ProteoGenomics Converter tool
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README.md

ProteoGenomics Converter tool (PGConverter)

Download PGConverter Latest: 1.7

This library is primarily to offer a command-line tool to convert between the following formats for proteogenomics related data: mzIdentML -> mzTab -> proBed -> bigBed. For more information about proBed, see the PSI proBed website. For more information about BED and bigBed, please see the UCSC website.

It is also possible to convert regular non-proteogenomics mzIdentML or PRIDE XML files to mzTab.

A secondary function of this library is to gather metadata and statistics about mzIdentML, mzTab, and PRIDE XML files for validation purposes.

Primarily this tool is powered by the ms-data-core-api library to read/write files.

Minimum requirements

  • Java 1.8, 64-bit
  • A dual-core CPU
  • 2+ GB RAM for complex mzIdentML files.

Instructions

  1. Download the tool as a zip archive file.
  2. Extract the zip file to a directory.
  3. From a terminal / command prompt, navigate to this new extracted directory and execute a command as described under the 'usage' section below.

Usage

File conversion

To convert, run the tool with the -c parameter, and the provide 'result' assay files using the -mzid, -mztab, or -pridexml parameter. You may specify an output file directly using the -outputfile parameter, or a general output format: this will the same name as the input file name with the extension of the -outputformat.

Convert from mzIdentML to mzTab, specifying an output file name

$ java -jar pg-converter.jar -c -mzid /path/to/data/foo.mzid -outputfile /path/to/output/output.mztab

Convert from PRIDE XML to mzTab, specifying an output format

$ java -jar pg-converter.jar -c -pridexml /path/to/data/foo.pride.xml -outputformat mztab

Convert from annotated mzTab to (sorted, filtered*) proBed

$ java -jar pg-converter.jar -c -mztab /path/to/data/foo.mztab -chromsizes /path/to/chrom.txt -outputformat probed

Convert from annotated mzIdentML to (sorted, filtered*) proBed

$ java -jar pg-converter.jar -c -mzid /path/to/data/foo.mztab -chromsizes /path/to/chrom.txt -outputformat probed

Convert from (sorted, filtered*) proBed to bigBed

$ java -jar pg-converter.jar -c -mztab /path/to/data/foo.pro.bed -chromsizes /path/to/chrom.txt -asqlfile /path/to/aSQL.as -bigbedconverter /path/to/bedToBigBed

NB *bigBed conversion requires the input proBed file to be sorted by the first 3 columns, and chromosomes without provided sizes need to be filtered out.

Assay 'result' file validation

To validate, run the tool with the -v parameter, and the provide your 'result' assay files, and related 'peak' files if applicable. Peak files can be added with the -peak parameter for a single peak file, or -peaks with paths separated by '##' for multiple related peak files. By default the report is saved as a serilized object, so to make a human-readiable plain text report use the -skipserialization flag, and provide an output report file to save the output.

mzIdentML validation

$ java -jar pg-converter.jar -v -mzid /path/to/data/foo.mzid -peak /path/to/data/bar1.mgf -skipserialization -reportfile /path/to/output/outputReport.txt

mzTab validation

$ java -jar pg-converter.jar -v -mztab /path/to/data/foo.mztab -peaks /path/to/data/bar1.mgf##/path/to/data/bar2.mgf -skipserialization -reportfile /path/to/output/outputReport.txt

PRIDE XML validation

$ java -jar pg-converter.jar -v -pridexml /path/to/data/foo.pride.xml -skipserialization -reportfile /path/to/output/outputReport.txt

XML schema validation

To perform XML schema validation on mzIdentML or PRIDE XML files, add the -schema or -schemaonly parameter. -schema will include schema validation before the "normal" validation, and -schemaonly will stop after the schema validation has finished (no "normal" validation).

mzIdentML schema validation and normal validation

$ java -jar pg-converter.jar -v -mzid /path/to/data/foo.mzid -peak /path/to/data/bar1.mgf -scehma -skipserialization -reportfile /path/to/output/outputReport.txt

PRIDE XML schema validation only, without normal validation

$ java -jar pg-converter.jar -v -pridexml /path/to/data/foo.pride.xml -schemaonly -skipserialization -reportfile /path/to/output/outputReport.txt

proBed validation

proBed validation is also supported, by using the default proBed ASQL (.as) schema, or by using the -asqlfile parameter.

proBed validation - default schema

$ java -jar pg-converter.jar -v -proBed /path/to/data/foo.pro.bed -reportfile /path/to/output/outputReport.txt
For a real example of proBed validation, please download the unit test example to a directory, and then run the PG-Converter tool using a command along the lines of:
$ java -jar pg-converter.jar -v -proBed /path/to/data/test.pro.bed

proBed validation - custom schema

$ java -jar pg-converter.jar -v -proBed /path/to/data/foo.pro.bed -asqlfile /path/to/data/foo.as -reportfile /path/to/output/outputReport.txt

Troubleshooting

Java memory usage

You may need to allocate more RAM for the tool to use. To do so, add an extra parameter at the start of the command along the lines of: -Xmx<heap size>g

You will also need to ensure that you're using 64-bit Java in order to use a higher allocation of RAM.

  • e.g. to specify 4GB of RAM:

$ java -Xmx4g -jar pg-converter.jar -c -mzid /path/to/data/foo.mzid -peaks /path/to/data/bar1.mgf##/path/to/data/bar2.mgf -outputfile /path/to/output/output.mztab

  • e.g. to specify 100GB of RAM:

$ java -Xmx100g -jar pg-converter.jar -v -mzid /path/to/data/foo.mzid -peak /path/to/data/bar1.mgf -skipserialization -reportfile /path/to/output/outputReport.txt

bigBed conversion

bigBed conversion requires extra supporting files. For further information please see the PSI proBed website, and the UCSC bigBed website.

In particular, the UCSC bedToBigBed converter tool is only available for linux and Mac (OSX), not Windows.

Contact

To get in touch, please either email pride-support@ebi.ac.uk or raise an issue on the issues page.