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pyOpenMS readthedocs documentation, additional utilities, addons, scripts, and examples.

Home Page: https://pyopenms.readthedocs.io

License: Other

Python 87.49% Shell 0.15% JavaScript 10.73% HTML 0.92% CSS 0.72%

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[DOC] Add example how target / decoy information, as well as protein accessions can be queried

OpenMS/OpenMS#4335

Buttons for mzTabTablewidget

Currently the .mzTab need to be hardcoded to be loaded into the widget.
An improvement would be to do this over a load button inside an empty widget.
Also other buttons as save could be implemented if one wants to change and save the table

getting started confuses total ion current and total ion chromatogra,

needs rework

change interface of SpectrumBrowser widget

Currently, it is called using a spectrum file name.
As a pure view class this should only take the MSExperiment and not add logic for loading files.

Spectral Viewer: efficient access to raw data

@timosachsenberg @JeeH-K please change this to access data more efficiently using get_peaks, the current approach below is very inefficient:

https://github.com/OpenMS/pyopenms-extra/blob/57d9c2675d958f536c92671470d9165abde42068/src/specViewer/SpecViewer.py#L110-L116

How to test jupyter notebooks after they are created?

can we run them and check if an error is produced?
how to report?

embed python console in GUI app: potentially interesting widget for power users

# -*- coding: utf-8 -*-
"""
ConsoleWidget is used to allow execution of user-supplied python commands
in an application. It also includes a command history and functionality for trapping
and inspecting stack traces.

"""
import initExample ## Add path to library (just for examples; you do not need this)

import pyqtgraph as pg
from pyqtgraph.Qt import QtCore, QtGui
import numpy as np
import pyqtgraph.console

app = pg.mkQApp()

## build an initial namespace for console commands to be executed in (this is optional;
## the user can always import these modules manually)
namespace = {'pg': pg, 'np': np}

## initial text to display in the console
text = """
This is an interactive python console. The numpy and pyqtgraph modules have already been imported 
as 'np' and 'pg'. 

Go, play.
"""
c = pyqtgraph.console.ConsoleWidget(namespace=namespace, text=text)
c.show()
c.setWindowTitle('pyqtgraph example: ConsoleWidget')

## Start Qt event loop unless running in interactive mode or using pyside.
if __name__ == '__main__':
    import sys
    if (sys.flags.interactive != 1) or not hasattr(QtCore, 'PYQT_VERSION'):
        QtGui.QApplication.instance().exec_()

plotting of 2D maps

Currently, the fastest way to generate 2D spectra plots is to use either TOPPView or ImageCreator. Both are not available in pyOpenMS and adding ImageCreator to the library would introduce new and possibly conflicting dependencies (e.g., QImage).
https://github.com/OpenMS/OpenMS/blob/develop/src/utils/ImageCreator.cpp
Do we have other options?
E.g. only move the bilinear interpolation and gridding to the library and expose a pyOpenMS interface that returns a numpy image that can be directly displayed in pyqtgraph.

example: plot spectrum and chromatogram in python

https://pyopenms.readthedocs.io/en/latest/datastructures.html#spectrum

convert more of the existing pyOpenMS tools that use argparse to use CTDopts

potentially important for a pyTOPP publication

algo parameter documentation

add to https://pyopenms.readthedocs.io/en/latest/parameter_handling.html
how to getDescription in a nice way

move "memory management" submenu to "advanced"

move LC-MS experiment menu item below chromatogram

and see if text still works

Spectrum alignment menu

Small example for SpectrumAlignment class (e.g., theoretical vs. observed)

Add observed spectrum https://github.com/OpenMS/pyopenms-extra/blob/master/src/data/YIC(Carbamidomethyl)DNQDTISSK.mzML already there) to repo
Generate theoretical spectrum with TSG
Call SpectrumAlignment
visualize aligned spectra (mirror plot?)

add examle how to align multiple feature maps using e.g., mapalignerposeclustering

iPyNB conversion for code in Notes not working

see Chemistry

Misleading docs about TIC

In the pyopenms docs there is an example about how to calculate the TIC from a MSExperiment. Isn't it better to use the TIC information in a Chromatogram:

tic = exp.getChromatograms()[0]
for rt, i in zip(*tic.get_peaks()):
    # use rt and i to construct the data structure of your choice

add pyTOPP documentation / retention time prediction

concept / why we use CTD?
example template
more advanced example e.g. using retention time prediction

Integrate https://mybinder.org/

might be a nice way to create interactive pyOpenMS jupyter notebooks from examples.
Not sure if it works with our dependencies though...

