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io.github.bigbio.external

Version of jmzTab library

https://github.com/bigbio/jmztab

Science Score: 67.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 2 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (11.8%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

Version of jmzTab library

Basic Info
  • Host: GitHub
  • Owner: bigbio
  • License: apache-2.0
  • Language: Java
  • Default Branch: master
  • Size: 5.21 MB
Statistics
  • Stars: 1
  • Watchers: 7
  • Forks: 0
  • Open Issues: 0
  • Releases: 2
Created over 5 years ago · Last pushed over 3 years ago
Metadata Files
Readme License Citation

README.md

jmzTab: Java library for reading and writing mzTab

Java CI with Maven DOI

The jmzTab library provide reading and writing capabilities, as well as supporting the validation of mzTab and the conversion of mzIdentML files to mzTab. Currently, the library contains converter for

jmzTabValidator

  • jmzTabValidator, 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.

Currently, the tool can be downloaded from the releases section:

java -jar jmztab-{version}.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 (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.

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

``` 3.0.4

io.github.bigbio.external jmztab ${jmztab.version} <!-- based on mzTab specification version 1.0 --> ```

The jmzTab library can currently only be found in the [maven central]'s maven repository:

<repository> <id>sonatype-release</id> <url>https://oss.sonatype.org/service/local/staging/deploy/maven2</url> </repository> <repository> <id>sonatype-snapshopt</id> <url>https://oss.sonatype.org/content/repositories/snapshots</url> </repository>

News

``` java MZTabColumnFactory prh = MZTabColumnFactory.getInstance(Section.ProteinHeader); prh.addDefaultStableColumns(); // add other optional columns prh.addBestSearchEngineScoreOptionalColumn(ProteinColumn.BESTSEARCHENGINESCORE, 1);

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

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

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

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.

Citation

Perez-Riverol, Y. (2021). JmzTab 3.0: Java library to parse, validate and convert mztab proteomics files (Version 3.0.12) [Computer software]. https://doi.org/10.5281/zenodo.5213712 DOI

Owner

  • Name: BigBio Stack
  • Login: bigbio
  • Kind: organization
  • Email: proteomicsstack@gmail.com
  • Location: Cambridge, UK

Provide big data solutions Bioinformatics

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Perez-Riverol"
  given-names: "Yasset"
  orcid: "https://orcid.org/0000-0001-6579-6941"
title: "JmzTab: Java library to parse, validate and convert mztab proteomics files"
version: 3.0.12
doi: 10.5281/zenodo.5213712
date-released: 2021-08-17
url: "https://github.com/bigbio/jmzTab"

GitHub Events

Total
Last Year

Issues and Pull Requests

Last synced: 8 months ago

All Time
  • Total issues: 0
  • Total pull requests: 9
  • Average time to close issues: N/A
  • Average time to close pull requests: 12 minutes
  • Total issue authors: 0
  • Total pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 9
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
Pull Request Authors
  • ypriverol (9)
Top Labels
Issue Labels
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Packages

  • Total packages: 1
  • Total downloads: unknown
  • Total dependent packages: 1
  • Total dependent repositories: 0
  • Total versions: 2
repo1.maven.org: io.github.bigbio.external:jmztab

JmzTab is a Java-based library to read mzTab files containing peptide/protein quantitative data

  • Versions: 2
  • Dependent Packages: 1
  • Dependent Repositories: 0
Rankings
Dependent repos count: 32.0%
Dependent packages count: 32.0%
Average: 35.9%
Stargazers count: 39.7%
Forks count: 39.8%
Last synced: 7 months ago

Dependencies

pom.xml maven
  • commons-cli:commons-cli 1.2
  • junit:junit 4.12
  • org.projectlombok:lombok 1.18.2
  • org.slf4j:jcl-over-slf4j 1.7.25
  • org.slf4j:slf4j-api 1.7.25
  • uk.ac.ebi.jmzidml:jmzidentml 1.2.11
  • uk.ac.ebi.pride.utilities:pride-utilities 2.0.18
  • uk.ac.ebi.pride:px-submission-core 2.0.15