__main__.py 6.77 KB
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#!/usr/bin/env python3

from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as FigureCanvas
from matplotlib.figure import Figure
from matplotlib.widgets import SpanSelector
from PyQt5 import QtCore
from PyQt5 import QtWidgets
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from PyQt5 import QtGui
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from rawprasslib import load_raw
import prasopes.graphtools as gt
import prasopes.filetools as ft
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import prasopes.zcetools as zce
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import prasopes.drltools as drl
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import prasopes.config as cf
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import sys
import matplotlib
import logging
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import os.path
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matplotlib.use("Qt5Agg")


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def load_file(chrom_plot, spc, d_set, ms_s, fn, chrom_s, settings):
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    """populates dataset and plots it"""
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    directory=settings.value("open_folder")
    if fn[0] is not None:
        directory=fn[0]
    filename = QtWidgets.QFileDialog.getOpenFileName(
            caption="Open spectrum",
            directory=directory,
            filter="Finnigan RAW files (*.raw, *.RAW)")[0]
    if filename is not '':
        d_set['chrom_dat'], d_set['masses'], d_set['matrix'] \
             = load_raw(filename, settings.value("tmp_location"))
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        gt.populate(chrom_plot, spc, d_set, ms_s, chrom_s)
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        fn[0] = filename

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def update_spectrum(event, chromatogram, spect, ds,
                    ms, fn, chrom, config):
    if fn[0] is not None and event.key is "f5":
        slims = [spect.get_xlim(), spect.get_ylim()]
        ds['chrom_dat'], ds['masses'], ds['matrix'] \
            = load_raw(fn[0], config.value("tmp_location"))
        gt.populate(chromatogram, spect, ds, ms, chrom)
        spect.set_xlim(slims[0])
        spect.set_ylim(slims[1])
        spect.get_figure().canvas.draw()


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def main():
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    # ds for data_set, ms for mass_spec_dataset, chrom for chrom_dataset
    ds = dict(chrom_dat=None, masses=None, matrix=None)
    ms = dict(x=[0], y=[0], line=None, annotation=[],
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              name="Spectrum", xlabel="m/z", ylabel="ion count",
              xtics=20)
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    chrom = dict(x=[0], y=[0], line=None, t_start=None, t_end=None,
                 name="Chromatogram", xlabel="time(min)",
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                 ylabel="total ion count", timesarg=None)
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    filename = [None]
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    drlcache = [None, None, None]
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    config = cf.settings()

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    p_logger = logging.getLogger('parseLogger')
    logging.basicConfig()
    p_logger.setLevel("WARN")

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    graph = Figure(figsize=(5, 4), dpi=100, facecolor="None")
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    chromatogram = graph.add_subplot(211, facecolor=(1, 1, 1, 0.8))
    spectrum = graph.add_subplot(212, facecolor=(1, 1, 1, 0.8))
    graph.tight_layout()

    mpl_canvas = FigureCanvas(graph)
    mpl_canvas.setStyleSheet("background-color:transparent;")
    mpl_canvas.setAutoFillBackground(False)
    mpl_canvas.setFocusPolicy(QtCore.Qt.ClickFocus)
    
    gt.pan_factory(chromatogram)
    gt.zoom_factory(chromatogram, 1.15)
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    gt.arrow_factory(spectrum, chromatogram, ds, ms, chrom)
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    gt.pan_factory(spectrum, ms)
    gt.zoom_factory(spectrum, 1.15, ms)
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    mass_selector = SpanSelector(
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        spectrum, lambda x_min, x_max: gt.pick_masses(
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            x_min, x_max, spectrum, ms), 'horizontal', minspan=0.01,
        useblit=True, rectprops=dict(alpha=0.15, facecolor='purple'),
        button=3)
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    time_selector = SpanSelector(
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         chromatogram, lambda x_min, x_max: gt.pick_times(
             x_min, x_max, spectrum, ds, chromatogram, ms, chrom), 
         'horizontal', useblit=True, rectprops=dict(
             alpha=0.15, facecolor='purple'), button=3)