IsotopeDistribution should provide dict conversion

Itwould make a lot of code simpler if we would return an

{"mass": [], "abundance": []}

Separate mixed code blocks in documentation

Especially in the introduction there are often core blocks with both python code and in the next line the output.
This should be avoided for binder.

add example on how to iterate over AASequence

Reconfigure the build process

e.g. which branches get built, which version of python/sphinx is used etc.
I do not have rights to change that on RTD settings.

IDViewer crashes if no TIC is present in mzML file and zooming is performed

Create example to export featuremap and idxml into pandas data frame

e.g., for easy integration into ML

pyopenms.Constants not working

on disc reading of spectra data

Currently, the Spectrum viewer widget loads the whole experiment into memory.
That way it is not feasible to inspect many different mzML files.
OpenMS provides an OnDiscExperiment that doesn't load the whole mzML file into memory but directly accesses
the spectra through an index in the mzML file.
It would be beneficial to change that.

Add link to jupyter notebook as well (e.g., next to binder button)

scikit learn does it like that and it might be useful

Code that should be wrapped in PyOpenMS

Wrapping:

./src/openms/include/OpenMS/METADATA/IonSource.h

static const std::string NamesOfPolarity[SIZE_OF_POLARITY];
static const std::string NamesOfInletType[SIZE_OF_INLETTYPE];
static const std::string NamesOfIonizationMethod[SIZE_OF_IONIZATIONMETHOD];

./src/openms/include/OpenMS/ANALYSIS/QUANTITATION/IsotopeLabelingMDVs.h:

static const std::string NamesOfDerivatizationAgent[static_cast<int>(DerivatizationAgent::SIZE_OF_DERIVATIZATIONAGENT)];
static const std::string NamesOfMassIntensityType[static_cast<int>(MassIntensityType::SIZE_OF_MASSINTENSITYTYPE)];

./src/openms/include/OpenMS/CHEMISTRY/EnzymaticDigestion.h

static const std::string NamesOfSpecificity[SIZE_OF_SPECIFICITY];

./src/openms/include/OpenMS/FORMAT/MSNumpressCoder.h

static const std::string NamesOfNumpressCompression[SIZE_OF_NUMPRESSCOMPRESSION];

./src/openms/include/OpenMS/METADATA/DataProcessing.h

static const std::string NamesOfProcessingAction[SIZE_OF_PROCESSINGACTION];

./src/openms/include/OpenMS/METADATA/Modification.h

static const std::string NamesOfSpecificityType[SIZE_OF_SPECIFICITYTYPE];

./src/openms/include/OpenMS/METADATA/SourceFile.h

static const std::string NamesOfChecksumType[SIZE_OF_CHECKSUMTYPE];

./src/openms/include/OpenMS/METADATA/Instrument.h

static const std::string NamesOfIonOpticsType[SIZE_OF_IONOPTICSTYPE];

./src/openms/include/OpenMS/METADATA/SpectrumSettings.h

static const std::string NamesOfSpectrumType[SIZE_OF_SPECTRUMTYPE];

./src/openms/include/OpenMS/METADATA/IonDetector.h

static const std::string NamesOfType[SIZE_OF_TYPE];
static const std::string NamesOfAcquisitionMode[SIZE_OF_ACQUISITIONMODE];

./src/openms/include/OpenMS/METADATA/Tagging.h

static const std::string NamesOfIsotopeVariant[SIZE_OF_ISOTOPEVARIANT];

./src/openms/include/OpenMS/METADATA/InstrumentSettings.h:

static const std::string NamesOfScanMode[SIZE_OF_SCANMODE];

./src/openms/include/OpenMS/METADATA/Precursor.h

static const std::string NamesOfActivationMethod[SIZE_OF_ACTIVATIONMETHOD];
static const std::string NamesOfActivationMethodShort[SIZE_OF_ACTIVATIONMETHOD];

./src/openms/include/OpenMS/METADATA/MSQuantifications.h

static const std::string NamesOfQuantTypes[SIZE_OF_QUANT_TYPES];

./src/openms/include/OpenMS/METADATA/MassAnalyzer.h

static const std::string NamesOfAnalyzerType[SIZE_OF_ANALYZERTYPE];
static const std::string NamesOfResolutionMethod[SIZE_OF_RESOLUTIONMETHOD];
static const std::string NamesOfResolutionType[SIZE_OF_RESOLUTIONTYPE];
static const std::string NamesOfScanDirection[SIZE_OF_SCANDIRECTION];
static const std::string NamesOfScanLaw[SIZE_OF_SCANLAW];
static const std::string NamesOfReflectronState[SIZE_OF_REFLECTRONSTATE];

