kegg-cli

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[!NOTE] You MUST make absolutely sure to comply with the conditions of using KEGG and its API: http://www.kegg.jp/kegg/legal.html and http://www.kegg.jp/kegg/rest/.

Table of Contents

• Installation
• Features
• Commands
  • info
  • get
  • list
  • find
  • conv
  • link
  • get_seq
• License
• Contributing

Features

• Query KEGG database information
• Retrieve entries from KEGG databases
• List database entries
• Search by keywords
• Convert between KEGG and external database IDs
• Find related entries between KEGG databases
• Download gene sequences (nucleotide or amino acid)

Installation

Via pip

pip install kegg-cli

From source

git clone https://www.github.com/vidyasagar0405/kegg-cli
cd kegg-cli
pip install .

Commands

you can use conventional KEGG API commands such as info, get, list, find, conv, link, see below for example usage check KEGG REST API documentation for more info: https://www.kegg.jp/kegg/rest/keggapi.html

info

kegg-cli info kegg

get

• Retrives gene entry

kegg-cli get eco:b0002

• Enclose ids in "double quotes", use -op/--option for options for available options check KEGG REST API

kegg-cli get "hsa:10458 ece:Z5100" -op aaseq

list

• Returns the list of KEGG organisms with taxonomic classification

kegg-cli list organism

• Returns the list of the genes

kegg-cli list "rsz:19816419 rsz:19816420" 

• Returns the list of human pathways

kegg-cli list pathway -org hsa

find

• Returns compound ids with the said formula

kegg-cli find C7H10O5 -db compound -op formula

• Returns genes involved in cancer in humans

kegg-cli find "cancer hsa"

• Returns Pathways with RNA in their name

kegg-cli find "rna" -db pathway

conv

• Converts KEGG geneIDS to NCBI proteinIDs

kegg-cli conv ncbi-proteinid "rsz:19816419 rsz:19816420 rsz:19816421 rsz:19816422"

• Converts KEGG geneIDS to NCBI geneIDs

kegg-cli conv ncbi-geneid "rsz:19816419 rsz:19816420 rsz:19816421 rsz:19816422" 

• Converts NCBI geneIDs to KEGG geneIDS

kegg-cli conv genes "ncbi-geneid:19816419 ncbi-geneid:19816420 ncbi-geneid:19816421 ncbi-geneid:19816422" 

• Converts NCBI proteinIDs to KEGG geneIDS

kegg-cli conv genes "ncbi-proteinid:YP_009046967 ncbi-proteinid:YP_009046968 ncbi-proteinid:YP_009046969 ncbi-proteinid:YP_009046970" 

link

• Returns genes linked to the rsz00966 pathway

kegg-cli link rsz rsz00966 

• Returns compounds linked to the rsz00966 pathway

kegg-cli link cpd map00010 

• Returns pathways linked to the given genes

kegg-cli link pathway "hsa:10458 ece:Z5100"

get-seq

It is not a part of KEGG REST API, but uses link and get API calls to get the nucleotide sequence (ntseq) or amino acid sequence (aaseq).

get-seq can be used in four different ways:

• Fetches the ntseq (default) of the given genes and saves it to a file named with time_date.fasta

kegg-cli get-seq "rsz:108806876 rsz:108839148" 

• Fetches the aaseq of the given genes and saves it to a file named with time_date.fasta

kegg-cli get-seq "rsz:108806876 rsz:108839148" --seq-type aaseq 

• Fetches the aaseq of the given genes and saves it to a file named path/to/file.fasta

kegg-cli get-seq "rsz:108806876 rsz:108839148" --seq-type aaseq -o path/to/file.fasta 

• Fetches the aaseq of the genes in the file (one per line) and saves it to a file named path/to/file.fasta

kegg-cli get-seq /home/vs/Documents/bioinfo/practise/kegg/rsz_rsz_M00005_genes.tsv --seq-type aaseq -o expected_aaseq.fasta 

• Fetches the aaseq of the genes in the second column (0 based indexing) of the file (one per line) and saves it to a file named path/to/file.fasta (delimiter can also be changed with --delimiter, defaults to '\t')

kegg-cli get-seq /home/vs/Documents/bioinfo/practise/kegg/rsz_rsz_M00005_genes.tsv --field 1 --seq-type aaseq -o expected_aaseq.fasta

• Fetches the ntseq of all the genes in the given pathway (make sure to add 'path:' prefix, to the pathway ID. One pathway at a time)

kegg-cli get-seq path:minc00966 --seq-type ntseq -o tests/data/expected_pathway_ntseq.fasta 

• Fetches the ntseq of all the genes in the given module (make sure to add 'md:' prefix, to the module ID. One module at a time)

kegg-cli get-seq md:rsz_M00005 --seq-type ntseq -o tests/data/expected_module_ntseq.fasta 

License

kegg-cli is distributed under the terms of the MIT license.

Contributing

Contributions are welcome! Please feel free to submit a Pull Request.