

  2. BLAST Suite

  3. mafft

For Windows users, please make sure:

  1. correct version and platform (x86/x64) for best performance.

  2. Biopython has lots of version, its python version must be same with python3’s you installed before. For example, you installed python 3.5.1 with x86_64 architecture (depends on your CPU, most of them on PC now support x86_64 mode). Then you have to install biopython for python 3.5.1 with same architecture.

  3. It is better to choose all-in-one package for mafft.

For Linux users, just run:

sudo apt-get install python3-biopython ncbi-blast+ mafft

Or

sudo yum install python3-biopython ncbi-blast+ mafft

Operating system

Although technically BarcodeFinder and its dependent software could run on various operating system, till now, only Linux and Microsoft Windows were tested.

Installation

  1. Download BarcodeFinder.py (~10kb)
  2. Finished :)

Usage

Put BarcodeFinder.py into same directory of input fasta files. Then run the command.

For Microsoft Windows user:

python BarcodeFinder.py

For Linux user:

python3 BarcodeFinder.py

If you want to change parameters set by default, see details by

python BarcodeFinder.py –h

or

python3 BarcodeFinder.py –h.

Information

The latest version of BarcodeFinder can be found on [github] (https://github.com/wpwupingwp/201609).

Main author

If you have problems or any other questions, feel free to send email to [Ping Wu] (wuping@ibcas.ac.cn).