Exemplo n.º 1
0
def testLoadMap():
    from_ = u"data/SHORT_MS2_FILE.mzXML"
    ds = ms.loadPeakMap(from_)
    assert osp.basename(ds.meta.get("source")) == osp.basename(from_)

    # with unicode
    ms.storePeakMap(ds, u"temp_output/utilstest.mzML")
    ds2 = ms.loadPeakMap(u"temp_output/utilstest.mzML")
    assert len(ds) == len(ds2)

    # without unicode
    ms.storePeakMap(ds2, "temp_output/utilstest.mzData")
    ds3 = ms.loadPeakMap("temp_output/utilstest.mzData")
    assert len(ds) == len(ds3)
Exemplo n.º 2
0
def testLoadMap():
    from_ = u"data/SHORT_MS2_FILE.mzXML"
    ds = ms.loadPeakMap(from_)
    assert osp.basename(ds.meta.get("source")) ==  osp.basename(from_)

    # with unicode
    ms.storePeakMap(ds, u"temp_output/utilstest.mzML")
    ds2 = ms.loadPeakMap(u"temp_output/utilstest.mzML")
    assert len(ds)==len(ds2)

    # without unicode
    ms.storePeakMap(ds2, "temp_output/utilstest.mzData")
    ds3 = ms.loadPeakMap("temp_output/utilstest.mzData")
    assert len(ds)==len(ds3)
Exemplo n.º 3
0
        def process(self, path):

            try:
                print "read ", path
                pm = ms.loadPeakMap(path)
            except Exception, e:
                print e
                print "reading FAILED"
                return None
Exemplo n.º 4
0
        def process(self, path):

            try:
                print "read ", path
                pm = ms.loadPeakMap(path)
            except Exception, e:
                print e
                print "reading FAILED"
                return None
def testMatchedFilter():

    pm = ms.loadPeakMap("data/test.mzXML")
    table = ms.runMatchedFilters(pm,
            destination="temp_output", configid="std", mzdiff=0, fwhm=50,
            steps=1, step=0.6)

    assert len(table) == 340, len(table)
    assert len(table.getColNames()) ==  18, len(table.getColNames())
    assert len(table.getColTypes()) ==  18
Exemplo n.º 6
0
        def process(self, path):
            import ms
            from ms._metabo import metaboFeatureFinder

            try:
                print "read ", path
                ds = ms.loadPeakMap(path)
            except Exception, e:
                print e
                print "reading FAILED"
                return None
Exemplo n.º 7
0
def testCentwaveFeatureDetector():

    print "load"
    ds = ms.loadPeakMap("data/test_mini.mzXML")
    print "loaded"
    det = libms.RConnect.CentwaveFeatureDetector(ppm=3, peakwidth=(8, 13), snthresh=40, prefilter=(8, 10000), mzdiff=1.5 )
    assert det.__doc__ != None
    table = det.process(ds)
    table.print_()
    assert len(table) == 1, len(table)

    assert len(table.getColNames()) ==  16, len(table.getColNames())
    assert len(table.getColTypes()) ==  16, len(table.getColTypes())
    assert "polarity" in table.getColNames()
def testRunCentwave():

    pm = ms.loadPeakMap("data/test_mini.mzXML")
    table = ms.runCentwave(pm,
                           ppm=3,
                           peakwidth=(8, 13),
                           snthresh=40,
                           prefilter=(8, 10000),
                           mzdiff=1.5 )
    #runCentwave("data/test.mzXML", destination="temp_output", configid="std")
    #assert len(glob.glob("temp_output/test.csv")) == 1
    ##assert len(tables) == 1
    #table=tables[0]
    assert len(table) == 1, len(table)
    assert len(table.getColNames()) ==  16, len(table.getColNames())
    assert len(table.getColTypes()) ==  16
Exemplo n.º 9
0
def testCentwaveFeatureDetector():

