Hello, I am using this nice Python API to access raw file metadata. Although I can easily obtain sample_information.user_text, I cannot extract "UserLabel" or "Sequence Row Level Name". Do I need to add these .NET <=> Python wrappers myself?

I have problems with the raw_file.select_instrument(Device.MS, 1) line using Python 3.10 on Windows 10.

File loads properly and lines such as raw_file.instrument_count and other sample-related functionality such as raw_file.sample_information.vial and others from https://github.com/ethz-institute-of-microbiology/fisher_py/blob/main/examples/raw_file_reader_example.py work well, but not those that directly refer to the instrument access, like raw_file.get_instrument_data().name

Instead of the intended functionality, there is an AssertionError for line 893 in https://github.com/ethz-institute-of-microbiology/fisher_py/blob/main/fisher_py/raw_file_reader/raw_file_access.py

The file I try to open is attached blank219.raw

blank219.zip

I just cannot figure out if the problem is with my installation or there is something else wrong?!?!

Sorry, more a question than an issue - I can access the mass spectra in two ways:

average_scan = raw_file.average_scans_in_scan_range(first_scan_number, last_scan_number, scan_filter, options)
spectrum = average_scan.segmented_scan
for i in range(len(spectrum.positions)):
    print(f'  {i} - {spectrum.positions[i]}, {spectrum.intensities[i]}')
for i in range(average_scan.centroid_scan.length):
    print(f'  {average_scan.centroid_scan.masses[i]} {average_scan.centroid_scan.intensities[i]}')

and there is also a function that Converts the segmented scan to centroid scan. Used to centroid profile data.

But how do I access the raw profile data?

The segmented_scan seems to set values which are below a certain threshold to zero respectively does not show m/z ranges outside the identified peaks but I want the full intensity vs. m/z date pairs for the whole scan range - or is this more of a nomenclature problem and the "segmented scan" is actually the "profile"?!?

Hello, Not really an issue, but wondering the equivalent call from older C++ interface XRawfile::IXRawfile2Ptr GetMassListFromScanNum() in the new dotNet / Python world? thx e.-

When I run a script multiprocessed on Linux I get this telemetry dumper:

• Assertion at mono-threads.c:499, condition `result' not met ================================================================= Native Crash Reporting ================================================================= Got a SIGABRT while executing native code. This usually indicates a fatal error in the mono runtime or one of the native libraries used by your application. ================================================================= ================================================================= Native stacktrace: ================================================================= 0x7f3f1127665d - /home/tochr/miniconda3/lib/python3.8/site-packages/../../libmonosgen-2.0.so.1 : 0x7f3f112769e9 - /home/tochr/miniconda3/lib/python3.8/site-packages/../../libmonosgen-2.0.so.1 : 0x7f3f11207bc2 - /home/tochr/miniconda3/lib/python3.8/site-packages/../../libmonosgen-2.0.so.1 : 0x7f3f11275ba2 - /home/tochr/miniconda3/lib/python3.8/site-packages/../../libmonosgen-2.0.so.1 : 0x7f3f11f7e3c0 - /lib/x86_64-linux-gnu/libpthread.so.0 : 0x7f3f11c5703b - /lib/x86_64-linux-gnu/libc.so.6 : gsignal 0x7f3f11c36859 - /lib/x86_64-linux-gnu/libc.so.6 : abort 0x7f3f1116fc2f - /home/tochr/miniconda3/lib/python3.8/site-packages/../../libmonosgen-2.0.so.1 : 0x7f3f1144b376 - /home/tochr/miniconda3/lib/python3.8/site-packages/../../libmonosgen-2.0.so.1 : 0x7f3f11465aaf - /home/tochr/miniconda3/lib/python3.8/site-packages/../../libmonosgen-2.0.so.1 : 0x7f3f1146613d - /home/tochr/miniconda3/lib/python3.8/site-packages/../../libmonosgen-2.0.so.1 : monoeg_assertion_message 0x7f3f1146617b - /home/tochr/miniconda3/lib/python3.8/site-packages/../../libmonosgen-2.0.so.1 : 0x7f3f1145ada9 - /home/tochr/miniconda3/lib/python3.8/site-packages/../../libmonosgen-2.0.so.1 : mono_thread_info_attach 0x7f3f113ab1e3 - /home/tochr/miniconda3/lib/python3.8/site-packages/../../libmonosgen-2.0.so.1 : 0x7f3f11f72609 - /lib/x86_64-linux-gnu/libpthread.so.0 : 0x7f3f11d33163 - /lib/x86_64-linux-gnu/libc.so.6 : clone ================================================================= Telemetry Dumper: =================================================================