./src/openms/include/OpenMS/METADATA/Sample.h

static const std::string NamesOfSampleState[SIZE_OF_SAMPLESTATE];

./src/openms/include/OpenMS/METADATA/ProteinIdentification.h

static const std::string NamesOfPeakMassType[SIZE_OF_PEAKMASSTYPE];

./src/openms/include/OpenMS/KERNEL/BaseFeature.h

static const std::string NamesOfAnnotationState[SIZE_OF_ANNOTATIONSTATE];

./src/openms_gui/include/OpenMS/VISUAL/LayerData.h

static const std::string NamesOfLabelType[SIZE_OF_LABEL_TYPE];

Examples:

Add example to readthedocs as this has been requested by users

add example: plot TIC from mzMLs

using getChromtograms()
and by manual calculation
https://pyopenms.readthedocs.io/en/latest/getting_started.html#tic-calculation

TheoreticalSpetrum generator

rename menu entry to "Fragment spectrum generation"
Plot spectrum with annotated ions in meta data arrays

add example on how to iterate over AASequence and print modified residues

Add basic protein inference example

Add target / decoy creation, PeptideIndexer, FDR, filtering
https://pyopenms.readthedocs.io/en/latest/peptide_search.html#simplesearch

also protein inference at the end

Formulate learning goals at top of each topic.

Maybe in a colored box e.g. something like

In this section, you will learn:

how to load, process and store mass spectra and chromatograms
how to plot spectra

add launch with Colab Button

It will be good to have Launch with Google Colab button similar to launch with binder option.

http://proteomics.ethz.ch/pyOpenMS_Manual.pdf is linked but doesn not exist anymore

http://proteomics.ethz.ch/pyOpenMS_Manual.pdf

Example how to score theoretical spectrum and observed spectrum using hyperscore

add short high-level background in introduction (e.g. chromatography)

few sentences so that the reader with no background can at least get an idea how to classify the information/topic that follows

Publicly available workflows or building blocks?

Hi,

I wonder if there is a repository of workflows are building blocks to build workflows with PyOpenMs?

In particular, I am looking for an implementation of a TMT 11 quantitative proteomics workflow.

possible faeature: adding a filter for the MS column

Some sample code how to add filters to (e.g., the MS column)

#!/usr/bin/env python
#-*- coding:utf-8 -*-

from PyQt5 import QtCore, QtGui
from PyQt5.QtWidgets import QApplication, QMainWindow, QVBoxLayout, \
        QHBoxLayout, QWidget, QDesktopWidget, QMessageBox, \
        QLabel, QAction, QFileDialog, QTableView, QSplitter, QComboBox, \
        QDialog, QToolButton, QLineEdit, QRadioButton, QGroupBox, QGridLayout, QMenu,\
        QFormLayout, QDialogButtonBox, QAbstractItemView
from PyQt5.QtCore import Qt, QAbstractTableModel, pyqtSignal, QItemSelectionModel, QSortFilterProxyModel
from PyQt5.QtGui import QStandardItemModel, QStandardItem, QPainter, QIcon, QBrush, QColor, QPen, QPixmap

import random

class myWindow(QMainWindow):
    def __init__(self, parent=None):
        super(myWindow, self).__init__(parent)
        self.centralwidget  = QWidget(self)
        self.view           = QTableView(self.centralwidget)
        self.gridLayout = QGridLayout(self.centralwidget)
        self.gridLayout.addWidget(self.view, 1, 0, 1, 3)
        self.setCentralWidget(self.centralwidget)
        self.model = QStandardItemModel(self)

        # fill table with values
        for rowName in range(15):
            self.model.invisibleRootItem().appendRow(
                [QStandardItem("MS {0}".format(random.randint(1,3)))] +
                [ 
                    QStandardItem("blablub")
                    for columns in range(4)
                    ]
                )

        self.proxy = QSortFilterProxyModel(self)
        self.proxy.setSourceModel(self.model)
        self.view.setModel(self.proxy)

        self.horizontalHeader = self.view.horizontalHeader()
        self.horizontalHeader.sectionClicked.connect(self.on_view_horizontalHeader_sectionClicked)

