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| # COGclassifier | ||
| Classify protein sequences into COG functional category | ||
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| [](https://pypi.python.org/pypi/cogclassifier) | ||
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| ## Table of Contents | ||
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| - [Overview](#overview) | ||
| - [Installation](#installation) | ||
| - [Workflow](#workflow) | ||
| - [Command Usage](#command-usage) | ||
| - [Output Contents](#output-contents) | ||
| - [Customize charts](#customize-charts) | ||
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| ## Overview | ||
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| COGclassifier is a tool for classifying prokaryote protein sequences into COG functional category. | ||
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| Fig.1: Barchart of COG funcitional category classification result for E.coli | ||
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| Fig.2: Piechart of COG funcitional category classification result for E.coli | ||
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| ## Installation | ||
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| COGclassifier is implemented in Python3 (Tested on Ubuntu20.04) | ||
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| Install PyPI stable version with pip: | ||
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| pip install cogclassifier | ||
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| COGclassifier requires `RPS-BLAST` for COG database search. | ||
| Download latest BLAST executable binary from [NCBI FTP site](https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/) and add to PATH. | ||
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| > :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](https://www.ncbi.nlm.nih.gov/books/NBK571452/) for details. | ||
| ## Workflow | ||
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| 1. Download COG & CDD resources | ||
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| 2. RPS-BLAST query sequences against COG database | ||
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| 3. Classify query sequences into COG functional category | ||
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| ## Command Usage | ||
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| ### Basic Command | ||
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| COGclassifier -i [query protein fasta file] -o [output directory] | ||
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| ### Options | ||
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| -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 | ||
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| ### Example Command | ||
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| Classify E.coli protein sequences into COG functional category ([ecoli.faa](https://github.com/moshi4/COGclassifier/blob/main/example/input/ecoli.faa?raw=true)): | ||
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| COGclassifier -i ./example/input/ecoli.faa -o ./ecoli_cog_classifier | ||
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| ## Output Contents | ||
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| COGclassifier outputs 4 result text files and 3 html format chart files. | ||
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| - **`rpsblast_result.tsv`** ([example](https://github.com/moshi4/COGclassifier/blob/main/example/output/mycoplasma_cog_classifier/rpsblast_result.tsv)) | ||
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| RPS-BLAST against COG database result (format = `outfmt 6`). | ||
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| - **`classifier_result.tsv`** ([example](https://github.com/moshi4/COGclassifier/blob/main/example/output/mycoplasma_cog_classifier/classifier_result.tsv)) | ||
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| Query sequences classified into COG functional category result. | ||
| This file contains all classified query sequences and associated COG information. | ||
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| <details> | ||
| <summary>Table of detailed tsv format information (9 columns)</summary> | ||
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| | 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 | | ||
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| </details> | ||
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| - **`classifier_count.tsv`** ([example](https://github.com/moshi4/COGclassifier/blob/main/example/output/ecoli_cog_classifier/classifier_count.tsv)) | ||
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| Count classified sequences per COG functional category result. | ||
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| <details> | ||
| <summary>Table of detailed tsv format information (4 columns)</summary> | ||
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| | 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 | | ||
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| </details> | ||
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| - **`classifier_stats.txt`** ([example](https://github.com/moshi4/COGclassifier/blob/main/example/output/ecoli_cog_classifier/classifier_stats.txt)) | ||
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| 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`** | ||
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| 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. | ||
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| - **`classifier_count_piechart.html`** | ||
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| Piechart of COG funcitional category classification result. | ||
| Functional category with percentages less than 1% don't display letter on piechart. | ||
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| - **`classifier_count_piechart_sort.html`** | ||
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| Piechart with descending sort by count. | ||
| Functional category with percentages less than 1% don't display letter on piechart. | ||
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| ## Customize charts | ||
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| COGclassifier also provides barchart & piechart plotting scripts to customize charts appearence. | ||
| Each script can plot the following feature charts. See [wiki](https://github.com/moshi4/COGclassifier/wiki) for details. | ||
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| - Features of **plot_cog_classifier_barchart** script | ||
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| - 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` | ||
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| - Features of **plot_cog_classifier_piechart** script | ||
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| - 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` |