def test_calccumsum_00_file():
data = loadfile(TESTDIR + "test00.21")
cn, c1, yd, yo, zd, zo = calccumsum(data)
assert_equal(cn, 1)
assert_equal(c1, 1)
assert_equal(yd, 1)
assert_equal(yo, 1)
assert_equal(zd, 1)
assert_equal(zo, 1)
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
# Loop over input identifiers, and skip if main()
# fails to produce some traces
spectra = []
labels = []
if opts.filelist:
if not os.path.isfile(opts.filelist):
sys.exit("File {} does not exist".format(opts.filelist))
IN_FILE = open(opts.filelist, "r")
for line in IN_FILE:
if line[0] != "#":
a = line.strip().split("\t")
if len(a[0]) > 0:
if len(a) == 1:
a.append(a[0])
sys.stderr.write("%s\t%s\n" % (a[0], a[1]))
contents = loadfile(a[0])
if contents != []:
spectra.append(contents)
labels.append(a[1])
if opts.option == 0:
plotstratifiedfracs(labels, spectra)
elif opts.option == 1:
plotstratifiedsizes(labels, spectra)
elif opts.option == -1:
summarizestrata(labels, spectra)
sys.exit()
else:
sys.exit("Valid graph types are -g 0, 1, and -1")
if opts.interactive:
sys.stderr.write("Interactive mode (no file output)\n")
plt.show()
"File {} does not exist".format(listfile)
IN_FILE = open(listfile, "r").readlines()
numplots = len(IN_FILE)
for line in IN_FILE:
if line[0] != "#":
a = line.strip().split("\t")
if len(a[0]) > 0:
if len(a) == 1:
a.append(a[0])
sys.stderr.write("%s %s \n" % (a[0], a[1]))
filename = a[0]
if len(a) == 3:
selectedcolor = a[2]
else:
selectedcolor = COLORS[n % len(COLORS)]
spectrum = loadfile(filename)
if spectrum != []:
plotme(spectrum, label=a[1], color=selectedcolor,
thresholdlist=listofthresholds,
numplots=numplots, dump=OPTS.dump, shaded=SHADED)
n = n + 1
if OPTS.suppresslegend == 0:
plt.legend(loc="upper left")
plt.savefig(OUTFILE)
else:
# for v in ARGS:
# print("#", v)
# filename = v
# spectrum = loadfile(filename)
# plotme(spectrum, filename, thresholdlist=listofthresholds,
# color=COLORS[n], dump=OPTS.dump, numplots=len(ARGS), shaded=SHADED)
def test_missingfile():
fixture = loadfile("nonexistentfile")
assert fixture == []
def test_loadfile_khmer():
fixture = loadfile(TESTDIR + "test_khmer.21")
assert type(fixture) == np.ndarray
def test_loadfile_stats():
fixture = loadfile(TESTDIR + "stats.txt")
assert type(fixture) == np.ndarray
def test_loadfile_npo():
fixture = loadfile(TESTDIR + "test_1.npo")
assert type(fixture) == np.ndarray
def test_loadfile_empty():
fixture = loadfile(TESTDIR + "emptyfile")
print(type(fixture))
assert fixture == []
def test_loadfile_SRR():
FIXTURE2 = loadfile(
"repeatresolutionpaper/counts-validationgenomedata/SRR000333.fastq.21")
[20000, 10000],
[200000, 100],
[1000000, 1],
[2000000, 1]], dtype="float")
FIXTURE3 = np.array([[2000, 1000000],
[20000, 10000],
[200000, 100],
[1000000, 1],
[2000000, 1]], dtype="int")
FIXTUREBAD1 = np.array([[0, 0]], dtype="int")
FIXTUREBAD2 = np.array([[0, 0]], dtype="float")
FIXTUREBAD3 = loadfile(TESTDIR + "testF1.21")
FIXTURE2 = loadfile(
"repeatresolutionpaper/counts-validationgenomedata/SRR000333.fastq.21")
def test_calccumsum_float():
data = FIXTURE1
cn, c1, yd, yo, zd, zo = calccumsum(data)
def test_calccumsum_int():
data = FIXTURE3
cn, c1, yd, yo, zd, zo = calccumsum(data)
def test_01():
data = loadfile(TESTDIR + "test01.21")
cn, c1, yd, yo, zd, zo = calccumsum(data)
pass
# Loop over input identifiers, and skip if main()
# fails to produce some traces
spectra = []
labels = []
if opts.filelist:
if not os.path.isfile(opts.filelist):
sys.exit("File {} does not exist".format(opts.filelist))
IN_FILE = open(opts.filelist, "r")
for line in IN_FILE:
if line[0] != "#":
a = line.strip().split("\t")
if len(a[0]) > 0:
if len(a) == 1:
a.append(a[0])
sys.stderr.write("%s\t%s\n" % (a[0], a[1]))
contents = loadfile(a[0])
if contents != []:
spectra.append(contents)
labels.append(a[1])
if opts.option == 0:
plotstratifiedfracs(labels, spectra)
elif opts.option == 1:
plotstratifiedsizes(labels, spectra)
elif opts.option == -1:
summarizestrata(labels, spectra)
sys.exit()
else:
sys.exit("Valid graph types are -g 0, 1, and -1")
if opts.interactive:
sys.stderr.write("Interactive mode (no file output)\n")
plt.show()
"File {} does not exist".format(listfile)
IN_FILE = open(listfile, "r").readlines()
numplots = len(IN_FILE)
for line in IN_FILE:
if line[0] != "#":
a = line.strip().split("\t")
if len(a[0]) > 0:
if len(a) == 1:
a.append(a[0])
sys.stderr.write("%s %s \n" % (a[0], a[1]))
filename = a[0]
if len(a) == 3:
selectedcolor = a[2]
else:
selectedcolor = COLORS[n % len(COLORS)]
spectrum = loadfile(filename)
if spectrum != []:
plotme(spectrum,
label=a[1],
color=selectedcolor,
thresholdlist=listofthresholds,
numplots=numplots,
dump=OPTS.dump,
shaded=SHADED)
n = n + 1
if OPTS.suppresslegend == 0:
plt.legend(loc="upper left")
plt.savefig(OUTFILE)
else:
# for v in ARGS:
# print("#", v)