def main():
usage = "usage: %prog profile_fn [options]"
parser = OptionParser(usage=usage, description="Make secondary structure prediction from a PSI-BLAST profile")
parser.add_option("-o", "--outfile",action = "store", dest="outfile", type="string",
help="outputfile, if not specfied output is stdout")
parser.add_option("-v", "--verbose",
action="store_true", dest="verbose")
(options, args) = parser.parse_args()
if len(args) != 1:
parser.error("incorrect number of arguments, expected 1")
profile_fn = args[0]
if options.outfile:
outfile = options.outfile
voutfn = options.outfile
else:
outfile = None
voutfn = 'stdout'
if options.verbose:
print "outfile: %s"%(str(voutfn))
assignment.assign(profile_fn, outfile)
def main():
usage = "usage: %prog profile_fn [options]"
parser = OptionParser(
usage=usage,
description=
"Make secondary structure prediction from a PSI-BLAST profile")
parser.add_option("-o",
"--outfile",
action="store",
dest="outfile",
type="string",
help="outputfile, if not specfied output is stdout")
parser.add_option("-v", "--verbose", action="store_true", dest="verbose")
(options, args) = parser.parse_args()
if len(args) != 1:
parser.error("incorrect number of arguments, expected 1")
profile_fn = args[0]
if options.outfile:
outfile = options.outfile
voutfn = options.outfile
else:
outfile = None
voutfn = 'stdout'
if options.verbose:
print "outfile: %s" % (str(voutfn))
assignment.assign(profile_fn, outfile)
def test_assign(self):
eligible_nurses = make_and_execute_sql_query(4, 0, 0, self.cursor)
eligible_nurse_objects, assignments = to_object(
eligible_nurses, self.assignments)
sorted_eligible_nurses = sort_eligible_nurse_objects_acuity(
eligible_nurse_objects)
eligible_max_nurses = calculate_weights(eligible_nurse_objects, 'F', 0,
self.patient_2, assignments,
self.cursor)
assignments = {1: {"num_patients": 2, "patients": []}}
output = assign(sorted_eligible_nurses, eligible_max_nurses,
assignments, 0, self.patient_1, 0, self.twins)
self.assertEqual(output, {1: {'num_patients': 3, 'patients': [1]}})
from matplotlib.ticker import AutoMinorLocator
import numpy as np
import assignment as asm
__author__ = 'Gerrit'
colors = ["#1f77b4", "#d62728", "#2ca02c", "#414451"]
plt.style.use("C:/Users/Gerrit/PycharmProjects/dis_style.mplstyle")
#ind = np.arange(len(total_data["total"]))+0.5
fig, ax = plt.subplots(nrows=1, ncols=1, sharex=True)
fig.set_figheight(12)
fig.set_figwidth(14)
profile_fn = "C:\Users\Gerrit\PycharmProjects\sparrow_res\example\T0515-D1.out"
ret = asm.assign(profile_fn)
x = range(1, 101, 1)
len(x)
len(ret.probability[0:100, 0])
#acc = plt.plot(x, ret.accuracy)
#print ret.probability[:,0]
he = ax.plot(x, ret.probability[0:100, 0], color=colors[0], linewidth=2, label="Helix")
st = ax.plot(x, ret.probability[0:100, 1], color=colors[1], linewidth=2, label="Strand")
co = ax.plot(x, ret.probability[0:100, 2], color=colors[2], linewidth=2, label="Coil")
handles, labels = ax.get_legend_handles_labels()
ax.legend(handles, labels, loc="lower right", numpoints=1)
#ax[0].set_xlim(0, ind[-1]+.5)
ax.set_xlim(1, x[-1])
start, end = ax.get_xlim()
def main():
spreadsheet_id = '1WydOez3OoBKLvxsdUaZQ8s9d5xBK7BY9dzBIyxJXzgk'
sheet_range = 'A1:H10'
table = sheets.get_data_for_range(spreadsheet_id, sheet_range)
assignment.assign(table)
def decompose(
inXd, inYd, inZd, xmind, xmaxd, ymind, ymaxd, zmind, zmaxd
): # inXd: list of x-coordinates \ inYd: list of y-coordinates \ inZd: list of z-coordinates