This only happens on linux, and happens on multiple independent linux systems. I installed fisher-py with 'conda install -c conda-forge pythonnet' and 'pip install fisher-py' and to repoduce the error:

from time import sleep from fisher_py import RawFile from multiprocessing import Pool def read_file(file): RawFile(file) sleep(10)

files = ['/path/to/file1.raw', '/path/to/file2.raw'] with Pool(2) as ps: list(ps.map(read_file, files))

Is there a way to disable the native Thermo peak picking using fisher-py? I know very little of the way this peak picking is implemented natively into the raw files, but looking at the ThermoRawFileParser (https://github.com/compomics/ThermoRawFileParser) an option -p is possible to disable this peak picking, returning, on average, 10+ times more peaks per spectra.

I would love if there was a way to achieve this using fisher-py, but from looking through the RawFile class and the documentation I can find no such option, is this manageable or completely not feasible with the current fisher-py?

I tried newer DLLs (OpenMcdf, ThermoFisher.CommonCore.Data, ThermoFisher.CommonCore.RawFileReader) in https://github.com/compomics/ThermoRawFileParser/releases/tag/v1.3.4 and the issue has been fixed. However, looks like the .pdbs are missing...

Description

I encountered a couple of errors when accessing MS/MS RAW files from our proteomics lab using fisher-py 1.0.17 on our CentOS 7.5 cluster, and also on my MacBook. Both of the errors were part of scan_event.py.

1. When the ms_order property was accessed, we got an error about a missing attribute. The relevant portion of the stack trace is:

     File "/Users/dpsmca/MprcExtractRaw/venv/lib/python3.9/site-packages/fisher_py/raw_file.py", line 71, in __init__
       scan_numbers, rt = self._get_ms_scan_numbers_and_retention_times_(MsOrderType.Ms)
     File "/Users/dpsmca/MprcExtractRaw/venv/lib/python3.9/site-packages/fisher_py/raw_file.py", line 126, in _get_ms_scan_numbers_and_retention_times_
       if scan_event.ms_order != ms_order:
     File "/Users/dpsmca/MprcExtractRaw/venv/lib/python3.9/site-packages/fisher_py/data/scan_event.py", line 296, in ms_order
       return MsOrderType(self._get_wrapped_object_().MsOrder)
   AttributeError: 'IScanEvent' object has no attribute 'MsOrder'
   

2. When get_reaction() was called, we got a similar error about the Reactions attribute. Stack trace:

     File "/Users/dpsmca/MprcExtractRaw/venv/lib/python3.9/site-packages/fisher_py/raw_file.py", line 81, in __init__
       scan_numbers, filter_masses = self._get_ms2_scan_numbers_and_masses_()
     File "/Users/dpsmca/MprcExtractRaw/venv/lib/python3.9/site-packages/fisher_py/raw_file.py", line 109, in _get_ms2_scan_numbers_and_masses_
       precursor_mass = self._get_scan_filter_precursor_mass_(scan_number)
     File "/Users/dpsmca/MprcExtractRaw/venv/lib/python3.9/site-packages/fisher_py/raw_file.py", line 138, in _get_scan_filter_precursor_mass_
       return scan_event.get_reaction(0).precursor_mass
     File "/Users/dpsmca/MprcExtractRaw/venv/lib/python3.9/site-packages/fisher_py/data/scan_event.py", line 599, in get_reaction
       return Reaction(self._get_wrapped_object_().Reactions[index])
   AttributeError: 'IScanEvent' object has no attribute 'Reactions'
   

Issues

• (1) is just a typo, I think -- looking at ThermoFisher.CommonCore.Data.xml, it appears that this should be MSOrder, with a capital S.

• (2) seems to work if you replace the direct access to Reactions[index] with a call to GetReaction(index).

I've created a pull request for this: #13

Thanks!

Implicit int-enum conversion is no longer a default. Considering how this project is set up, I've added the necessary codec to do the conversion.

However, as of this PR's creation, there is a bug upstream in that codec waiting to be fixed and v3 is still in alpha.

Two fixes for for problems encountered in scan_event.py:

• get_reaction(index) replaced direct access to Reactions[index] with call to GetReaction(index)
• ms_order() fixed capitalization typo: was MsOrder, should be MSOrder

Currently the two for loops

for i in range(average_scan.centroid_scan.length):
    print(f'  {average_scan.centroid_scan.masses[0]} {average_scan.centroid_scan.intensities[i]}')

have average_scan.centroid_scan.masses[0] but shouldn't that also be iterated as average_scan.centroid_scan.masses[i] since otherwise for all intensities only the mass of the first scan is shown?!?