def main(filename, opt=6, label=None, n=0, opts=None, colorlist=[], stylelist=None): '''loads file and invokes makegraphs and printstats. Appends graphics from each file onto the figure. opt is a symbol for the graph type; n is the serial number of successful traces.''' logfh = open(opts["logfile"], "a") if opts["filetype"].upper() == "MGM": spectrum = getmgrkmerspectrum(filename, mgrkey=MGRKEY) elif opts["filetype"] == "file": spectrum = loadfile(filename) else: raise ValueError( "%s is invalid type (valid types are mgm and file)" % opts.filetype) if spectrum == []: # Abort this trace--but try to graph the others return n if label is None: label = filename if spectrum.shape[1] > 0: spectrum = spectrum[np.lexsort((spectrum[:, 1], spectrum[:, 0]))] sys.stderr.write("Making graphs for %s\n" % filename) try: makegraphs( spectrum, filename, option=opt, label=label, n=n, dump=opts["dump"], opts=opts, colorlist=colorlist, stylelist=stylelist) # sys.stderr.write("Printing stats in logfile %s %d\n" % # (opts.logfile, n)) printstats(spectrum, filename, filehandle=logfh, n=n) n += 1 except ValueError as err: # This catches no data or defective data sys.stderr.write("Error printing stats for %s\n" % filename) else: sys.stderr.write("Error with dataset %s\n" % filename) return n
def main(filename, opt=6, label=None, n=0, opts=None, colorlist=[], stylelist=None): '''loads file and invokes makegraphs and printstats. Appends graphics from each file onto the figure. opt is a symbol for the graph type; n is the serial number of successful traces.''' logfh = open(opts.logfile, "a") if opts.filetype.upper() == "MGM": spectrum = getmgrkmerspectrum(filename, mgrkey=MGRKEY) elif opts.filetype == "file": spectrum = loadfile(filename) else: raise ValueError( "%s is invalid type (valid types are mgm and file)" % opts.filetype) if spectrum == []: # Abort this trace--but try to graph the others return n if label is None: label = filename if spectrum.shape[1] > 0: spectrum = spectrum[np.lexsort((spectrum[:, 1], spectrum[:, 0]))] sys.stderr.write("Making graphs for %s\n" % filename) try: makegraphs( spectrum, filename, option=opt, label=label, n=n, dump=opts.dump, opts=opts, colorlist=colorlist, stylelist=stylelist) # sys.stderr.write("Printing stats in logfile %s %d\n" % # (opts.logfile, n)) printstats(spectrum, filename, filehandle=logfh, n=n) n += 1 except ValueError as err: # This catches no data or defective data sys.stderr.write("Error printing stats for %s\n" % filename) else: sys.stderr.write("Error with dataset %s\n" % filename) return n
def test_makegraphs_list_5(): p = makegraphs([FIXTURE1, FIXTURE2], ["FIXTURE1", "SRR000331"], option=5)
def test_makegraphs_list(): p = makegraphs([FIXTURE1, FIXTURE2], ["FIXTURE1", "SRR000331"])
def test_makegraphs_30(): p = makegraphs(FIXTURE1, "tempfilename", option=30)
def test_makegraphs_name(): p = makegraphs(FIXTURE1, "tempfilename", option=6, label="ridiculouslabel", name="graph title")
def test_makegraphs_label(): p = makegraphs(FIXTURE1, "tempfilename", option=6, label="ridiculouslabel")
def test_makegraphs_m2d(): p = makegraphs(FIXTURE1, "tempfilename", option=- 2, dump=True, suppress=True)
def test_makegraphs_labels(): p = makegraphs(FIXTURE1, "tempfilename", ylabel="Y label", xlabel="X label")
def test_makegraphs_6d(capsys): p = makegraphs(FIXTURE1, "tempfilename", option=6, dump=True) out, err = capsys.readouterr() assert len(out) < 30
def test_makesgraphs(): for i in range(-3, 29): print("testing visualization {:d}".format(i)) p = makegraphs(FIXTURE1, "tempfilename", option=i)