assert tn.getColNames()[0]=="id"
assert list(tn.id) == range(len(t))
tn.renameColumns(int='iii')
assert set(tn.getVisibleCols()) == { 'iii', 'long', 'id' }
tn.addColumn('x', 'hi', str, '%s')
assert set(tn.getVisibleCols()) == { 'iii', 'long', 'id', 'x' }
assert tn.getColNames()[-1]=="x"
assert list(tn.x) == ["hi"]*len(tn)
before = set(os.listdir("temp_output"))
tn.storeCSV(u"temp_output/x.csv")
tnre = ms.loadCSV("temp_output/x.csv")
assert len(tnre) == len(tn)
assert tnre.getColNames() == tn.getColNames()
assert tnre.id.values == tn.id.values
assert tnre.iii.values == tn.iii.values
assert tnre.long.values == tn.long.values
assert tnre.x.values == tn.x.values
tn.storeCSV("temp_output/x.csv", onlyVisibleColumns=False)
after = set(os.listdir("temp_output"))
# file written twice !
assert len(after-before) == 2
for n in after-before:
# maybe we have some x.csv.? from previous run of this
def test_handling_of_wrong_answer_from_metlin():
t = ms.loadCSV("data/metlin_input.csv")
assert len(t) == 2, len(t)
tn = ms.matchMetlin(t, "mass__0", ["M"], 3)
assert len(tn) == 12, len(tn)
assert set(tn.formula__1.values) == set(["C7H14O6", "C13H10N2"])
"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)
ms.inspect(result)
def testCSVParsing():
tab = ms.loadCSV("data/mass.csv", )
fms = '"%.2fm" % (o/60.0)'
assert tab.getFormat("RT_min") == "%.2f", tab.getFormat("RT_min")
import ms
universal = ms.loadCSV(r"tables\universal_metabolites.csv")
universal.renameColumns(
RT_max="rtmax",
RT_min="rtmin",
M0="m0",
link_to_pubchem="url",
compouind_name="name",
MF="mf",
)
universal.replaceColumn("rtmax", universal.rtmax * 60)
universal.replaceColumn("rtmin", universal.rtmin * 60)
universal.set(universal.colFormats, "rtmin", '"%.2fm" % (o/60.0)')
universal.set(universal.colFormats, "rtmax", '"%.2fm" % (o/60.0)')
universal._print()
universal.store(r"tables\universal_metabolites.table", True)
assert tn.getColNames()[0] == "id"
assert list(tn.id) == range(len(t))
tn.renameColumns(int='iii')
assert set(tn.getVisibleCols()) == {'iii', 'long', 'id'}
tn.addColumn('x', 'hi', str, '%s')
assert set(tn.getVisibleCols()) == {'iii', 'long', 'id', 'x'}
assert tn.getColNames()[-1] == "x"
assert list(tn.x) == ["hi"] * len(tn)
before = set(os.listdir("temp_output"))
tn.storeCSV(u"temp_output/x.csv")
tnre = ms.loadCSV("temp_output/x.csv")
assert len(tnre) == len(tn)
assert tnre.getColNames() == tn.getColNames()
assert tnre.id.values == tn.id.values
assert tnre.iii.values == tn.iii.values
assert tnre.long.values == tn.long.values
assert tnre.x.values == tn.x.values
tn.storeCSV("temp_output/x.csv", onlyVisibleColumns=False)
after = set(os.listdir("temp_output"))
# file written twice !
assert len(after - before) == 2
for n in after - before:
# maybe we have some x.csv.? from previous run of this
#function so we can not assume that we find x.csv and
#x.csv.1
import ms
universal = ms.loadCSV(r"tables\universal_metabolites.csv")
universal.renameColumns(RT_max="rtmax", RT_min="rtmin", M0="m0", link_to_pubchem="url", compouind_name="name", MF="mf", )
universal.replaceColumn("rtmax", universal.rtmax * 60)
universal.replaceColumn("rtmin", universal.rtmin * 60)
universal.set(universal.colFormats, "rtmin", '"%.2fm" % (o/60.0)')
universal.set(universal.colFormats, "rtmax", '"%.2fm" % (o/60.0)')
universal._print()
universal.store(r"tables\universal_metabolites.table", True)
message += "maybe this caused this exception !"
if len(e.args) > 0:
e0 = e.args[0] + "\n" + message
e.args = (e0, ) + e.args[1:]
raise e
import os, ms, glob
from libms.Chemistry.Elements import Elements
here = os.path.abspath(os.path.dirname(__file__))
for path in [here] + repositoryPathes:
path = os.path.join(path, "tables")
for p in glob.glob("%s/*.csv" % path):
try:
table = ms.loadCSV(p)
except Exception, e:
import traceback
traceback.print_exc()
print "PARSING", p, "FAILED"
continue
name, _ = os.path.splitext(os.path.basename(p))
name = name.replace(" ", "_")
table.title = name
exec("%s=table" % name)
print "LOADED", name, "FROM", p
# table files overrun csv files !
for p in glob.glob("%s/*.table" % path):
try:
table = ms.loadTable(p)
except Exception, e:
def test_handling_of_wrong_answer_from_metlin():
t = ms.loadCSV("data/metlin_input.csv")
assert len(t) == 2, len(t)
tn = ms.matchMetlin(t, "mass__0", ["M"], 3)
assert len(tn) == 12, len(tn)
assert set(tn.formula__1.values) == set(["C7H14O6", "C13H10N2"])
message += "maybe this caused this exception !"
if len(e.args)>0:
e0 = e.args[0] + "\n" + message
e.args = (e0,) + e.args[1:]
raise e
import os, ms, glob
from libms.Chemistry.Elements import Elements
here = os.path.abspath(os.path.dirname(__file__))
for path in [here] + repositoryPathes:
path = os.path.join(path, "tables")
for p in glob.glob("%s/*.csv" % path):
try:
table = ms.loadCSV(p)
except Exception, e:
import traceback
traceback.print_exc()
print "PARSING",p,"FAILED"
continue
name, _ = os.path.splitext(os.path.basename(p))
name = name.replace(" ","_")
table.title = name
exec("%s=table" % name)
print "LOADED", name, "FROM", p
# table files overrun csv files !
for p in glob.glob("%s/*.table" % path):
try:
table = ms.loadTable(p)
except Exception, e:
def testCSVParsing():
tab = ms.loadCSV("data/mass.csv", )
fms = '"%.2fm" % (o/60.0)'
assert tab.getFormat("RT_min") == "%.2f", tab.getFormat("RT_min")
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)
ms.inspect(result)