"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)
import sys
sys.path.insert(0, "..")
import ms
t = ms.loadTable("integrated_features.table")
t2 = t.copy()
tj = t.join(t2, t.id == t2.id)
tj.rtmin__0 -= 20
tj.rtmax__0 -= 20
pm = tj.peakmap__0.values[0]
for s in pm.spectra:
s.rt -= 20
ms.inspect(tj)
# 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 show():
ms.inspect(table)
def show():
ms.inspect(table)
#encoding: utf-8
import sys
sys.path.insert(0, "..")
import ms
table = ms.loadTable("features.table")
print table.rows[0]
ms.inspect([table])
#encoding: utf-8
import sys
sys.path.insert(0, "..")
import ms
table = ms.loadTable("features.table")
table2 = ms.loadTable("integrated_features.table")
ms.inspect([table, table2])
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)
def mzAlign(table,
fullC13=False,
tol=15 * MMU,
mz_reference_table=None,
destination=None,
minR2=0.95,
minPoints=5,
interactive=False):
"""
performs affine linear mz-correction for a feature table.
you need a ``mz_reference_table`` with the theoretical ideal masses
and retention times of some universal metabolites. This table needs
columns ``m0`` for the neutral mass, ``rtmin``, ``rtmax`` for the
retention time window for restricting the match of the table against
the ``mz_reference_table`` and the molecular formula ``mf``.
If you specify ``fullC13=True`` the ``mf`` is used to correct ``m0``.
``destination`` is a directory which will be used for storing the
result and intermediate data. If you do not specify this value, a
dialog for choosing the destination directory will be opened.
The input table **is not mofied** in place, the function returns the
aligned table.
"""
import ms
import tab
import os
import numpy as np
from _mzalign_helpers import (_buildHypotheseTable, _findMzMatches,
_findParametersAutomatically,
_findParametersManually, _plotAndSaveMatch,
_applyTransform)
if not interactive:
assert minR2 <= 1.0
assert minPoints > 1
sources = set(table.source.values)
assert len(sources) == 1
source = sources.pop()
if mz_reference_table is None:
mz_reference_table = tab.universal_metabolites
univ = mz_reference_table
univ.requireColumn("m0")
univ.requireColumn("rtmin")
univ.requireColumn("rtmax")
univ.requireColumn("mf")
assert univ.get(univ.colTypes, "m0") == float,\
"col m0 is not float"
assert univ.get(univ.colTypes, "rtmin") == float,\
"col rtmin is not float"
assert univ.get(univ.colTypes, "rtmax") == float,\
"col rtmax is not float"
polarities = set(table.polarity.values)
assert len(polarities) == 1, "multiple polarities in table"
polarity = polarities.pop()
hypot = _buildHypotheseTable(polarity, univ.copy(), fullC13)
if destination is not None:
basename = os.path.basename(source)
fname, _ = os.path.splitext(basename)
hypot.store(os.path.join(destination, fname + "_hypot.table"), True)
real, tobe, matches = _findMzMatches(hypot, table, tol)
if len(real) <= 1:
print "NOT ENOUGH MATCHES"
return
if interactive:
ms.inspect(matches, offerAbortOption=True)
elif len(tobe) < minPoints:
raise Exception("could only match %d peaks" % len(tobe))
if not interactive:
transform, used = _findParametersAutomatically(tobe.copy(), real.copy(),\
minR2, minPoints)
else:
transform, used = _findParametersManually(tobe.copy(), real.copy())
if transform is None:
print "ABORTED"
return
if destination is not None:
matches.addColumn("error", np.linalg.norm(transform(real)-tobe), float,\
"%.3e")
matches.store(os.path.join(destination, fname + "_mzalign.table"),
True)
matches.storeCSV(os.path.join(destination, fname + "_mzalign.csv"))
path = os.path.join(destination, fname + "_mzalign.png")
_plotAndSaveMatch(tobe, real, used, transform, path)
transformedTable = _applyTransform(table, transform)
print "DONE"
return transformedTable
::
"""
run("""common = joined.filter(joined.onEarth_1==1)
common._print()""")
MMU=0.001
print """
The ``tab`` module contains some databases, eg the substances from pubchem
categorized as *metabolomic compounds*::
"""
run("""import tab # some standard tables
pc = tab.pc_full
ms.inspect(pc)""")
print """
Before matching our data against the large pubchem table, we build an index on tthis table in order to speed up the following ``leftJoin`` call. Building an index is done by sorting the corresponding column::
"""
run("""pc.sortBy("m0")
matched=joined.leftJoin(pc, (joined.onEarth_1==1)
& joined.m0.approxEqual(pc.m0, 15*MMU))""")
run("matched.meta=dict()")
run("""print matched.numRows()""")
run("""ms.inspect(matched)""")