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)
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)
def process(self, path):
try:
print "read ", path
pm = ms.loadPeakMap(path)
except Exception, e:
print e
print "reading FAILED"
return None
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
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
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
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 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)
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
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)
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
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)
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)
# 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)
def test():
import ms
pm = ms.loadPeakMap("emzed_files/example1.mzXML")
t = metaboFeatureFinder(pm, epdet_width_filtering="auto")
ms.inspect(t)
def test():
import ms
pm = ms.loadPeakMap("emzed_files/example1.mzXML")
t = metaboFeatureFinder(pm, epdet_width_filtering="auto")
ms.inspect(t)