knext 1.0.0

Kyoto Encylopedia of Genes and Genomes Markup Language File parser and converter

KNeXT downloads and parses Kyoto Encylopedia of Genes and Genomes (KEGG) markup language files (KGML). The tool employs NetworkX’s framework to create gene-only networks, but mixed (gene, compound, pathway) networks can also be generated. All output files are in TSV format. KNeXT also retrieves a TXT file of node x-y axis coordinates for use in NetworkX’s graph visualization library, and it is able to convert KEGG IDs into Uniprot and NCBI IDs.

Usage

Primary line: get-kgml [SPECIES_NAME]

  KEGG NetworkX Topological (KNeXT) parser uses the KEGG
  API to gather all KGML files for a single species
  in 3 to 4 letter KEGG organism code.

Options:
  --help,   shows options and website for KEGG organism codes

Primary line: parse-genes [OPTIONS]

  KNeXT parser deploy's NetworkX's
  framework to create gene-only representations of KGML files.

Options:
  file      KGML file
  --unique  TSV file's genes have a terminal modifier
  --graphics        outputs x-y axis coordinates
  --help    shows options and file types

  folder    folder containing KGML files
  --unique  TSV file's genes have a terminal modifier
  --graphics        outputs x-y axis coordinates
  --help    shows options and file types

Primary line: parse-mixed [OPTIONS]

  KNeXT parser creates mixed
  (genes, compounds, pathways) representations of KGML files.

Options:
  file      KGML file
  --unique  TSV file's nodes have a terminal modifier
  --graphics        outputs x-y axis coordinates
  --help    shows options and file types

  folder    folder containing KGML files
  --unique  TSV file's nodes have a terminal modifier
  --graphics        outputs x-y axis coordinates
  --help    shows options and file types

Primary line: convert-network [OPTIONS]

  KNeXT parser converts KEGG entry IDs in TSV output files into
  UniProt or NCBI IDs.

Options:
  file      PATH:   path to TSV file
  species   TEXT:   KEGG 3 to 4 letter organism code
  --uniprot optional flag for output:       use if UniProt IDs are the desired output
  --unique  optional flag for output:       use if the TSV file has terminal modifiers
  --graphics        PATH:   graphics file
  --help    optional flag:  shows options

Options:
  folder    PATH:   path to folder containing TSV files
  species   TEXT:   KEGG 3 to 4 letter organism code
  --uniprot optional flag for output:         use if UniProt IDs are the desired output
  --unique  optional flag for output:         use if the TSV file has terminal modifiers
  --graphics        PATH:       path to folder containing graphics files
  --help    optional flag:            shows options

For example, KNeXT can obtain all KGML files for Homo sapiens:

$ get-kgml hsa

The resulting output folder can be used to parse the files:

$ parse-genes folder kgml_hsa --graphics

The resulting output folder can be used to convert the TSV files and graphics file:

$ convert-network folder kegg_gene_network_hsa hsa --graphics kegg_gene_network_hsa

Inputs

KNeXT only accepts KGML files downloaded from KEGG

The output of which can be used in successive commands. All input formats must be in TSV format. Column names are mandatory and should not be changed.

Data Frames

Example TSV file with KEGG ID’s

entry1	entry2	type	value	name
hsa:100271927-98	hsa:22800-12	PPrel	–>	activation
hsa:100271927-98	hsa:22808-12	PPrel	–>	activation
hsa:100271927-98	hsa:3265-12	PPrel	–>	activation

Example TSV file for uniprot conversion with –unique output

entry1	entry2	type	value	name
Q9Y243-23	O15111-59	PPrel	–>	activation
Q9Y243-23	Q6GYQ0-240	PPrel,PPrel	–|,+p	inhibition,phosphorylation
Q9Y243-23	O14920-59	PPrel	–>	activation

Installation

The current release is v1.0.0 Installation is via pip:

$ pip install https://github.com/everest/knext/knext-1.0.0.tar.gz

Repo can be downloaded and installed through poetry:

$ git clone https://github.com/everest/knext.git
$ cd knext
$ poetry shell
$ poetry install
$ poetry run [get-kgml, parse-genes, parse-mixed, or convert-network]

Requirements

Requirements are (also see pyproject.toml):

• Python >= 3.9

• typer

• requests

• pandas

• networkx

• pytest