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)