bigbio/pgatk-io

High performance io library for proteogenomics

pgatk-io

About pgatk-io

The pgatk-io library is a java framework to manipulate mass spectrometry and proteomics file formats. It has an special focus on novel file formats like Apache Spark Parquet and Json file formats for proteomics.

Support Matrix

This table summarizes the current level of support for each feature across the different file formats. See discussion below for details on each feature.

Feature	MGF	APL (Maxquant)	mzXML	mzML	PRIDE Json	Pep Avro
Random Access	✔️	✔️	✔️	✔️	✔️
Fast Iterable Access	✔️	✅	✔️	❌	❌	✔️
Gzip Support	❌	❌	❌	❌	❌
Numpress Support	❌	❌	✅	✅	❌

File formats

• MGF - http://www.matrixscience.com/help/data_file_help.html
• mzXML - http://tools.proteomecenter.org/wiki/index.php?title=Formats:mzXML#:~:text=mzXML%20is%20an%20open%20data,foundation%20of%20our%20proteomic%20pipelines
• mzML - https://www.psidev.info/mzML
• ArchiveSpectrum (PRIDE Json) - http://bigbio.xyz/pgatk-io/io/github/bigbio/pgatk/io/pride/ArchiveSpectrum.html
• AnnotatedSpectrum (Pep Avro) - http://bigbio.xyz/pgatk-io/io/github/bigbio/pgatk/io/pride/AnnotatedSpectrum.html

License

pgatk-io is licensed under Apache License 2.0.

Main Features

• Based on a custom build class to efficiently parse text files line by line all parsers can handle arbitrary large files in minimal memory, allowing easy and efficient processing of peak list files using the Java programming language.

• For every implementation a Random Access and Iterable Access Reader is provided.

  • In the Random access developers can access to any individual Spectrum using the Identifier of the Spectrum or the index.
  • In the Iterable access developers can access one by one each of the spectra with the next function

Getting Help

If you have questions or need additional help, please create an issue in the library repo in github (https://github.com/bigbio/pgatk-io/issues). Please send us your feedback, including error reports, improvement suggestions, new feature requests and any other things you might want to suggest.

Similar libraries:

• ms-data-core-api Perez-Riverol Y., Uszkoreit J., Sanchez A., Ternent T., Del Toro N., Hermjakob H., Vizcaíno J.A., Wang R. ms-data-core-api: an open-source, metadata-oriented library for computational proteomics. Bioinformatics, 2015 Sep 1;31(17):2903-5 ms-data-core-api

• jmzReader Griss J, Reisinger F, Hermjakob H, Vizcaíno JA. jmzReader: A Java parser library to process and visualize multiple text and XML-based mass spectrometry data formats. Proteomics. 2012 Mar;12(6):795-8. doi: 10.1002/pmic.201100578.

pgatk-io's Issues

Add support for PRIDE JSON streams

Currently, the PRIDE Json reader expects on JSON object per line.
Ideally, the reader should be updated to also support JSON streams as returned by the API directly.

Use GitHub Actions to Deploy automatically to GitHub Packages

@ypriverol

GitHub now also provides a maven repository which is accessible through GitHub actions.

I suggest to move this package to the GitHub mvn repo to automatically update the latest snapshot version as soon as we have a successful merge into master.

Otherwise, we have to update the mvn package manually which is causing some issues on my side.

Implement support for msp reader and writer.

We need to implement a read/write for the msp file format. The documentation of the format can be found here https://chemdata.nist.gov/mass-spc/ftp/mass-spc/peplib.pdf

IMapStorage::put no longer throws exception

@ypriverol

In the latest version, IMapStorage::put no longer throws a PgatkIOException exception.

How should we handle errors that occur at that stage?