def CHECK(self,Q,t,P): #/ -------------------------------------------------------------------------- x1 = Q[iX1] y1 = Q[iY1] x2 = Q[iX2] y2 = Q[iY2] x3 = Q[iX3] y3 = Q[iY3] x4 = Q[iX4] y4 = Q[iY4] rad1 = P[jR1] rad2 = P[jR2] rad3 = P[jR3] rad4 = P[jR4] r12 = rad1 + rad2 r13 = rad1 + rad3 r14 = rad1 + rad4 r23 = rad2 + rad3 r24 = rad2 + rad4 r34 = rad3 + rad4 dx12 = x1 - x2 dy12 = y1 - y2 dx13 = x1 - x3 dy13 = y1 - y3 dx14 = x1 - x4 dy14 = y1 - y4 dx23 = x2 - x3 dy23 = y2 - y3 dx24 = x2 - x4 dy24 = y2 - y4 dx34 = x3 - x4 dy34 = y3 - y4 if (t > 21912800.0): v2 = (Q[iVX4]*Q[iVX4]) + (Q[iVY4]*Q[iVY4]) if (v2 < 1.0e+9): cc = math.sqrt(v2) Q[iVX4] += Acc*Q[iVX4]/cc Q[iVY4] += Acc*Q[iVY4]/cc self.iCount += 1 self.tCount += AccInc print fpformat.sci(Q[iX4],5), fpformat.sci(Q[iY4],5), fpformat.sci(Q[iVX4],5), fpformat.sci(Q[iVY4],5), fpformat.sci(Acc,5), fpformat.sci(cc,5) rv = 0 if ((r12*r12) > ((dx12*dx12)+(dy12*dy12))): rv = 1 elif ((r13*r13) > ((dx13*dx13)+(dy13*dy13))): rv = 2 elif ((r14*r14) > ((dx14*dx14)+(dy14*dy14))): rv = 3 elif ((r23*r23) > ((dx23*dx23)+(dy23*dy23))): rv = 4 elif ((r24*r24) > ((dx24*dx24)+(dy24*dy24))): rv = 5 elif ((r34*r34) > ((dx34*dx34)+(dy34*dy34))): rv = 6 return rv
def test_failing_values(self):
# Now for 'unreasonable n and d'
self.assertEquals(fix(1.0, 1000), '1.' + ('0' * 1000))
self.assertEquals(sci("1" + ('0' * 1000), 0), '1e+1000')
# This behavior is inconsistent. sci raises an exception; fix doesn't.
yacht = "Throatwobbler Mangrove"
self.assertEquals(fix(yacht, 10), yacht)
try:
sci(yacht, 10)
except NotANumber:
pass
else:
self.fail("No exception on non-numeric sci")
def test_failing_values(self):
# Now for 'unreasonable n and d'
self.assertEquals(fix(1.0, 1000), '1.'+('0'*1000))
self.assertEquals(sci("1"+('0'*1000), 0), '1e+1000')
# This behavior is inconsistent. sci raises an exception; fix doesn't.
yacht = "Throatwobbler Mangrove"
self.assertEquals(fix(yacht, 10), yacht)
try:
sci(yacht, 10)
except NotANumber:
pass
else:
self.fail("No exception on non-numeric sci")
def outputStdDataFile(file,tags,data,stepRanges):
""" This function takes the contents of tags and data, and outputs them
to a std format *prn file. This is for testing purposes.