    print "load"
    ds = ms.loadPeakMap("data/test_mini.mzXML")
    print "loaded"
    det = libms.RConnect.CentwaveFeatureDetector(ppm=3,
                                                 peakwidth=(8, 13),
                                                 snthresh=40,
                                                 prefilter=(8, 10000),
                                                 mzdiff=1.5)
    assert det.__doc__ != None
    table = det.process(ds)
    table.print_()
    assert len(table) == 1, len(table)

    assert len(table.getColNames()) == 16, len(table.getColNames())
    assert len(table.getColTypes()) == 16, len(table.getColTypes())
    assert "polarity" in table.getColNames()
Exemplo n.º 10
0
def test_ffm():
    import ms
    pm = ms.loadPeakMap("data/test.mzXML")
    pm = pm.extract(rtmin=6, rtmax=12, mzmin=350, mzmax=400)

    #ftab = ms.feature_detectors.runMetaboFeatureFinder(pm)
    #assert len(ftab) == 19, len(ftab)
    #ftab.print_()

    #ftab2 = ms.feature_detectors.runMetaboFeatureFinder(pm, config_id="std")
    #assert len(ftab2) == 30, len(ftab2)
    #ftab2.print_()

    ftab2 = ms.feature_detectors.runMetaboFeatureFinder(pm, ms_level=1)
    assert len(ftab2) == 19, len(ftab2)
    ftab2.print_()

    al1, al2 = ms.rtAlign([ftab2, ftab2],
                          refTable=ftab2,
                          destination=".",
                          nPeaks=10)
Exemplo n.º 11
0
def run(integrator, areatobe, rmsetobe):
    assert len(str(integrator))>0

    try:
        ds = run.ds
    except:
        ds = run.ds =  ms.loadPeakMap("data/SHORT_MS2_FILE.mzData")

    integrator.setPeakMap(ds)

    rtmin = ds.spectra[0].rt
    rtmax = ds.spectra[30].rt

    mzmin = ds.spectra[0].peaks[10,0]
    mzmax = ds.spectra[0].peaks[-10,0]

    result = integrator.integrate(mzmin, mzmax, rtmin, rtmax, 1)
    area=result.get("area")
    rmse=result.get("rmse")

    print "area: is=%e  tobe=%e" % (area, areatobe)
    print "rmse: is=%e  tobe=%e" % (rmse, rmsetobe)


    if area > 0:
        assert abs(area-areatobe)/areatobe < .01,  area
    else:
        assert area == 0.0, area
    if rmse > 0:
        assert abs(rmse-rmsetobe)/rmsetobe < .01,  rmse
    else:
        assert rmse == 0.0, rmse

    params = result.get("params")

    rts = [ spec.rt for spec in ds.spectra ]

    x, y = integrator.getSmoothed(rts, params)

    return x,y, params
Exemplo n.º 12
0
def test_ffm():
    import ms
    pm = ms.loadPeakMap("data/test.mzXML")
    pm = pm.extract(rtmin=6, rtmax=12, mzmin=350, mzmax=400)


    #ftab = ms.feature_detectors.runMetaboFeatureFinder(pm)
    #assert len(ftab) == 19, len(ftab)
    #ftab.print_()


    #ftab2 = ms.feature_detectors.runMetaboFeatureFinder(pm, config_id="std")
    #assert len(ftab2) == 30, len(ftab2)
    #ftab2.print_()


    ftab2 = ms.feature_detectors.runMetaboFeatureFinder(pm, ms_level=1)
    assert len(ftab2) == 19, len(ftab2)
    ftab2.print_()

    al1, al2 = ms.rtAlign([ftab2, ftab2], refTable=ftab2, destination=".",
            nPeaks=10)
Exemplo n.º 13
0
def run(integrator, areatobe, rmsetobe):
    assert len(str(integrator)) > 0

    try:
        ds = run.ds
    except:
        ds = run.ds = ms.loadPeakMap("data/SHORT_MS2_FILE.mzData")