# xmind: subdomain lower x boundary \ xmaxd: subdomain upper x boundary \ ymind: subdomain lower x boundary
# ymaxd: subdomain upper y boundary \ zmind: subdomain lower x boundary \ zmaxd: subdomain upper z boundary
# xybufd: spatial buffer \ zbufd: temporal buffer
sett.sdNum += 1
xminDiff = xmind % sett.p3
xmaxDiff = xmaxd % sett.p3
yminDiff = ymind % sett.p3
ymaxDiff = ymaxd % sett.p3
zminDiff = zmind % sett.p4
zmaxDiff = zmaxd % sett.p4
xminP = xmind - xminDiff + sett.p3
xmaxP = xmaxd - xmaxDiff + sett.p3
yminP = ymind - yminDiff + sett.p3
ymaxP = ymaxd - ymaxDiff + sett.p3
zminP = zmind - zminDiff + sett.p4
zmaxP = zmaxd - zmaxDiff + sett.p4
xC, yC, zC = 0, 0, 0
xIter = xminP
while xIter < xmaxP:
xC += 1
xIter += sett.p3
yIter = yminP
while yIter < ymaxP:
yC += 1
yIter += sett.p3
zIter = zminP
while zIter < zmaxP:
zC += 1
zIter += sett.p4
xDim = xmaxd - xmind
yDim = ymaxd - ymind
zDim = zmaxd - zmind
sdVolume = xDim * yDim * zDim
bufVolume = (xDim + 2 * sett.p1) * (yDim + 2 * sett.p1) * (zDim +
2 * sett.p2)
bufRatio = sdVolume / bufVolume
if len(
inXd
) is 0: # if there are no data points or no regular grid points within subdomain, pass
pass
elif xC is 0:
pass
elif yC is 0:
pass
elif zC is 0:
pass
elif len(inXd) <= sett.p5 or bufRatio <= sett.p6:
fn = sett.dir1 + os.sep + "pts_" + str(sett.sdNum) + ".txt"
fn1 = open(fn, "w")
fn1.write(
str(xmind) + ", " + str(xmaxd) + ", " + str(ymind) + ", " +
str(ymaxd) + ", " + str(zmind) + ", " + str(zmaxd) + "\n")
for x, y, z in list(zip(inXd, inYd, inZd)):
fn1.write(str(x) + ", " + str(y) + ", " + str(z) + "\n")
fn1.close()
else: # if number of points in subdomain is higher than threshold, keep decomposing.
sdXYZ = ass.assign(inXd, inYd, inZd, xmaxd, xmind, ymaxd, ymind, zmaxd,
zmind)
decompose(sdXYZ[0], sdXYZ[1], sdXYZ[2], xmind, sdXYZ[-3], ymind,
sdXYZ[-2], zmind, sdXYZ[-1]) # recursive function call 1
decompose(sdXYZ[3], sdXYZ[4], sdXYZ[5], sdXYZ[-3], xmaxd, ymind,
sdXYZ[-2], zmind, sdXYZ[-1]) # recursive function call 2
decompose(sdXYZ[6], sdXYZ[7], sdXYZ[8], xmind, sdXYZ[-3], sdXYZ[-2],
ymaxd, zmind, sdXYZ[-1]) # recursive function call 3
decompose(sdXYZ[9], sdXYZ[10], sdXYZ[11], sdXYZ[-3], xmaxd, sdXYZ[-2],
ymaxd, zmind, sdXYZ[-1]) # recursive function call 4
decompose(sdXYZ[12], sdXYZ[13], sdXYZ[14], xmind, sdXYZ[-3], ymind,
sdXYZ[-2], sdXYZ[-1], zmaxd) # recursive function call 5
decompose(sdXYZ[15], sdXYZ[16], sdXYZ[17], sdXYZ[-3], xmaxd, ymind,
sdXYZ[-2], sdXYZ[-1], zmaxd) # recursive function call 6
decompose(sdXYZ[18], sdXYZ[19], sdXYZ[20], xmind, sdXYZ[-3], sdXYZ[-2],
ymaxd, sdXYZ[-1], zmaxd) # recursive function call 7
decompose(sdXYZ[21], sdXYZ[22], sdXYZ[23], sdXYZ[-3], xmaxd, sdXYZ[-2],
ymaxd, sdXYZ[-1], zmaxd) # recursive function call 8
from matplotlib.ticker import AutoMinorLocator
import numpy as np
import assignment as asm
__author__ = 'Gerrit'
colors = ["#1f77b4", "#d62728", "#2ca02c", "#414451"]
plt.style.use("C:/Users/Gerrit/PycharmProjects/dis_style.mplstyle")
#ind = np.arange(len(total_data["total"]))+0.5
fig, ax = plt.subplots(nrows=1, ncols=1, sharex=True)
fig.set_figheight(12)
fig.set_figwidth(14)
profile_fn = "C:\Users\Gerrit\PycharmProjects\sparrow_res\example\T0515-D1.out"
ret = asm.assign(profile_fn)
x = range(1, 101, 1)
len(x)
len(ret.probability[0:100, 0])
#acc = plt.plot(x, ret.accuracy)
#print ret.probability[:,0]
he = ax.plot(x,
ret.probability[0:100, 0],
color=colors[0],
linewidth=2,
label="Helix")
st = ax.plot(x,
ret.probability[0:100, 1],
color=colors[1],
linewidth=2,
label="Strand")
