def printChart(self, xLimit=50):
cEnd = chr(27) + "[0m"
fGreen = chr(27) + "[32m"
fYellow = chr(27) + "[33m"
print fGreen + "\n\nChart sorted by the longest requests. Limited for %s requests" % (xLimit) + cEnd
print "-" * 70
print fYellow
sortedRequestTimes = sorted(self.nginxRequestTimeList, reverse=True)
valuesForChart = sortedRequestTimes[0:xLimit]
aplotter.plot(valuesForChart, plot_slope=False, output=str)
def printChart(self, xLimit=50):
cEnd = chr(27) + '[0m'
fGreen = chr(27) + '[32m'
fYellow = chr(27) + '[33m'
print fGreen + "\n\nChart sorted by the longest requests. Limited for %s requests" % (
xLimit) + cEnd
print "-" * 70
print fYellow
sortedRequestTimes = sorted(self.nginxRequestTimeList, reverse=True)
valuesForChart = sortedRequestTimes[0:xLimit]
aplotter.plot(valuesForChart, plot_slope=False, output=str)
def plot(self):
print("entered plot()")
print('****** Sin([0,2pi]) ******')
scale=0.1
n=int(2*math.pi/scale)
plotx=[scale*i for i in xrange(n)]
ploty=[math.sin(scale*i) for i in xrange(n)]
aplotter.plot(plotx,ploty)
print('****** Some discrete data sequence ******')
data=[ord(c) for c in 'ASCII Plotter example']
aplotter.plot(data)
def main(args):
OptionParser.format_description = lambda self, formatter: self.description
OptionParser.format_epilog = lambda self, formatter: self.epilog
parser = OptionParser(usage="", description=prehelp % VERSION, epilog=posthelp % AUTH_LIST)
parser.add_option("", "--id", dest="id", default=None, help="KBase Metagenome ID")
parser.add_option("", "--url", dest="url", default=API_URL, help="communities API url")
parser.add_option("", "--user", dest="user", default=None, help="OAuth username")
parser.add_option("", "--passwd", dest="passwd", default=None, help="OAuth password")
parser.add_option("", "--token", dest="token", default=None, help="OAuth token")
parser.add_option(
"",
"--plot",
dest="plot",
action="store_true",
default=False,
help="display plot in ASCII art instead of table of numbers for: bp_profile, drisee, kmer, rarefaction, or taxa level",
)
parser.add_option(
"",
"--stat",
dest="stat",
default="sequence",
help="type of stat to display, use keyword: 'sequence', 'bp_profile', 'drisee', 'kmer', 'rarefaction', or taxa level name, default is sequence",
)
# get inputs
(opts, args) = parser.parse_args()
if not opts.id:
sys.stderr.write("ERROR: id required\n")
return 1
# get auth
token = get_auth_token(opts)
# build call url
url = opts.url + "/metagenome/" + opts.id + "?verbosity=stats"
# retrieve / output data
result = obj_from_url(url, auth=token)
stats = result["statistics"]
if opts.stat == "sequence":
for s in sorted(stats["sequence_stats"].iterkeys()):
safe_print("%s\t%s\n" % (s, stats["sequence_stats"][s]))
elif opts.stat == "bp_profile":
if not stats["qc"]["bp_profile"]["percents"]["data"]:
sys.stderr.write("ERROR: %s has no bp_profile statistics\n" % opts.id)
return 1
if opts.plot:
cols = stats["qc"]["bp_profile"]["percents"]["columns"][1:5]
data = map(lambda x: x[1:5], stats["qc"]["bp_profile"]["percents"]["data"])
plot_histo(cols, data, 20, 80)
else:
safe_print("\t".join(stats["qc"]["bp_profile"]["percents"]["columns"]) + "\n")
for d in stats["qc"]["bp_profile"]["percents"]["data"]:
safe_print("\t".join(map(str, d)) + "\n")
elif opts.stat == "drisee":
if not stats["qc"]["drisee"]["percents"]["data"]:
sys.stderr.write("ERROR: %s has no drisee statistics\n" % opts.id)
return 1
if opts.plot:
x, y = [], []
for d in stats["qc"]["drisee"]["percents"]["data"]:
x.append(d[0])
y.append(d[7])
aplotter.plot(x, y, output=sys.stdout, draw_axes=True, plot_slope=True, min_x=0, min_y=0)
else:
safe_print("\t".join(stats["qc"]["drisee"]["percents"]["columns"]) + "\n")
for d in stats["qc"]["drisee"]["percents"]["data"]:
safe_print("\t".join(map(str, d)) + "\n")
elif opts.stat == "kmer":
if not stats["qc"]["kmer"]["15_mer"]["data"]:
sys.stderr.write("ERROR: %s has no kmer statistics\n" % opts.id)
return 1
if opts.plot:
x, y = [], []
for d in stats["qc"]["kmer"]["15_mer"]["data"]:
x.append(math.log(d[3], 10))
y.append(math.log(d[0], 10))
aplotter.plot(x, y, output=sys.stdout, draw_axes=True, plot_slope=True, min_x=0, min_y=0)
else:
safe_print("\t".join(stats["qc"]["kmer"]["15_mer"]["columns"]) + "\n")
for d in stats["qc"]["kmer"]["15_mer"]["data"]:
safe_print("\t".join(map(str, d)) + "\n")
elif opts.stat == "rarefaction":
if not stats["rarefaction"]:
sys.stderr.write("ERROR: %s has no rarefaction statistics\n" % opts.id)
return 1
if opts.plot:
x, y = [], []
for r in stats["rarefaction"]:
x.append(int(r[0]))
y.append(float(r[1]))
