bigbio/sparkms

Spark package to perform downstream analysis of big data proteomics

bigbio documentation

This is a project documentation of all the pipelines and tools developed by bigbio stack (bigbio.xyz) group. This a detailed documentation of the each component.

sparkms's Issues

Group peptide evidences and protein evidences

Peptide Evidence:

A peptide evidence is the combination of a peptide sequence and protein accession.

1. We should be able to group by peptide evidences(peptide sequence+protein accession) for all the psms in all projects.
2. We should be able to group all the peptide evidences(peptide sequence+protein accession) by protein accession.

Ask for usage

Hello,

Thank you for providing the source code.
However, I cannot find any instructions on how to use it even in the README file.
Can I ask about the usage for utilizing this source code?

Structure project minor issues

Some comments after reviewing the code:

• I recommend having a general running script called sparkms.py which will be the major entry point for the package, we should move it to this folder https://github.com/bigbio/sparkms/tree/main/sparkms. The script will only give access to the different commands, check this structure https://github.com/bigbio/py-pgatk/blob/master/pypgatk/pypgatk_cli.py, this main script can have access to all click sub-command like https://github.com/bigbio/py-pgatk/tree/master/pypgatk/commands.
• General description of the PRIDE JSON format and the parquet format is needed. For people that would like to update or extended the library good to know the file format structure.