lewisresearchgroup / ms-mint Goto Github PK

Hello,

I've seen you cross-post a few places regarding mzMLb reading and writing. The current development version of https://github.com/levitsky/pyteomics has support for mzMLb reading, and the last release of psims includes an mzML to mzMLb conversion tool:

from psims.transform.mzml import MzMLToMzMLb

MzMLToMzMLb("mzml_path", "mzmlb_path").write()

Both require h5py and hdf5plugin.

Hi Soren,

Every time I run MINT after picking peaks, I get this error 504 Gateway Time-out nginx/1.18.0 (Ubuntu). Could you please fix it for me? I want to download the results from Promastigotes_spent_media workspace.

MINT version: 0.0.53 65.gd5fff28.dirty
OS: Linux-5.4.0-77-generic-x86_64-with-debian-10.10
Versions: ---

Hi, I was reading your question about MsFileReader. Looks like you may already have a solution that I'm looking for.
compomics/ThermoRawFileParser#116

Similar to your question, I'd like to have a way to dynamically generate XIC from my DIA proteomics data. Ideally, the mzML file would be reformatted to "feather" file in long format, such that I can extract the XIC with arrow calls in R. The storage space is not a concern as long as the read and filter speed is adequate.

Thanks!
Wen

While using

mint.run()

I got this error message:

maxtasksperchild: None
ERROR:root:process_ms1_files_in_parallel(): invalid literal for int() with base 10: 'scanId=2702'
ERROR:root:process_ms1_files_in_parallel(): invalid literal for int() with base 10: 'scanId=2456'
ERROR:root:process_ms1_files_in_parallel(): invalid literal for int() with base 10: 'scanId=2711'
ERROR:root:process_ms1_files_in_parallel(): invalid literal for int() with base 10: 'scanId=2499'

Seems to be an error related to how scanId is passed to int(), if the string scanId was not removed before passed to int()

Notebook in:
Alkaloids_extraction.pdf