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)