cogclassifier 0.1.0

Classify prokaryote protein sequences into COG functional category

COGclassifier

Table of Contents

• Overview
• Installation
• Workflow
• Command Usage
• Output Contents
• Customize charts

Overview

COGclassifier is a tool for classifying prokaryote protein sequences into COG functional category.

Fig.1: Barchart of COG funcitional category classification result for E.coli

Fig.2: Piechart of COG funcitional category classification result for E.coli

Installation

COGclassifier is implemented in Python3 (Tested on Ubuntu20.04)

Install PyPI stable version with pip:

pip install cogclassifier

COGclassifier requires RPS-BLAST for COG database search.
Download latest BLAST executable binary from NCBI FTP site and add to PATH.

:warning: 'mt_mode' option has been added since v2.12.0 or newer versions of BLAST. 'mt_mode=1' option setting makes effective use of multi-threading and is faster, so it is recommended that you install the latest version. See NCBI's article Threading By Query for details.

Workflow

1. Download COG & CDD resources

2. RPS-BLAST query sequences against COG database

3. Classify query sequences into COG functional category

Command Usage

Basic Command

COGclassifier -i [query protein fasta file] -o [output directory]

Options

-h, --help            show this help message and exit
-i , --infile         Input query protein fasta file
-o , --outdir         Output directory
-d , --download_dir   Download COG & CDD FTP data directory (Default: './cog_download')
-t , --thread_num     RPS-BLAST num_thread parameter (Default: MaxThread - 1)
-e , --evalue         RPS-BLAST e-value parameter (Default: 0.01)
-v, --version         Print version information

Example Command

Classify E.coli protein sequences into COG functional category (ecoli.faa):

COGclassifier -i ./example/input/ecoli.faa -o ./ecoli_cog_classifier

Output Contents

COGclassifier outputs 4 result text files and 3 html format chart files.

• rpsblast_result.tsv (example)

  RPS-BLAST against COG database result (format = outfmt 6).

• classifier_result.tsv (example)

  Query sequences classified into COG functional category result.
  This file contains all classified query sequences and associated COG information.

  Table of detailed tsv format information (9 columns)

  Columns	Contents	Example Value
  QUERY_ID	Query ID	NP_414544.1
  COG_ID	COG ID of RPS-BLAST top hit result	COG0083
  CDD_ID	CDD ID of RPS-BLAST top hit result	223161
  EVALUE	RPS-BLAST top hit evalue	2.5e-150
  IDENTITY	RPS-BLAST top hit identity	45.806
  GENE_NAME	Abbreviated gene name	ThrB
  COG_NAME	COG gene name	Homoserine kinase
  COG_LETTER	Letter of COG functional category	E
  COG_DESCRIPTION	Description of COG functional category	Amino acid transport and metabolism

• classifier_count.tsv (example)

  Count classified sequences per COG functional category result.

  Table of detailed tsv format information (4 columns)

  Columns	Contents	Example Value
  LETTER	Letter of COG functional category	J
  COUNT	Count of COG classified sequence	259
  COLOR	Symbol color of COG functional category	#FCCCFC
  DESCRIPTION	Description of COG functional category	Translation, ribosomal structure and biogenesis

• classifier_stats.txt (example)

  The percentages of the classified sequences are described as example below.

  86.35% (3575 / 4140) sequences classified into COG functional category.

• classifier_count_barchart.html

  Barchart of COG funcitional category classification result.
  COGclassifier uses Altair visualization library for plotting html format charts.
  In web browser, Altair charts interactively display tooltips and can export image as PNG or SVG format.

  

• classifier_count_piechart.html

  Piechart of COG funcitional category classification result.
  Functional category with percentages less than 1% don't display letter on piechart.

  

• classifier_count_piechart_sort.html

  Piechart with descending sort by count.
  Functional category with percentages less than 1% don't display letter on piechart.

  

Customize charts

COGclassifier also provides barchart & piechart plotting scripts to customize charts appearence. Each script can plot the following feature charts. See wiki for details.

• Features of plot_cog_classifier_barchart script

  • Adjust figure width, height, barwidth
  • Plot charts with percentage style instead of count number style
  • Fix maximum value of Y-axis
  • Descending sort by count number or not
  • Plot charts from user-customized classifier_count.tsv

• Features of plot_cog_classifier_piechart script

  • Adjust figure width, height
  • Descending sort by count number or not
  • Show letter on piechart or not
  • Plot charts from user-customized classifier_count.tsv