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everest-castaneda / knext

Kyoto Encylopedia of Genes and Genomes (KEGG) NetworkX Topological parser automates downloading, parsing, and converting from a KEGG Markup Language File to a TSV file that is usable in network analyses.
MIT License
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KEGG NetworkX Topological (KNeXT) parser

KNeXT downloads and parses Kyoto Encylopedia of Genes and Genomes (KEGG) markup language files (KGML). This 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. KNeXT also maximizes metadata information through preserving each edge's information and adding gene, compound, and pathways names.

Usage

.. code:: text

Primary line: knext get-kgml [SPECIES_NAME]

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

Options:
  --help,   shows options and website for KEGG organism codes
  -d/--d,   directory in which to save output

Primary line: knext genes [Input]

  KNeXT parser deploy's NetworkX's
  framework to create gene-only representations of KGML files.
  Genes between compounds are propagated before compounds are dropped.

Options:
  Input KGML file or folder of KGML files to parse
  -r/--results  file or folder where output should be stored    
  -g/--graphics outputs TXT file of x-y axis coordinates
  -u/--unique   TSV file's genes have a terminal modifier
  -n/--names    TSV file includes a column with gene names
        Notice: increases parsing time and internet connection required
  --help    shows options and file types

Primary line: knext mixed [Input]

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

Options:
  Input KGML file or folder of KGML files to parse
  -r/--results  file or folder where output should be stored
  -g/--graphics outputs TXT file of x-y axis coordinates
  -u/--unique   TSV file's genes have a terminal modifier
  -n/--names TSV file includes a column with compound, gene, and pathway names
     Notice: increases parsing time and internet connection required
  --help    shows options and file types

Primary line: knext convert [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:

.. code:: text

$ knext get-kgml hsa

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

.. code:: text

$ knext genes kgml_hsa --graphics

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

.. code:: text

$ knext convert kegg_gene_network_hsa hsa --graphics kegg_gene_network_hsa

Graphics text file usage

.. code:: text

import networkx as nx
import pandas as pd
import json
edges = pd.read_csv('edges.tsv', sep = '\t')
file_header = open('graphics.txt').read()
pos = json.loads(file_header)
graph = nx.from_pandas_edgelist(edges, source = 'entry1', target = 'entry2')
nx.draw(graph, pos = pos)

Inputs

KNeXT only accepts KGML files downloaded from KEGG <https://www.genome.jp/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 '''''''''''

.. csv-table:: Example TSV file with KEGG ID's :header: 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

.. csv-table:: Example TSV file for uniprot conversion with --unique output :escape: ` :header: 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 :code:v1.2.1 Installation is via pip:

.. code:: bash

$ pip install knext

Repo can be downloaded and installed through poetry__:

.. code:: bash

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

.. __: https://python-poetry.org/

Requirements

Requirements are (also see pyproject.toml):

.. : https://typer.tiangolo.com/ .. : https://click.palletsprojects.com/en/8.1.x/ .. : https://requests.readthedocs.io/en/latest/ .. : https://pandas.pydata.org/ .. : https://networkx.org/ .. : https://docs.pytest.org/en/7.2.x/ .. : https://pathlib.readthedocs.io/en/pep428/ .. : https://docs.pytest.org/en/7.1.x/contents.html