    integrator.setPeakMap(ds)

    rtmin = ds.spectra[0].rt
    rtmax = ds.spectra[30].rt

    mzmin = ds.spectra[0].peaks[10, 0]
    mzmax = ds.spectra[0].peaks[-10, 0]

    result = integrator.integrate(mzmin, mzmax, rtmin, rtmax, 1)
    area = result.get("area")
    rmse = result.get("rmse")

    print "area: is=%e  tobe=%e" % (area, areatobe)
    print "rmse: is=%e  tobe=%e" % (rmse, rmsetobe)

    if area > 0:
        assert abs(area - areatobe) / areatobe < .01, area
    else:
        assert area == 0.0, area
    if rmse > 0:
        assert abs(rmse - rmsetobe) / rmsetobe < .01, rmse
    else:
        assert rmse == 0.0, rmse

    params = result.get("params")

    rts = [spec.rt for spec in ds.spectra]

    x, y = integrator.getSmoothed(rts, params)

    return x, y, params
Exemplo n.º 14
0
def testPeakPicking():
    pp = libms.PeakPicking.PeakPickerHiRes()
    ds = ms.loadPeakMap("data/gauss_data.mzML")
    ds2 = pp.pickPeakMap(ds)
    assert len(ds) == len(ds2)
    assert ds2.spectra[0].peaks.shape == (9570, 2)
Exemplo n.º 15
0
                                 default=0.5)
        mode = gui.ChoiceItem(
            "mode of operation", ["explore", "targeted extraction"],
            default=1,
            help="for explore mode no parameter table is needed")
        path_para = gui.FileOpenItem("parameter table", ("csv"))
        path_data = gui.FileOpenItem("data file to process",
                                     ("mzXML", "mzML", "mzData"))

    frontend = SRMExplorer()
    exit_code = frontend.show()

    if exit_code == 1:  # means: ok button pressed

        print "LOAD DATA"
        peakmap = ms.loadPeakMap(frontend.path_data)

        if frontend.mode == 1:
            transitions = ms.loadCSV(frontend.path_para)
            # Edit parameter table
            required_columns = [
                "name", "fragment", "precursor", "rtmin", "rtmax"
            ]
            assert transitions.hasColumns(*required_columns),\
                    "Please check column names in parameter table !!"
            transitions.title = "SRM parameter table"
        else:
            transitions = None

        print "PROCESS DATA"
        result = process_srm_data(peakmap, transitions, frontend.delta_mz)
Exemplo n.º 16
0
    # here we build the result:
    for i in range(1, len(table)):
        result = result.leftJoin(table[i])
    return result


def add_postfix_to_column_names(table, postfix):
    mapping = dict((name, name + postfix) for name in table.colNames)
    table.renameColumns(mapping)


if __name__ == "__main__":

    import libms.gui.DialogBuilder as gui

    class SRMExplorer(gui.WorkflowFrontend):
        n_digits = gui.IntItem("no of significant digits\nof precursor m/z",
                                default=2)
        path = gui.FileOpenItem("data file to process",
                                ("mzXML", "mzML", "mzData"))


    frontend = SRMExplorer()
    exit_code = frontend.show()
    if exit_code:
        print "LOAD DATA"
        peakmap = ms.loadPeakMap(frontend.path)
        print "PROCESS DATA"
        result = process_srm_data(peakmap, frontend.n_digits)
        ms.inspect(result)
Exemplo n.º 17
0
def test():
    import ms
    pm = ms.loadPeakMap("emzed_files/example1.mzXML")
    t = metaboFeatureFinder(pm, epdet_width_filtering="auto")
    ms.inspect(t)
Exemplo n.º 18
0
def test():
    import ms
    pm = ms.loadPeakMap("emzed_files/example1.mzXML")
    t = metaboFeatureFinder(pm, epdet_width_filtering="auto")
    ms.inspect(t)