COGclassifier

Table of Contents

• Overview
• Installation
• Workflow
• Usage
• Output Contents
• Customize Charts

Overview

COG(Cluster of Orthologous Genes) is a database that plays an important role in the annotation, classification, and analysis of microbial gene function. Functional annotation, classification, and analysis of each gene in newly sequenced bacterial genomes using the COG database is a common task. However, there was no COG functional classification command line software that is easy-to-use and capable of producing publication-ready figures. Therefore, I developed COGclassifier to fill this need. COGclassifier can automatically perform the processes from searching query sequences into the COG database, to annotation and classification of gene functions, to generation of publication-ready figures (See figure below).

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

Python 3.9 or later is required for installation. Installation of RPS-BLAST(ncbi-blast+) is also necessary.

Install bioconda package:

conda install -c conda-forge -c bioconda cogclassifier

Install PyPI stable package:

pip install cogclassifier

Workflow

Description of COGclassifier’s automated workflow. This workflow was created based in part on cdd2cog.

1. Setup COG & CDD resources

Download & load 4 required COG & CDD files from FTP site.

• cog-24.fun.tab (https://ftp.ncbi.nih.gov/pub/COG/COG2024/data/cog-24.fun.tab)
  Descriptions of COG functional categories.
  This resource file is included in the package as cog_func_category.tsv.

  Show more information

  Tab-delimited plain text file with descriptions of COG functional categories
  The categories form four functional groups:
  1. INFORMATION STORAGE AND PROCESSING
  2. CELLULAR PROCESSES AND SIGNALING
  3. METABOLISM
  4. POORLY CHARACTERIZED
  Columns:
  1. Functional category ID (one letter)
  2. Functional group (1-4, as above)
  3. Hexadecimal RGB color associated with the functional category
  4. Functional category description
  Each line corresponds to one functional category. The order of the categories is meaningful (reflects a hierarchy of functions; determines the order of display)

  (From https://ftp.ncbi.nih.gov/pub/COG/COG2024/data/Readme.COG2024.txt)

• cog-24.def.tab (https://ftp.ncbi.nih.gov/pub/COG/COG2024/data/cog-24.def.tab)
  COG descriptions such as ‘COG ID’, ‘COG functional category’, ‘COG name’, etc…
  This resource file is included in the package as cog_definition.tsv.

  Show more information

  Tab-delimited plain text file with COG descriptions
  Columns:
  1. COG ID
  2. COG functional category (could include multiple letters in the order of importance)
  3. COG name
  4. Gene name associated with the COG (optional)
  5. Functional pathway associated with the COG (optional)
  6. PubMed ID, associated with the COG (multiple entries are semicolon-separated; optional)
  7. PDB ID of the structure associated with the COG (multiple entries are semicolon-separated; optional)
  Each line corresponds to one COG. The order of the COGs is arbitrary (displayed in the lexicographic order)

  (From https://ftp.ncbi.nih.gov/pub/COG/COG2024/data/Readme.COG2024.txt)

• cddid.tbl.gz (https://ftp.ncbi.nih.gov/pub/mmdb/cdd/)
  Summary information about the CD(Conserved Domain) model.

  Show more information

  “cddid.tbl.gz” contains summary information about the CD models in this distribution, which are part of the default “cdd” search database and are indexed in NCBI’s Entrez database. This is a tab-delimited text file, with a single row per CD model and the following columns:

  PSSM-Id (unique numerical identifier)
  CD accession (starting with ‘cd’, ‘pfam’, ‘smart’, ‘COG’, ‘PRK’ or “CHL’)
  CD “short name”
  CD description
  PSSM-Length (number of columns, the size of the search model)

  (From https://ftp.ncbi.nih.gov/pub/mmdb/cdd/README)

• Cog_LE.tar.gz (https://ftp.ncbi.nih.gov/pub/mmdb/cdd/little_endian/)
  COG database, a part of CDD(Conserved Domain Database), for RPS-BLAST search.

2. RPS-BLAST search against COG database

Run query sequences RPS-BLAST against COG database [Default: E-value = 1e-2]. Best-hit (=lowest e-value) blast results are extracted and used in next functional classification step.

3. Classify query sequences into COG functional category

From best-hit results, extract relationship between query sequences and COG functional category as described below.