"""
filename = "test_" + file
print "\nCreating std format output file: " + filename
output = open(filename,'w')
tagstring = "Index "
numvars = len(tags)
for i in range(numvars):
tagstring += tags[i] + " "
tagstring += "\n"
output.write(tagstring)
sizeTmp = len(stepRanges)
size = stepRanges[sizeTmp-1]+1
for i in range(size):
numberstring = str(i) + " "
for j in range(numvars):
numberstring += str(fpformat.sci(data[i,j],8)) + " "
numberstring += "\n"
output.write(numberstring)
finalstring = "End of Xyce(TM) Simulation\n"
output.write(finalstring)
return
def checkSci(self, n, digits):
result = sci(n, digits)
if isinstance(n, StringType):
n = repr(n)
expected = "%.*e" % (digits, float(n))
# add the extra 0 if needed
num, exp = expected.split("e")
if len(exp) < 4:
exp = exp[0] + "0" + exp[1:]
expected = "%se%s" % (num, exp)
self.assertEquals(result, expected)
def checkSci(self, n, digits):
result = sci(n, digits)
if isinstance(n, StringType):
n = repr(n)
expected = "%.*e" % (digits, float(n))
# add the extra 0 if needed
num, exp = expected.split("e")
if len(exp) < 4:
exp = exp[0] + "0" + exp[1:]
expected = "%se%s" % (num, exp)
self.assertEquals(result, expected)
def parseLatLong(latlong):
"""
Parse Lat or Long in METAR notation into float values. N and E
are +, S and W are -. Expects one positional string and returns
one float value.
"""
# I know, I could invert this if and put
# the rest of the function into its block,
# but I find it to be more readable this way
if latlong is None:
return None
s = latlong.upper().strip()
elms = s.split('-')
ud = elms[-1][-1]
elms[-1] = elms[-1][:-1]
elms = [int(i) for i in elms]
coords = 0.0
elen = len(elms)
if elen > 2:
coords = coords + float(elms[2]) / 3600.0
if elen > 1:
coords = coords + float(elms[1]) / 60.0
coords = coords + float(elms[0])
if ud in ('W', 'S'):
coords = -1.0 * coords
f, i = math.modf(coords)
if elen > 2:
f = float(fpformat.sci(f, 4))
elif elen > 1:
f = float(fpformat.sci(f, 2))
else:
f = 0.0
return f + i
def parseLatLong(latlong):
"""
Parse Lat or Long in METAR notation into float values. N and E
are +, S and W are -. Expects one positional string and returns
one float value.
"""
# I know, I could invert this if and put
# the rest of the function into its block,
# but I find it to be more readable this way
if latlong is None:
return None
s = latlong.upper().strip()
elms = s.split('-')
ud = elms[-1][-1]
elms[-1] = elms[-1][:-1]
elms = [int(i) for i in elms]
coords = 0.0
elen = len(elms)
if elen > 2:
coords = coords + float(elms[2])/3600.0
if elen > 1:
coords = coords + float(elms[1])/60.0
coords = coords + float(elms[0])
if ud in ('W', 'S'):
coords = -1.0*coords
f, i = math.modf(coords)
if elen > 2:
f = float(fpformat.sci(f, 4))
elif elen > 1:
f = float(fpformat.sci(f, 2))
else:
f = 0.0
return f+i
def parseLatLong(self, latlong):
"""
Parse Lat or Long in METAR notation into float values. N and E are +, S
and W are -. Expects one positional string and returns one float value.
