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compomics / moFF

A modest Feature Finder (moFF) to extract MS1 intensities from Thermo raw file
Apache License 2.0
33 stars 11 forks source link

Added missing "pymzml" import statement to moff.py #12

Closed jgriss closed 7 years ago

jgriss commented 7 years ago

The import statement seemed to be missing in moff.py

This change was necessary for me to get the tool running when using mzML.

Thanks for the very nice tool!

Best regards, Johannes

jgriss commented 7 years ago

The second commit (48cf823) was necessary as otherwise the tool crashed when using 40 threads. Apparently, the log file wasn't created in time for some concurrent event to happen. I didn't perform any extensive debugging on this.

464d97c removes some excessive print statements when processing mzML files.

Maux82 commented 7 years ago

Hi, Thank you very much for updating fo the code related to mzML file. Indeed I worked a lot to speed up the moFF using the new thermo library on their raw file that I forget to add the import of pymzML after my test..

Actually , I did not tested the multithreading with mzML file so thank you again for you contribution. The logging on a file in the multithreading is python 2.7 is not realy straightforward so I did some workarounds How are the time performance on mzML file actually ? If you know how to speed up the XiC computation using pymzML or other just let me know, I think that file access in pymzML is not the really fast if you ask one Xic at the time. At the moment I m more focused on the Thermo raw file but I know that many users use mzML file.

jgriss commented 7 years ago

Hi,

Small update on the times: On my server processing a RAW file takes 3-4 sec. Processing an mzML file (same RAW file converted using msConvert) takes around 600-700 seconds...

So the mzML processing is rather slow.