    app = QtWidgets.QApplication(sys.argv)
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    main_window = QtWidgets.QMainWindow(windowTitle="Prasopes")
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    openact = QtWidgets.QAction(QtGui.QIcon.fromTheme(
        "document-open"), "&Open...")
    openact.setShortcut(QtCore.Qt.CTRL + QtCore.Qt.Key_O)
    openact.triggered.connect(lambda: load_file(
        chromatogram, spectrum, ds, ms, filename, chrom, config))
    exportact = QtWidgets.QAction(QtGui.QIcon.fromTheme(
        "document-save-as"), "&Export...")
    exportact.setShortcut(QtCore.Qt.CTRL + QtCore.Qt.Key_E)
    exportact.triggered.connect(lambda: ft.export_dial(
        ms, chrom, filename, main_window))
    settingsact = QtWidgets.QAction(QtGui.QIcon.fromTheme(
        "preferences-system"), "&Settings...")
    settingsact.triggered.connect(lambda: cf.dial(main_window))
    quitact = QtWidgets.QAction(QtGui.QIcon.fromTheme(
        "application-exit"), "&Quit")
    quitact.setShortcut(QtCore.Qt.CTRL + QtCore.Qt.Key_Q)
    quitact.triggered.connect(main_window.close)
    zceact = QtWidgets.QAction(QtGui.QIcon.fromTheme(
        "applications-utilities"), "&TSQ zce...")
    zceact.setShortcut(QtCore.Qt.CTRL + QtCore.Qt.Key_T)
    zceact.triggered.connect(lambda: zce.dialog(
        main_window, ds, filename))
    drlact = QtWidgets.QAction(QtGui.QIcon.fromTheme(
        "applications-utilities"), "&DRL...")
    drlact.setShortcut(QtCore.Qt.CTRL + QtCore.Qt.Key_D)
    drlact.triggered.connect(lambda: drl.main_window(
        main_window, ds, filename, drlcache))




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    file_menu = QtWidgets.QMenu('&File', main_window)
    main_window.menuBar().addMenu(file_menu)
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    file_menu.addAction(openact)
    file_menu.addAction(exportact)
    file_menu.addSeparator()
    file_menu.addAction(settingsact)
    file_menu.addSeparator()
    file_menu.addAction(quitact)
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    tools_menu = QtWidgets.QMenu('&Tools', main_window)
    main_window.menuBar().addMenu(tools_menu)
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    tools_menu.addAction(zceact)
    tools_menu.addAction(drlact)
    """tools_menu.addAction('&TSQ zce', lambda: zce.dialog(
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        main_window, ds, filename), QtCore.Qt.CTRL + QtCore.Qt.Key_T)
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    tools_menu.addAction('&DRL..', lambda: drl.main_window(
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        main_window, ds, filename, drlcache),
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        QtCore.Qt.CTRL + QtCore.Qt.Key_D)"""
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    main_widget = QtWidgets.QWidget(main_window)
    main_window.setCentralWidget(main_widget)

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    toolBar = QtWidgets.QToolBar(main_window)
    toolBar.setAllowedAreas(QtCore.Qt.TopToolBarArea)
    toolBar.setFloatable(False)
    toolBar.setMovable(False)
    toolBar.setToolButtonStyle(QtCore.Qt.ToolButtonTextBesideIcon)
    toolBar.addAction(openact)
    toolBar.addAction(exportact)
    toolBar.addSeparator()
    toolBar.addAction(zceact)
    toolBar.addAction(drlact)

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    layout = QtWidgets.QVBoxLayout(main_widget)
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    layout.addWidget(toolBar)
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    layout.addWidget(mpl_canvas)
    mpl_canvas.setFocus()

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    mpl_canvas.mpl_connect('key_press_event', lambda event:
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        update_spectrum(event, chromatogram, spectrum, ds, ms,
                        filename, chrom, config))


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    if len(sys.argv) == 2:
        raw_file = sys.argv[1]
        filename[0] = raw_file
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        ds['chrom_dat'], ds['masses'], ds['matrix'] = load_raw(
                raw_file, config.value("tmp_location"))
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        gt.populate(chromatogram, spectrum, ds, ms, chrom)
    else:
        gt.pop_plot(spectrum, ms)
        gt.pop_plot(chromatogram, chrom)

    main_window.show()
    sys.exit(app.exec_())
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if __name__ == "__main__":
    main()