New Atlantis Labs MinPath remixed by Josh L. Espinoza ([email protected])

MinPath

Developer: Yuzhen Ye [email protected]
Affiliation: School of Informatics, Computing and Engineering, Indiana University, Bloomington

Description:

MinPath (Minimal set of Pathways) is a parsimony approach for biological pathway reconstructions using protein family predictions, achieving a more conservative, yet more faithful, estimation of the biological pathways for a query dataset.

KEGG and MetaCyc pathways included in Minpath were updated as of May 10, 2021.

If you need older releases of MinPath, please check out this website

And if you need to use the web-based MinPath, please go to this website

Changes in `minpath-nal`

This version is meant to provide easier access to MinPath. Designed with interoperability with PyKOfamScan.

Requires glpk to be installed in the same conda environment (i.e., os.path.join(os.environ["CONDA_PREFIX"], "bin", "glpsol"))
Executtables and database files are now in bin/
Changed executable from MinPath.py to minpath
Include utility scripts:
- reformat_minpath_report.py

1. Introduction

MinPath is free software under the terms of the GNU General Public License as published by the Free Software Foundation.

If you use MinPath, please cite, Yuzhen Ye and Thomas G. Doak. A parsimony approach to biological pathway reconstruction/inference for genomes and metagenomes (PLoS Computational Biology, 5(8):e1000465, 2009)

2. Installation

conda install -c new-atlantis-labs minpath-nal

3. Requirements

3.1 files of reference pathways with function to pathway (subsystem) mapping

3.1.1 Files required for KEGG pathway reconstruction by MinPath (placed under data/)

KEGG-pathway.txt, KEGG-family.txt, KEGG-mapping.txt
These files are updated regularly

3.1.2 File required for MetaCyc metabolic pathway reconstruction by MinPath (placed under data/)

MetaCyc-pathway.txt, MetaCyc-family.txt, MetaCyc-mapping.txt
These files are updated regularly

3.1.3 File required for SEED subsystem reconstruction by MinPath (placed under data/)

figfam_subsystem.dat (this file isn't updated since 2010) (note: current file is copied from figfam release6: Release6/FigfamsData.Release.6/release_history/figfam_subsystem.dat; please note it is an outdated version. )

3.1.4 Any pathway system

what you need to prepare is a pathway-function mapping file similar to KEGG-mapping.txt or MetaCyc-mapping.txt
format of this file: one row for a mapping of a function to a pathway; pathway-id comes before functions, seperated by a tab;

3.2 The original implementation shipped with glpk but this version requires a the dependency in a conda environment.

4. Running MinPath

4.1 Simply call MinPath.py to check its usage. Also check out the included examples as follows.

4.2 Examples (under examples/ directory):

under examples/

#for KEGG pathway
minpath -ko demo.ko -report demo.ko.minpath -details demo.ko.minpath.details

#for MetaCyc pathway
minpath -ec demo.ec -report demo.ec.minpath -details demo.ec.minpath.details

#for SEED subsystem
minpath -fig demo.fig -report demo.fig.minpath -details demo.fig.minpath.details

#for any pathway
minpath -any demo.any -map ../data/MetaCyc-mapping.txt -report demo.any.minpath -details demo.any.minpath.details

Input of MinPath: ko (or fig, ec, or any) annotations (check demo.ko, demo.fig and demo.ec under examples/ directory) Format of the inputs: one line per annotation; the first column is the protein/sequence id, and the second column is the annotation0; the two columns are seperated by a tab

Outputs of MinPath: demo.ko.minpath, and demo.ko.minpath.details (and so on)

How to read the MinPath report file?

e.g, demo.ko.minpath ... path 00030 kegg n/a naive 1 minpath 1 fam0 42 fam-found 18 name Pentose phosphate pathway path 00031 kegg n/a naive 1 minpath 0 fam0 12 fam-found 2 name Inositol metabolism ...

path 00030, path 00031 are the KEGG pathway IDs (if your input file has fig families, the pathways will then be SEED subsystems)
kegg n/a, indicates pathway reconstruction of your input dataset if not available (note: this information is only available for the genomes annotated in KEGG database); for input with fig families, KEGG is replaced by SEED
naive 1 or 0: the pathway is reconstructed, or not, by the naive mapping approach
minpath 1 or 0: the pathway is kept, or removed by MinPath
fam0: the total number of families involved in the corresponding pathway
fam-found: the total number of involved families that are annotated
name: the description of the corresponding pathway (subsystem)

4.4 How to read the MinPath detailed report file?

This report file lists all the pathways found MinPath, and a list of families each pathway includes e.g. demo.ko.minpath.details ... path 00010 fam0 56 fam-found 27 # Glycolysis / Gluconeogenesis K00001 hits 6 # E1.1.1.1, adh K00002 hits 1 # E1.1.1.4, adh ...

path 00010 is the KEGG pathway ID, and fam0 and fam-found are the same as in 4.3
this pathway includes families, K00001 and K00002, and so on (here K numbers are used for KEGG families, and FIG ids for FIG families)
family K00001 has 6 hits (i.e., 6 proteins/reads are annotated as this family)

MinPath on the web:

http://omics.informatics.indiana.edu/MinPath (please check the project home page for updates and newer version of the MinPath)

Acknowledgments

Development was supported by NIH grant 1R01HG004908 to YY

jolespin / minpath-nal Goto Github PK

minpath-nal's Introduction