Skip to content
This repository has been archived by the owner on Jul 27, 2022. It is now read-only.

Latest commit

 

History

History
210 lines (162 loc) · 9.54 KB

README.md

File metadata and controls

210 lines (162 loc) · 9.54 KB
Raw

jmzTab

Build Status

NOTE: If you are looking for the reference implementation for mzTab-M for Metabolomics (2.0), please go here.

The jmzTab library provide reading and writing capabilities, as well as supporting the validation of mzTab (1.0) for Proteomics MS data and the conversion of PRIDE XML and mzIdentML files to mzTab. Currently, the library contains converter for

In addition, it is important to highlight that jmzTab is already integrated and used in external software such as the LipidDataAnalyzer, and in an mzQuantML to mzTab converter included in the mzq-lib library.

The jmzTab library is divided in different modules:

The latest versions of these modules from version 3.0.9 onwards can be downloaded individually from the ISAS Artifactory repository.

When you use jmzTab library, please cite the following publication:

Tools

As examples of implementation, two Utilities were developed:

  • mzTabGUI, which a simple desktop application which provides mzTab validation functionality (for Warn or Error levels), and conversion of PRIDE XML and mzIdentML files to mzTab. After the conversion, the tool will also perform an automatic validation of the mzTab file.
  • mzTabCLI, a command line interface (CLI), which provides a more flexible way of processing mzTab files in a batch mode. It also has validation and conversion functionality.

From version 3.0.9 on, both tools can be downloaded from:

For version prior to 3.0.9, both tools can be downloaded from:

In mzTabCLI Demo, we provide a couple of examples to help user call command line interface quickly.

  • print command line help
java -jar mzTabCLI.jar -help

The output will like following:

usage: jmztab
 -check inFile=<inFile>             Choose a file from input directory. This parameter should not be null!
 -convert inFile=<inFile format=<format>   Converts the given format file (PRIDE or mzIdentML) to an mztab file.
 -h,--help                   print help message
 -message code=<code>             print Error/Warn detail message based on code number.
 -outFile <arg>              Dump output data to the given file. If not set, output data will be dumped on stdout.

More information about the tools can be found in the Wiki

Using the jmzTab library

All components of the jmzTab library were developed as maven projects. For information of how to using jmzTab API, please visit the Wiki documents.

Maven

The jmzTab library can easily be used in Maven projects. You can include the following snippets in your Maven pom file.

For parsing and writing mzTab

<properties>
    <jmztab.version>3.0.4</jmztab.version>
</properties>

<dependency>
    <groupId>uk.ac.ebi.pride</groupId>
    <artifactId>jmztab-modular-model</artifactId>
    <version>${jmztab.version}</version>
    <!-- based on mzTab specification version 1.0 -->
</dependency>
<dependency>
    <groupId>uk.ac.ebi.pride</groupId>
    <artifactId>jmztab-modular-util</artifactId>
    <version>${jmztab.version}</version>
    <!-- based on mzTab specification version 1.0 -->
</dependency>

For converting to mzTab

<properties>
    <jmztab.version>3.0.4</jmztab.version>
</properties>

<dependency>
    <groupId>uk.ac.ebi.pride</groupId>
    <artifactId>jmztab-modular-converters</artifactId>
    <version>${jmztab.version}</version>
    <!-- based on mzTab specification version 1.0 -->
</dependency>

Since version 3.0.9, the jmzTab library is available from the LIFS Bintray repository. To retrieve it from there, please adapt your pom.xml / settings.xml as follows:

<profile>
    <id>lifs-repos</id>
    <repositories>
     <repository>
         <snapshots>
             <enabled>false</enabled>
         </snapshots>
         <id>bintray-lifs</id>
         <name>bintray-lifs</name>
         <url>https://dl.bintray.com/lifs/maven</url>
     </repository>
    </repositories>
</profile>

To compile mzTab against the LIFS Bintray repository, please add the following entry to you ~/.m2/settings.xml file:

<activeProfiles>
  <activeProfile>lifs-repos</activeProfile>
</activeProfiles>

or use the -Plifs-repos command line switch when running Maven to enable the LIFS Bintray maven repositories for parent pom and artifact resolution.

The jmzTab library versions prior to 3.0.9 can currently only be found in the EBI's maven repository. In order to work against those versions, please adapt your pom.xml / settings.xml as follows:

<profile>
    <id>ebi-repos</id>
    <repositories>
        <repository>
            <id>nexus-ebi-release-repo</id>
            <url>http://www.ebi.ac.uk/Tools/maven/repos/content/groups/ebi-repo/</url>
        </repository>
        <repository>
            <id>nexus-ebi-snapshot-repo</id>
            <url>http://www.ebi.ac.uk/Tools/maven/repos/content/groups/ebi-snapshots/</url>
        </repository>
    </repositories>
</profile>

To compile mzTab against the EBI repositories, please add the following entry to your ~/.m2/settings.xml file:

<activeProfiles>
  <activeProfile>ebi-repos</activeProfile>
</activeProfiles>

or use the -Pebi-repos command line switch when running Maven to enable the ebi maven repositories for parent pom and artifact resolution.

News

jmzTab version 3.0.9 - (25. September 2019)

  • adding support for more than 99 optional columns #11
  • fix for new line issues on Windows #10

jmzTab version 3.0.4 - (18. October 2016)

  • general refinements and bug fixing

jmzTab version 3.0.2 - (12. February 2015)

  • general refinements and bug fixing
  • removes from the mzTabCLI the need to separate the input and output directory from the file
  • allow parsing the file with the columns in different order to the one define in the specification.Due to this new feature the defaults columns need to be added manually to the factory. Examples:
MZTabColumnFactory prh = MZTabColumnFactory.getInstance(Section.Protein_Header);
prh.addDefaultStableColumns();
// add other optional columns
prh.addBestSearchEngineScoreOptionalColumn(ProteinColumn.BEST_SEARCH_ENGINE_SCORE, 1);

MZTabColumnFactor peh = MZTabColumnFactory.getInstance(Section.Peptide_Header);
peh.addDefaultStableColumns();
// add other optional columns
peh.addBestSearchEngineScoreOptionalColumn(ProteinColumn.BEST_SEARCH_ENGINE_SCORE, 1);

MZTabColumnFactory psh = MZTabColumnFactory.getInstance(Section.PSM_Header);
psh.addDefaultStableColumns();
// add other optional columns
psh.addSearchEngineScoreOptionalColumn(PSMColumn.SEARCH_ENGINE_SCORE, 1, null);

MZTabColumnFactory smh = MZTabColumnFactory.getInstance(Section.PSM_Header);
smh.addDefaultStableColumns();
// add other optional columns
smh.addSearchEngineScoreOptionalColumn(PSMColumn.SEARCH_ENGINE_SCORE, 1, null);

jmzTab version 3.0.0 - (1. August 2014)

  • update version of the library to the Specification Document 1.0.0 (June 2014)
  • new modular version of the jmzTab library. This version allows a easier integration in other projects because minimises the dependencies per module.
  • first version of mzIdentML converter
  • general refinements and bug fixing
  • update mzTab examples

mzTab Specification Document 1.0 RC 5 - (11. December 2013)

  • A completely updated version of the mzTab format specification
  • Version currently submitted to the PSI document process

For more information please see the ReleaseNote.