def Experiment_store(names, peakz):
for n, p in itertools.izip(names, peakz):
expr = Experiment(n, p)
expr.sele_rt_range(["1m", "50m"])
store_expr("/home/juicebox/Desktop/StrawberryExotic/parameters_v/bigFold2/"+n+".p130_s30_%2_n3expr", expr)
print(n, "checked")
def Experiment_store(names, peakz):
for n, p in itertools.izip(names, peakz):
expr = Experiment(n, p)
expr.sele_rt_range(["1m", "50m"])
store_expr("/home/cocopalacelove/Desktop/StrawberryExotic/output/"+n+"UID.expr", expr)
print(n, "checked")
def store_as_expr(run, peak_list, args):
# create an experiment
print "creating expression file for run ",run
expr = Experiment(run, peak_list)
print "created expression file "
# set time range for all experiments
expr.sele_rt_range([args.trimstart+"m", args.trimend+"m"])
filename, fileext = os.path.splitext(run)
print "storing expression file at", os.path.join(exprdir,(filename+".expr"))
store_expr( os.path.join(exprdir,(filename+".expr")), expr )
return expr
def store_as_expr(run, peak_list, args):
# create an experiment
print "creating expression file for run ", run
expr = Experiment(run, peak_list)
print "created expression file "
# set time range for all experiments
expr.sele_rt_range([args.trimstart + "m", args.trimend + "m"])
filename, fileext = os.path.splitext(run)
print "storing expression file at", os.path.join(exprdir,
(filename + ".expr"))
store_expr(os.path.join(exprdir, (filename + ".expr")), expr)
return expr
def Experiment_store(names, peakz, name_tag, sdir2):
"""
Stores peak information used in the peak alignment scripts ()
Using CMD args for the names and storage directory
@param names: .cdf file names processed by this script
@param peakz: peak data corresponding to each .cdf file
@param name_tag: Identifier expressing peak detection variables used in this processing run
@param sdir2: Location to store to .expr files corresponding to each .cdf file
@return: list of files saved
"""
for n, p in itertools.izip(names, peakz):
expr = Experiment(n, p)
expr.sele_rt_range(["1m", "50m"])
store_expr(sdir2 + n + name_tag + ".expr", expr)
print(n, "checked")
# do peak detection on pre-trimmed data
# get the list of Peak objects
pl = BillerBiemann(im, points, scans)
# trim by relative intensity
apl = rel_threshold(pl, r)
# trim by threshold
peak_list = num_ions_threshold(apl, n, t)
print "Number of Peaks found:", len(peak_list)
# ignore TMS ions and set mass range
for peak in peak_list:
peak.crop_mass(50,540)
peak.null_mass(73)
peak.null_mass(147)
# find area
area = peak_sum_area(im, peak)
peak.set_area(area)
# create an experiment
expr = Experiment("a0806_077", peak_list)
# set time range for all experiments
expr.sele_rt_range(["6.5m", "21m"])
store_expr("output/a0806_077.expr", expr)
for peak in peak_list:
peak.crop_mass(50,540)
peak.null_mass(73)
peak.null_mass(147)
# find peak areas
area = peak_sum_area(im, peak)
peak.set_area(area)
area_dict = peak_top_ion_areas(im, peak)
peak.set_ion_areas(area_dict)
# create an experiment
expr = Experiment(expr_code, peak_list)
# use same retention time range for all experiments
lo_rt_limit = "6.5m"
hi_rt_limit = "21m"
print "\t -> Selecting retention time range between '%s' and '%s'" % \
(lo_rt_limit, hi_rt_limit)
expr.sele_rt_range([lo_rt_limit, hi_rt_limit])
# store processed data as experiment object
output_file = "output/" + expr_code + ".expr"
print "\t -> Saving the result as '%s'" % ( output_file )
store_expr(output_file, expr)
# ignore TMS ions and use same mass range for all experiments
for peak in peak_list:
peak.crop_mass(50, 540)
peak.null_mass(73)
peak.null_mass(147)
# find peak areas
area = peak_sum_area(im, peak)
peak.set_area(area)
area_dict = peak_top_ion_areas(im, peak)
peak.set_ion_areas(area_dict)
# create an experiment
expr = Experiment(expr_code, peak_list)
# use same retention time range for all experiments
lo_rt_limit = "6.5m"
hi_rt_limit = "21m"
print "\t -> Selecting retention time range between '%s' and '%s'" % \
(lo_rt_limit, hi_rt_limit)
expr.sele_rt_range([lo_rt_limit, hi_rt_limit])
# store processed data as experiment object
output_file = "output/" + expr_code + ".expr"
print "\t -> Saving the result as '%s'" % (output_file)
store_expr(output_file, expr)
def Experiment_store(names, peakz, name_tag, sdir2):
for n, p in itertools.izip(names, peakz):
expr = Experiment(n, p)
expr.sele_rt_range(["1m", "50m"])
store_expr(sdir2 + n + name_tag + ".expr", expr)
print(n, "checked")
pl = BillerBiemann(im, pk_points, pk_scans)
# trim by relative intensity
apl = rel_threshold(pl, r)
# trim by number of ions above threshold
peak_list = num_ions_threshold(apl, n, t)
print " done."
print " [ Number of peaks found: %d ]" % ( len(peak_list) )
# find peak areas
for peak in peak_list:
area = peak_sum_area(im, peak)
peak.set_area(area)
# store the results
print " Saving data ...",
# create an experiment object
expr = Experiment(expr_code, peak_list)
# select the time range to between 310 and 1258 seconds
expr.sele_rt_range(["310s", "1258s"])
store_expr(outfile + ".expr", expr)
print " done."
# do peak detection on pre-trimmed data
# get the list of Peak objects
pl = BillerBiemann(im, points, scans)
# trim by relative intensity
apl = rel_threshold(pl, r)
# trim by threshold
peak_list = num_ions_threshold(apl, n, t)
print "Number of Peaks found:", len(peak_list)
# ignore TMS ions and set mass range
for peak in peak_list:
peak.crop_mass(50, 540)
peak.null_mass(73)
peak.null_mass(147)
# find area
area = peak_sum_area(im, peak)
peak.set_area(area)
# create an experiment
expr = Experiment("a0806_077", peak_list)
# set time range for all experiments
expr.sele_rt_range(["6.5m", "21m"])
store_expr("output/a0806_077.expr", expr)