"""
# I know, I could invert this if and put
# the rest of the function into its block,
# but I find this to be more readable
if latlong is None:
return None
s = string.strip(string.upper(latlong))
elms = string.split(s, "-")
ud = elms[-1][-1]
elms[-1] = elms[-1][:-1]
elms = map(string.atoi, elms)
coords = 0.0
elen = len(elms)
if elen > 2:
coords = coords + float(elms[2]) / 3600.0
if elen > 1:
coords = coords + float(elms[1]) / 60.0
coords = coords + float(elms[0])
if ud in ("W", "S"):
coords = -1.0 * coords
f, i = math.modf(coords)
if elen > 2:
f = float(fpformat.sci(f, 4))
elif elen > 1:
f = float(fpformat.sci(f, 2))
else:
f = 0.0
return f + i
def test_basic_cases(self):
self.assertEquals(fix(100.0 / 3, 3), '33.333')
self.assertEquals(sci(100.0 / 3, 3), '3.333e+001')
def mapPeptides2STRING(blastDir,
organism,
fastafilename,
id_pos_res,
id_seq,
number_of_processes,
datadir,
fast=False,
leave_intermediates=False):
sys.stderr.write("Mapping using blast\n")
incoming2string = {}
string2incoming = {}
# Speedup, only blast sequences with site specified
tempfile.tempdir = '/output'
blast_tmpfile = tempfile.NamedTemporaryFile()
#f = open('/output/blast_tmp', 'wb')
if id_pos_res == {}:
for id in id_seq:
wr = '>' + id + '\n' + id_seq[id] + '\n'
blast_tmpfile.write(wr)
else:
for id in id_pos_res:
try:
wr = '>' + id + '\n' + id_seq[id] + '\n'
blast_tmpfile.write(wr)
#print(wr)
#f.write(wr)
except:
sys.stderr.write("No sequence available for '%s'\n" % id)
blast_tmpfile.flush()
blastDB = os.path.join(datadir,
"%s.protein.sequences.fa" % (organism)).replace(
' ', '\\ ')
# print("blastdb path is" + blastDB)
# Check if blast database is actually initialized, if not: do it
if not os.path.isfile(blastDB + '.pin'):
#print("Is this it??")
command = "%s/formatdb -i %s" % (blastDir.rsplit("/", 1)[0], blastDB)
sys.stderr.write(
"Looks like blast database is not initialized, trying to run:\n%s\n"
% command)
myPopen(command)
command = "%s -a %s -p blastp -e 1e-10 -m 8 -d %s -i %s | sort -k12nr" % (
blastDir, number_of_processes, blastDB, blast_tmpfile.name)
#print(blastDir, blastDB, '/output/blast_tmp')
#if os.path.isfile(blast_tmpfile.name):
#print('File exists')
# to save time - jhkim
if fast and os.path.isfile(fn_blast_output):
#print('fast')
blast_out = ReadLines(fn_blast_output)
else:
#print('mopen')
blast_out = myPopen(command)
if leave_intermediates:
WriteString(fn_blast_output, "".join(blast_out))
#print(blast_out)
for line in blast_out:
tokens = line.split('\t')
incoming = tokens[0]
if incoming not in incoming2string:
# get rid of organism prefix
string = tokens[1].replace("%s." % organism, "")
identity = float(tokens[2])
evalue = float(tokens[-2])
if string in string2incoming:
sys.stderr.write('Best hit for ' + incoming +
' is not reciprocal\n')
if identity < 90:
sys.stderr.write('Best hit for ' + incoming + ' has only ' +
fpformat.fix(identity, 2) + ' %identity\n')
if evalue > 1e-40:
sys.stderr.write('Best hit for ' + incoming +
' has high E-value ' +
fpformat.sci(evalue, 2) + ' \n')
if incoming in incoming2string:
incoming2string[incoming][string] = True
else:
incoming2string[incoming] = {string: True}
if string in string2incoming:
string2incoming[string][incoming] = True
else:
string2incoming[string] = {incoming: True}
else:
pass
return incoming2string, string2incoming
'''
def mapPeptides2STRING(blastDir, organism, fastafilename, id_pos_res, id_seq, number_of_processes, datadir, fast = True, leave_intermediates = False):
sys.stderr.write("Mapping using blast\nLength id_seq: %s\n"%len(id_seq))