aplotter.plot(x, y, output=sys.stdout, draw_axes=True, plot_slope=True, min_x=0, min_y=0)
else:
safe_print("x\ty\n")
for r in stats["rarefaction"]:
safe_print("%s\t%s\n" % (str(r[0]), str(r[1])))
elif opts.stat in stats["taxonomy"]:
ranked = sorted(stats["taxonomy"][opts.stat], key=lambda x: (-int(x[1]), x[0]))
if opts.plot:
top = map(lambda x: int(x[1]), ranked)[:50]
aplotter.plot(top, output=sys.stdout, draw_axes=True, plot_slope=False, min_x=0, min_y=0)
else:
for t in ranked:
safe_print("%s\t%s\n" % (t[0], str(t[1])))
else:
sys.stderr.write("ERROR: invalid stat type\n")
return 1
return 0
def main(args):
OptionParser.format_description = lambda self, formatter: self.description
OptionParser.format_epilog = lambda self, formatter: self.epilog
parser = OptionParser(usage='',
description=prehelp % VERSION,
epilog=posthelp % AUTH_LIST)
parser.add_option("",
"--id",
dest="id",
default=None,
help="KBase Metagenome ID")
parser.add_option("",
"--url",
dest="url",
default=API_URL,
help="communities API url")
parser.add_option("",
"--user",
dest="user",
default=None,
help="OAuth username")
parser.add_option("",
"--passwd",
dest="passwd",
default=None,
help="OAuth password")
parser.add_option("",
"--token",
dest="token",
default=None,
help="OAuth token")
parser.add_option(
"",
"--plot",
dest="plot",
action="store_true",
default=False,
help=
"display plot in ASCII art instead of table of numbers for: bp_profile, drisee, kmer, rarefaction, or taxa level"
)
parser.add_option(
"",
"--stat",
dest="stat",
default='sequence',
help=
"type of stat to display, use keyword: 'sequence', 'bp_profile', 'drisee', 'kmer', 'rarefaction', or taxa level name, default is sequence"
)
# get inputs
(opts, args) = parser.parse_args()
if not opts.id:
sys.stderr.write("ERROR: id required\n")
return 1
# get auth
token = get_auth_token(opts)
# build call url
url = opts.url + '/metagenome/' + opts.id + '?verbosity=stats'
# retrieve / output data
result = obj_from_url(url, auth=token)
stats = result['statistics']
if opts.stat == 'sequence':
for s in sorted(stats['sequence_stats'].iterkeys()):
safe_print("%s\t%s\n" % (s, stats['sequence_stats'][s]))
elif opts.stat == 'bp_profile':
if not stats['qc']['bp_profile']['percents']['data']:
sys.stderr.write("ERROR: %s has no bp_profile statistics\n" %
opts.id)
return 1
if opts.plot:
cols = stats['qc']['bp_profile']['percents']['columns'][1:5]
data = map(lambda x: x[1:5],
stats['qc']['bp_profile']['percents']['data'])
plot_histo(cols, data, 20, 80)
else:
safe_print(
"\t".join(stats['qc']['bp_profile']['percents']['columns']) +
"\n")
for d in stats['qc']['bp_profile']['percents']['data']:
safe_print("\t".join(map(str, d)) + "\n")
elif opts.stat == 'drisee':
if not stats['qc']['drisee']['percents']['data']:
sys.stderr.write("ERROR: %s has no drisee statistics\n" % opts.id)
return 1
if opts.plot:
x, y = [], []
for d in stats['qc']['drisee']['percents']['data']:
x.append(d[0])
y.append(d[7])
aplotter.plot(x,
y,
output=sys.stdout,
draw_axes=True,
plot_slope=True,
min_x=0,
min_y=0)
else:
safe_print(
"\t".join(stats['qc']['drisee']['percents']['columns']) + "\n")
for d in stats['qc']['drisee']['percents']['data']:
safe_print("\t".join(map(str, d)) + "\n")
elif opts.stat == 'kmer':
if not stats['qc']['kmer']['15_mer']['data']:
sys.stderr.write("ERROR: %s has no kmer statistics\n" % opts.id)
return 1
if opts.plot:
x, y = [], []
for d in stats['qc']['kmer']['15_mer']['data']:
x.append(math.log(d[3], 10))
y.append(math.log(d[0], 10))
aplotter.plot(x,
y,
output=sys.stdout,
draw_axes=True,
plot_slope=True,
min_x=0,
min_y=0)
else:
safe_print("\t".join(stats['qc']['kmer']['15_mer']['columns']) +
"\n")
for d in stats['qc']['kmer']['15_mer']['data']:
safe_print("\t".join(map(str, d)) + "\n")
elif opts.stat == 'rarefaction':
if not stats['rarefaction']:
sys.stderr.write("ERROR: %s has no rarefaction statistics\n" %
opts.id)
return 1
if opts.plot:
x, y = [], []
for r in stats['rarefaction']:
x.append(int(r[0]))
y.append(float(r[1]))
aplotter.plot(x,
y,
output=sys.stdout,
draw_axes=True,
plot_slope=True,
min_x=0,
min_y=0)
else:
safe_print("x\ty\n")
for r in stats['rarefaction']:
safe_print("%s\t%s\n" % (str(r[0]), str(r[1])))
elif opts.stat in stats['taxonomy']:
ranked = sorted(stats['taxonomy'][opts.stat],
key=lambda x: (-int(x[1]), x[0]))
if opts.plot:
top = map(lambda x: int(x[1]), ranked)[:50]
aplotter.plot(top,
output=sys.stdout,
draw_axes=True,
plot_slope=False,
min_x=0,
min_y=0)
else:
for t in ranked:
safe_print("%s\t%s\n" % (t[0], str(t[1])))
else:
sys.stderr.write("ERROR: invalid stat type\n")
return 1
return 0