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MannLabs / alphapept

A modular, python-based framework for mass spectrometry. Powered by nbdev.
https://mannlabs.github.io/alphapept/
Apache License 2.0
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Search fails on mzML files? #544

Open lazear opened 1 year ago

lazear commented 1 year ago

Describe the bug

Hi, no specific bug... I just can't get AlphaPept to run! I have a collection of mzML files from PXD003881 converted using ThermoRawFileParser that I am trying to analyze with default settings. AlphaPept will spend a minute or two processing the FASTA file and then fail when it begins the search process. I have attached the log below, please let me know if there is more information I can provide.

Version (please complete the following information):

Additional context

.alphapept\failed: https://gist.github.com/lazear/5ff36a97f6f41b13a81120105bf50083 full log: https://gist.github.com/lazear/9102f3206ea44d5c875c904a349656bd

straussmaximilian commented 1 year ago

Hi,

Thanks for reporting. It looks like there was an issue when compiling the installer when lxml was not packaged. I will try to fix this in the next release. If you want to process Thermo files, I suggest processing them directly. The issues with mzML we had in the past were that you could end up with different mzML files depending on which conversion settings you use, and we wanted to have the raw file reading as part of the search engine package.

The mzML format was to have a generic import format for "everything else," which so far was SciEx. For the next release, we will have a native reader in Python for Thermo, Bruker, and Sciex, so this use case will probably be obsolete.

Best,

Max

Btw: I think you did fantastic work with sage! Very cool. Any plans to include an MS1 feature finder? There is some code here, maybe this is something that would be great in Rust?

lazear commented 1 year ago

I was able to run it with the raw files - I will try installing the python package next time for mzMLs. Slick interface!

I've been rewriting my MS1 quant (added MBR, isotopic scoring, etc), so I'm trying out AlphaPept, etc to try and verify what I'm doing. I'll definitely be snooping around in the codebase for some inspiration :)