1. Best-hit results -> CDD ID
2. CDD ID -> COG ID (From cddid.tbl.gz)
3. COG ID -> COG Functional Category Letter (From cog-24.def.tab)
4. COG Functional Category Letter -> COG Functional Category Definition (From cog-24.fun.tab)

If functional category with multiple letters exists, first letter is treated as functional category (e.g. COG4862 has multiple letters KTN. A letter K is treated as functional category).

Using the above information, the number of query sequences classified into each COG functional category is calculated and functional annotation and classification results are output.

Usage

Basic Command

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

Options

$ COGclassifier --help
                                                                                                                      
Usage: COGclassifier [OPTIONS]                                                                                       
                                                                                                                      
A tool for classifying prokaryote protein sequences into COG functional category                                     
                                                                                                                      
╭─ Options ──────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ *  --infile        -i        Input query protein fasta file [required]                                             │
│ *  --outdir        -o        Output directory [required]                                                           │
│    --download_dir  -d        Download COG & CDD resources directory [default: /home/user/.cache/cogclassifier_v2]  │
│    --thread_num    -t        RPS-BLAST num_thread parameter [default: MaxThread - 1]                               │
│    --evalue        -e        RPS-BLAST e-value parameter [default: 0.01]                                           │
│    --quiet         -q        No print log on screen                                                                │
│    --version       -v        Print version information                                                             │
│    --help          -h        Show this message and exit.                                                           │
╰────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯

Example Command

Click here to download example protein fasta files.

COGclassifier -i ./example/ecoli.faa -o ./ecoli_cogclassifier

Output Contents

• rpsblast.tsv (example)
  RPS-BLAST against COG database result (format = outfmt 6).

• cog_classify.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

• cog_count.tsv (example)
  Count classified sequences per COG functional category result.

  Table of detailed tsv format information (5 columns)

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

• cogclassifier.log (example)
  COGclassifier log file.

• cog_count_barchart.[png|html]
  Barchart of COG funcitional category classification result.
  COGclassifier uses Altair visualization library for plotting charts.

  

• cog_count_piechart.[png|html]
  Piechart of COG funcitional category classification result.
  Functional category with percentages less than 1% don’t display letter on piechart.

  

Customize Charts

COGclassifier also provides barchart & piechart plotting API/CLI to customize charts appearence. See notebooks and command below for details.

plot_cog_count_barchart

$ plot_cog_count_barchart --help
                                                                                              
Usage: plot_cog_count_barchart [OPTIONS]                                                      
                                                                                              
Plot COGclassifier count barchart figure                                                      
                                                                                              
╭─ Options ───────────────────────────────────────────────────────────────────────────────────╮
│ *  --infile         -i        Input COG count result file ('cog_count.tsv') [required]      │
│ *  --outfile        -o        Output barchart figure file (*.png|*.svg|*.html) [required]   │
│    --width                    Figure pixel width [default: 440]                             │
│    --height                   Figure pixel height [default: 340]                            │
│    --bar_width                Figure bar width [default: 15]                                │
│    --y_limit                  Y-axis max limit value                                        │
│    --percent_style            Plot percent style instead of number count                    │
│    --sort                     Enable descending sort by number count                        │
│    --dpi                      Figure DPI [default: 100]                                     │
│    --help           -h        Show this message and exit.                                   │
╰─────────────────────────────────────────────────────────────────────────────────────────────╯

plot_cog_count_piechart

$ plot_cog_count_piechart --help
                                                                                              
Usage: plot_cog_count_piechart [OPTIONS]                                                      
                                                                                              
Plot COGclassifier count piechart figure                                                      
                                                                                              
╭─ Options ───────────────────────────────────────────────────────────────────────────────────╮
│ *  --infile       -i        Input COG count result file ('cog_count.tsv') [required]        │
│ *  --outfile      -o        Output piechart figure file (*.png|*.svg|*.html) [required]     │
│    --width                  Figure pixel width [default: 380]                               │
│    --height                 Figure pixel height [default: 380]                              │
│    --show_letter            Show functional category lettter on piechart                    │
│    --sort                   Enable descending sort by number count                          │
│    --dpi                    Figure DPI [default: 100]                                       │
│    --help         -h        Show this message and exit.                                     │
╰─────────────────────────────────────────────────────────────────────────────────────────────╯