The dia-pasef from roestlab

packaging problems

I will try to get this project packaged but I'm facing some problems.

This project is called dia-pasef, but the python package is called diapysef it that correct? Should the Bioconda package be named after the pypi package?
A License file is missing, the pypi package is indicating MIT, but here no indication of a License file.
- is https://github.com/Roestlab/dia-pasef/blob/master/src/diapysef/setup.py#L17 correct?
there is also no release here, so its hard to say which version is on pypi

Thanks!
Bjoern

There is no libtimsdata.so file

Hello,
I am a postgraduate student. Recently, I want to use diapysef to convert tdf file. However, Bruker sdk is not found. The libtimsdata.so is just a link file in diapysef. Which URL do I need to download? Can you tell me?
Thank you very much!!

Python 2.0 and Linux

dia-pasef/src/diapysef/scripts/convertTDFtoMzML.py

Line 1 in fe8e361

# -*- coding: utf-8 -*-

can you add

#!/usr/bin/env python
from __future__ import print_function

to the top of all the scripts? this helps a lot on Linux

Automate diapysef PyPI deployment on release

Use github workflows to automatically update PyPI release to reflect updated changes in diapysef

sys exit

dia-pasef/src/diapysef/scripts/plot_dia_windows.py

Line 9 in fe8e361

print("Usage: plot_dia_windows.py window_file precursor_map")

I suggest to add sys.exit() here

scikit-image missing from setup.py

scikit-image is not included in setup.py, which on a fresh pip install causes an error if the package is not already installed. Fix by adding scikit-image to setup.py.

Traceback (most recent call last):
  File "/gpfs/fs1/home/h/hroest/singjust/bin/py39/bin/diapysef", line 5, in <module>
    from diapysef.main import cli
  File "/gpfs/fs1/home/h/hroest/singjust/bin/py39/lib/python3.9/site-packages/diapysef/__init__.py", line 4, in <module>
    from .plotting import *
  File "/gpfs/fs1/home/h/hroest/singjust/bin/py39/lib/python3.9/site-packages/diapysef/plotting.py", line 22, in <module>
    from skimage.morphology import disk, binary_dilation
ModuleNotFoundError: No module named 'skimage'

pip install error of latests version 1.0.3

Automated build and push of version 1.0.3 seems to fail during pip install

$ pip install diapysef
Collecting diapysef
  Downloading diapysef-1.0.3.tar.gz (697 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 697.7/697.7 kB 6.3 MB/s eta 0:00:00
  Preparing metadata (setup.py) ... error
  error: subprocess-exited-with-error
  
  × python setup.py egg_info did not run successfully.
  │ exit code: 1
  ╰─> [8 lines of output]
      Traceback (most recent call last):
        File "<string>", line 2, in <module>
        File "<pip-setuptools-caller>", line 34, in <module>
        File "/tmp/pip-install-6etgn60b/diapysef_28657bc4376c4d70b8640a95b96094da/setup.py", line 13, in <module>
          long_description=readme(),
        File "/tmp/pip-install-6etgn60b/diapysef_28657bc4376c4d70b8640a95b96094da/setup.py", line 4, in readme
          with open('PYPI_README.rst') as f:
      FileNotFoundError: [Errno 2] No such file or directory: 'PYPI_README.rst'
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed

× Encountered error while generating package metadata.
╰─> See above for output.

note: This is an issue with the package mentioned above, not pip.
hint: See above for details.

DEFINE src

This is not the best message to display. "src" could literally mean src folder for diapasef, or it could metaphorically mean a source folder of a project. Define src please for those who many not be Native English speaking people.

To activate that functionality place libtimsdata.so (Linux) or timsdata.dll in the src folder.

Also maybe if possible indicate where to place if installing from pip...

$ ls /usr/local/lib/python3.7/site-packages/diapysef*                      
/usr/local/lib/python3.7/site-packages/diapysef:
__init__.py             data               plotting.py                                          two_dimension_gradient_ascent_peak_finder.py
__pycache__             diapysef.py        proto_two_dimension_gradient_ascent_peak_finding.py  two_dimension_gradient_ascent_peak_finding.py
conversions.py          main.py            splitting_consumer.py                                two_dimension_quantification.py
convert_tdf_to_mzml.py  merge_consumer.py  targeted_data_extraction.py                          util.py
coverage.py             pasefdata.py       timsdata.py

/usr/local/lib/python3.7/site-packages/diapysef-1.0.1.dist-info:
INSTALLER  METADATA  RECORD  REQUESTED  WHEEL  entry_points.txt  top_level.txt

Implement non-linear RT alignment

Add non-linear RT alignment here:

dia-pasef/src/diapysef/diapysef/conversions.py

Lines 82 to 96 in ed8e182

    
           if rt_alignment is 'linear': 
        
               print("Aligning retention time...") 
        