incoming2string = {}
string2incoming = {}
#for id in id_seq:
# sys.stderr.write("ID_Seq: " + id + '\n')
# Speedup, only blast sequences with site specified
sys.stderr.write("tempfile: %s"%tempfile)
#import pdb; pdb.set_trace()
blast_tmpfile = tempfile.NamedTemporaryFile()
#blast_tmpfile = "/home/gary/NetwoKINtmp/tmpXIao_unzip.txt"
if id_pos_res == {}:
for id in id_seq:
blast_tmpfile.write('>'+id+'\n'+id_seq[id]+'\n')
else:
for id in id_pos_res:
try:
blast_tmpfile.write('>'+id+'\n'+id_seq[id]+'\n')
except:
sys.stderr.write("No sequence available for '%s'\n"%id)
blast_tmpfile.flush()
# blastDB = os.path.join(datadir, "%s.protein.sequences.fa"%(organism)).replace(' ', '\\ ')
#Changed
blastDB = "/home/gary/Documents/20180925_NetworKIN_Hornberger_RapMIC_Redo/NetworKIN_release3.0/MouseProteome_20150814_noIsoforms_HumanEnsembl74_noNAs.fasta"
#sys.stderr.write("blastDB is initialized: %s"%os.path.isfile(blastDB+'.pin'))
# Check if blast database is actually initialized, if not: do it
if not os.path.isfile(blastDB+'.pin'):
command = "%s/formatdb -i %s"%(blastDir.rsplit("/", 1)[0], blastDB)
sys.stderr.write("Looks like blast database is not initialized, trying to run:\n%s\n"%command)
myPopen(command)
savefile = True
if savefile:
command = "%s -a %s -p blastp -e 1e-10 -m 8 -d %s -i %s | sort -k12nr -> blast_out_Ensembl74.txt"%(blastDir, number_of_processes, blastDB, blast_tmpfile.name)
else:
command = "%s -a %s -p blastp -e 1e-10 -m 8 -d %s -i %s | sort -k12nr"%(blastDir, number_of_processes, blastDB, blast_tmpfile.name)
sys.stderr.write("\nBlast command: %s\n"%command)
# to save time - jhkim
# TRUE if you want to use the existing Blast output file
if True and os.path.isfile("/home/gary/Documents/20180925_NetworKIN_Hornberger_RapMIC_Redo/NetworKIN_release3.0/blast_out_Ensembl74.txt"):
sys.stderr.write("Reading Blast Output\n")
blast_out = ReadLines("/home/gary/Documents/20180925_NetworKIN_Hornberger_RapMIC_Redo/NetworKIN_release3.0/blast_out_Ensembl74.txt")
else:
sys.stderr.write("Performing blast search\n")
sys.stderr.write("fn_blast_output: %s"%fn_blast_output)
blast_out = myPopen(command)
if leave_intermediates:
WriteString(fn_blast_output, "".join(blast_out))
sys.stderr.write("Length blast_out: %s\n"%len(blast_out))
for line in blast_out:
#sys.stderr.write(":%s\n"%line)
if not line:
sys.stderr.write("Empty line detected\n")
continue
tokens = line.split('\t')
if not len(tokens) > 5:
continue
incoming = tokens[0]
if incoming not in incoming2string:
# get rid of organism prefix
string = tokens[1].replace("%s."%organism, "")
identity = float(tokens[2])
evalue = float(tokens[-2])
if string in string2incoming:
sys.stderr.write('Best hit for '+incoming+' is not reciprocal\n')
if identity < 90:
sys.stderr.write('Best hit for '+incoming+' has only '+fpformat.fix(identity, 2)+' %identity\n')
if evalue > 1e-40:
sys.stderr.write('Best hit for '+incoming+' has high E-value '+fpformat.sci(evalue, 2)+' \n')
if incoming in incoming2string:
incoming2string[incoming][string] = True
else:
incoming2string[incoming] = { string: True }
if string in string2incoming:
string2incoming[string][incoming] = True
else:
string2incoming[string] = { incoming: True }
else:
pass
sys.stderr.write("Length incoming2string: %s\n"%len(incoming2string))
sys.stderr.write("Length string2incoming: %s\n"%len(string2incoming))
return incoming2string, string2incoming
def test_basic_cases(self):
self.assertEquals(fix(100.0/3, 3), '33.333')
self.assertEquals(sci(100.0/3, 3), '3.333e+001')
