COPaKB-DB-Updater

BD2K Center of Excellence for Big Data Computing at UCLA

Alan Kha            akhahaha@gmail.com
Hannah Chou         hannahjchou@gmail.com

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Overview

Updates the COPaKB database.

Usage

usage: DBUpdater [-all <version description> <directory> <instrument>
       <enzyme> | -dis | -h | -hpa <file> | -prot <file> | -spec <file>
       [module ID] <instrument> <enzyme> | -specdir <directory>
       <instrument> <enzyme> | -ver <description>]
Updates the COPaKB database.

 -all,--all <version description> <directory> <instrument> <enzyme>
                    Add/update version, proteins, spectra, and diseases
 -dis,--disease     Update diseases
 -h,--help          Show usage
 -hpa,--hpa <file>  Update HPA proteins from HPA XML file
 -prot,--proteins <file>
                    Update proteins from FASTA file
 -spec,--spectra <file> [module ID] <instrument> <enzyme>
                    Update Spectra from COPA file
 -specdir,--spectradirectory <directory> <instrument> <enzyme>
                    Update Spectra from COPA files in directory
 -ver,--version <description>
                    Add new version

Notes

• JUnit tests are not necessarily complete nor usable