               # Generate the iRT calibrators 
        
               calibrators = [] 
        
               pp = PdfPages(pdfout) 
        
               for file in raw_files: 
        
                   cal = calibrate(msms_irt[msms_irt.raw == file], pdf = pp) 
        
                   calibrators.append(cal) 
        
               pp.close() 
        
               # Apply rt calibrators 
        
               calibrators = pd.DataFrame(columns = ['Raw file', 'intercept', 'slope'], data = calibrators) 
        
               ms = pd.merge(ms, calibrators, on = 'Raw file') 
        
               ms['irt'] = ms.intercept + ms.slope * ms['Calibrated retention time'] 
        
               ms = ms.drop(columns=['intercept', 'slope'])

use for example statsmodels lowess (example code https://github.com/msproteomicstools/msproteomicstools/blob/master/msproteomicstoolslib/math/Smoothing.py#L416 )

Missing values in Normalized retention time, library intensity

dia-pasef/src/diapysef/diapysef/conversions.py

Line 47 in 30c0478

def pasef_to_tsv(evidence, msms,

IM arrays were not writen into mzml file

Hi, I'm using the lastest version diapysef 0.3.5 to convert diaPASEF data to mzml for further analysis with OSW, but got the following error msg, and IM array was indeed not in converted mzml file

---------------------------------------------------
FATAL: uncaught exception!
---------------------------------------------------
last entry in the exception handler:
exception of type IllegalArgument occurred in line 332, function void __cdecl OpenMS::ChromatogramExtractorAlgorithm::extractChromatograms(const class boost::shared_ptr<class OpenSwath::ISpectrumAccess>,class std::vector<class boost::shared_ptr<struct OpenSwath::OSChromatogram>,class std::allocator<class boost::shared_ptr<struct OpenSwath::OSChromatogram> > > &,const class std::vector<struct OpenMS::ChromatogramExtractorAlgorithm::ExtractionCoordinates,class std::allocator<struct OpenMS::ChromatogramExtractorAlgorithm::ExtractionCoordinates> > &,double,bool,double,const class OpenMS::String &) of C:\jenkins\ws\openms\RC\openms_release_packaging\9447518b\source\src\openms\source\ANALYSIS\OPENSWATH\ChromatogramExtractorAlgorithm.cpp
error message: Requested ion mobility extraction but no ion mobility array found.
---------------------------------------------------

I think this was caused by the order to write value arrays into spectrum in function handle_compressed_frame in script convertTDFtoMzML.py

Currently this function would first add an ion mobility array to pyopenms.MSSpectrum(), and called set_peaks after that. But this might overwrite float_data_arrays_ in MSSpectrum for each spec, since set_peaks would call spec_.clear(0) at first before adding new 1d peaks.
When I placed the sframe.setFloatDataArrays([fda]) from line 235 to line 244 after the calling of sframe.set_peaks( (mz, intens) ) in line 243, IM array could be written to mzml correctly.

I think this is also related to an issue in OpenMS [https://github.com/OpenMS/OpenMS/issues/4827]

The pyopenms version is 2.7.0

Best regards,
Ronghui

roestlab / dia-pasef Goto Github PK

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dia-pasef's Issues

packaging problems

There is no libtimsdata.so file

Python 2.0 and Linux

Automate diapysef PyPI deployment on release

sys exit

scikit-image missing from setup.py

pip install error of latests version 1.0.3

DEFINE src

Implement non-linear RT alignment

Missing values in Normalized retention time, library intensity

IM arrays were not writen into mzml file

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	if rt_alignment is 'linear':
	print("Aligning retention time...")
	# Generate the iRT calibrators
	calibrators = []
	pp = PdfPages(pdfout)
	for file in raw_files:
	cal = calibrate(msms_irt[msms_irt.raw == file], pdf = pp)
	calibrators.append(cal)
	pp.close()

	# Apply rt calibrators
	calibrators = pd.DataFrame(columns = ['Raw file', 'intercept', 'slope'], data = calibrators)
	ms = pd.merge(ms, calibrators, on = 'Raw file')
	ms['irt'] = ms.intercept + ms.slope * ms['Calibrated retention time']
	ms = ms.drop(columns=['intercept', 'slope'])