    @QtCore.pyqtSlot(int)
    def on_view_horizontalHeader_sectionClicked(self, logicalIndex):
        if logicalIndex != 0: return # allow filter on first column only

        self.logicalIndex  = logicalIndex
        self.menuValues = QMenu(self)
        self.signalMapper = QtCore.QSignalMapper(self)  

        valuesUnique = [    self.model.item(row, self.logicalIndex).text()
                            for row in range(self.model.rowCount())
                            ]

        actionAll = QAction("All", self)
        actionAll.triggered.connect(self.on_actionAll_triggered)
        self.menuValues.addAction(actionAll)
        self.menuValues.addSeparator()

        for actionNumber, actionName in enumerate(sorted(list(set(valuesUnique)))):              
            action = QAction(actionName, self)
            self.signalMapper.setMapping(action, actionNumber)  
            action.triggered.connect(self.signalMapper.map)  
            self.menuValues.addAction(action)

        self.signalMapper.mapped.connect(self.on_signalMapper_mapped)  

        headerPos = self.view.mapToGlobal(self.horizontalHeader.pos())        

        posY = headerPos.y() + self.horizontalHeader.height()
        posX = headerPos.x() + self.horizontalHeader.sectionPosition(self.logicalIndex)

        self.menuValues.exec_(QtCore.QPoint(posX, posY))

    @QtCore.pyqtSlot()
    def on_actionAll_triggered(self):
        filterColumn = self.logicalIndex
        filterString = QtCore.QRegExp(  "",
                                        QtCore.Qt.CaseInsensitive,
                                        QtCore.QRegExp.RegExp
                                        )

        self.proxy.setFilterRegExp(filterString)
        self.proxy.setFilterKeyColumn(filterColumn)

    @QtCore.pyqtSlot(int)
    def on_signalMapper_mapped(self, i):
        stringAction = self.signalMapper.mapping(i).text()
        filterColumn = self.logicalIndex
        filterString = QtCore.QRegExp(  stringAction,
                                        QtCore.Qt.CaseSensitive,
                                        QtCore.QRegExp.FixedString
                                        )

        self.proxy.setFilterRegExp(filterString)
        self.proxy.setFilterKeyColumn(filterColumn)

if __name__ == "__main__":
    import sys

    app  = QApplication(sys.argv)
    main = myWindow()
    main.show()
    main.resize(400, 600)
    sys.exit(app.exec_())

create github action with pyopenms installed from nightly conda
e.g. move code snippets into files
run on changes

Updating dependencies
Resolving dependencies...

Package operations: 0 installs, 1 update, 0 removals

  • Updating pyopenms (2.4.0 -> 2.6.0)

  EnvCommandError

  Command D:\mvp-end-device-agent\.venv\Scripts\pip.exe install --no-deps -U file:///C:/Users/Plasmion/AppData/Local/pypoetry/Cache/artifacts/e5/19/70/ec2071b487ede5fe00136b514692e0ba8dbd27f9303bfa7f79dd9c2fa6/pyopenms-2.6.0-cp38-cp38-win_amd64.whl errored with the following return code 2, and output: 
  Processing c:\users\plasmion\appdata\local\pypoetry\cache\artifacts\e5\19\70\ec2071b487ede5fe00136b514692e0ba8dbd27f9303bfa7f79dd9c2fa6\pyopenms-2.6.0-cp38-cp38-win_amd64.whl
  ERROR: Exception:
  Traceback (most recent call last):
    File "D:\mvp-end-device-agent\.venv\lib\site-packages\pip\_internal\cli\base_command.py", line 228, in _main
      status = self.run(options, args)
    File "D:\mvp-end-device-agent\.venv\lib\site-packages\pip\_internal\cli\req_command.py", line 182, in wrapper
      return func(self, options, args)
    File "D:\mvp-end-device-agent\.venv\lib\site-packages\pip\_internal\commands\install.py", line 323, in run
      requirement_set = resolver.resolve(
    File "D:\mvp-end-device-agent\.venv\lib\site-packages\pip\_internal\resolution\legacy\resolver.py", line 183, in resolve
      discovered_reqs.extend(self._resolve_one(requirement_set, req))
    File "D:\mvp-end-device-agent\.venv\lib\site-packages\pip\_internal\resolution\legacy\resolver.py", line 391, in _resolve_one
      dist = abstract_dist.get_pkg_resources_distribution()
    File "D:\mvp-end-device-agent\.venv\lib\site-packages\pip\_internal\distributions\wheel.py", line 29, in get_pkg_resources_distribution
      with ZipFile(self.req.local_file_path, allowZip64=True) as z:
    File "d:\python\python386\lib\zipfile.py", line 1269, in __init__
      self._RealGetContents()
    File "d:\python\python386\lib\zipfile.py", line 1336, in _RealGetContents
      raise BadZipFile("File is not a zip file")
  zipfile.BadZipFile: File is not a zip file

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