sorgerlab/kegg_metabolite_mapping

Name: kegg_metabolite_mapping

Owner: sorgerlab

Description: null

Created: 2018-02-02 21:10:48.0

Updated: 2018-02-02 21:11:01.0

Pushed: 2018-02-02 21:19:30.0

Homepage: null

Size: 4

Language: Python

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README

Introduction

This tools maps metabolite names from a CSV file in a format produced by a particular assay and tries to map them to KEGG Compound IDs via the Human Metabolite Database and some further manual curation.

Setup

Download the “All Metabolites” file from HMDB at http://www.hmdb.ca/downloads . Unzip it into the input directory to obtain hmdb_metabolites.xml (1.6GB).

Usage

python map_metabolites.py input/data.csv > output/mapping.csv