Exemplo n.º 1
0
	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
Exemplo n.º 2
0
    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")
Exemplo n.º 3
0
    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")
Exemplo n.º 4
0
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
Exemplo n.º 5
0
    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)
Exemplo n.º 6
0
    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)
Exemplo n.º 7
0
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
Exemplo n.º 8
0
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
Exemplo n.º 9
0
    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
Exemplo n.º 10
0
 def test_basic_cases(self):
     self.assertEquals(fix(100.0 / 3, 3), '33.333')
     self.assertEquals(sci(100.0 / 3, 3), '3.333e+001')
Exemplo n.º 11
0
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
Exemplo n.º 12
0
'''
Exemplo n.º 13
0
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
Exemplo n.º 14
0
 def test_basic_cases(self):
     self.assertEquals(fix(100.0/3, 3), '33.333')
     self.assertEquals(sci(100.0/3, 3), '3.333e+001')