def inbox_by_context_name():
import sys
sys.error("Don't do this")
for t in Thing.objects.all():
if t.context.name.lower().find(INBOX_CONTEXT_STR) >= 0:
t.status = t.STATE_INBOX
t.save()
def ippft( f , niter=6 , eps=1e-8 ):
## Check whether the input Pseudo Polar Grid is a 2D array
## and it is a square matrix
if f.ndim != 2:
sys.error('ERROR: input for inversePseudoPolarFT is not a 2D array!')
if f.shape[0] != f.shape[1]:
sys.error('WARNING: input for inversePseudoPolarFT is not a square matrix')
## Convert input Pseudo Polar Grid to myComplex format
f = f.astype( myComplex )
## Get size of the output object
n = int( 0.5 * f.shape[0] )
## Create preconditioning matrix to decrease the
## conditioning number of the Pseudo Polar Operator
M = np.array( np.sqrt( abs( np.arange(-n,n)/myFloat(n) ) ) )
M[n] = np.sqrt( 1.0/myFloat(4*n) )
M = np.ones( ( 2*n , 1 ) ) * M;
M[:,:] = M[:,:]**2;
## Initialization of the preconditioned conjugate method
xk = ppft_adj( np.multiply( M , f ) )
pk = xk - ppft_adj( M * ppft( xk ) )
rk = np.empty( ( n , n ) , dtype=myComplex )
rk[:,:] = pk[:,:]
f[:,:] = 0
ppAdj = np.zeros( ( n , n ) , dtype=myComplex )
## Print setu-up parameters for the IPPFT
print(' PCG-IPPFT: stopping threshold: ' , eps )
print(' PCG-IPPFT: max number of CG-iterations: ' , niter )
## Start conjugate gradient iterations
it = 0
while it < niter:
err = np.linalg.norm( pk )
print(' Iter = ' , it , ' cost function = ' , err )
if err > eps:
f[:,:] = ppft( pk )
f[:,:] = np.multiply( M , f )
ppAdj[:,:] = ppft_adj( f )
a0 = np.sum( np.abs(rk) * np.abs(rk) )
a1 = np.sum( np.conjugate(pk) * ppAdj )
a = a0 / myComplex( a1 )
xk[:,:] += a*pk
rk[:,:] -= a * ppAdj
bb = np.sum( np.abs(rk) * np.abs(rk) )
b = bb/a0
pk[:,:] = rk + b * pk
else: break
it += 1
## Final informative prints
print(' PCG-IPPFT: number of CG-iterations used: ' , it )
print(' PCG-IPPFT: cost function: ' , err )
print(' .... PCG for inverse PPFT done!')
return xk
def ppft_adj( f ):
if f.ndim != 2:
sys.error('ERROR: input for adjointPseudoPolarFT is not a 2D array!')
nx,ny = f.shape
if nx != ny or nx % 2:
n = int( np.ceil( max(nx,ny)/2. ) * 2 )
else: n = nx
n = int( n/2 )
f_out = np.zeros( ( n , n ), dtype=myComplex )
f_aux = np.zeros( ( 2*n , n ) , dtype=myComplex )
## Vertical hourglass
f_aux[:,:] = np.transpose( f[:n,:] )
for i in range( -n , n ):
f_aux[i+n,:] = frft_ctr( f_aux[i+n,:] , i/myFloat( n ) )
f_aux[:,:] = np.roll( f_aux , n , axis=0 )
f_aux[:,:] = 2 * n * scipy.fftpack.ifft( f_aux , 2*n , axis=0 , overwrite_x=True )
f_aux[:,:] = np.fft.fftshift( f_aux , axes=(0,) )
f_out[:,:] = f_aux[n/2:3*n/2,:]
## Horizontal hourglass
f_aux = f_aux.reshape( n , 2*n )
f_aux[:,:] = f[n:,:]
for i in range( -n , n ):
f_aux[:,i+n] = frft_ctr( f_aux[:,i+n] , i/myFloat( n ) )
f_aux[:,:] = np.roll( f_aux , n , axis=1 )
f_aux[:,:] = scipy.fftpack.fft( f_aux , 2*n , axis=1 , overwrite_x=True )
f_aux[:,:] = scipy.fftpack.fftshift( f_aux , axes=(1,) )
f_out[:,:] = 1/(n*np.sqrt(2)) * ( f_out[:,:] + f_aux[:,n/2:3*n/2] )
return f_out
def readGenes (fname):
"""
Take a file name that is bed-like (needs at least 3 columns) - will conserve strand and name if they exist
Name will be the dictionary key for the output coverages
"""
genes = {}
i = 1
with open(fname) as fn:
for line in fn:
if line.startswith('#'):
continue
try:
chrom,start,end,name,score,strand = line.strip().split('\t')[:6]
except:
try:
a = line.strip().split('\t')
length = len(a)
ext = 6-length
a.extend(['.'] * ext)
chrom, start, end, name, score, strand = a
except:
sys.error(fname, 'Not a valid bed')
if name == '.':
name = 'peak'+str(i)
else:
name = os.path.basename(name) #macs puts the full path in this name field, if it hasn't been cleaned up yet this will
if args.m:
start = (int(start)+int(end)) / 2
end = int(start +1 )
iv = HTSeq.GenomicInterval(chrom, start, end, strand)
genes[str(name)] = iv
i += 1
return(genes)
def close(self, exit = False):
""" close finishes socket sessions. Best used after each run. exit=True, shuts down labview; Not recommended"""
# close the remote channel through labview
try:
self.tSock.sendto('0005,0010,r', (self.host, self.tPort))
except:
raise sys.error("Could not close remote channel. Socket connection broken.")
if exit:
try:
self.tSock.sendto('0005,0010,x', (self.host, self.tPort))
except:
raise sys.error("Could not exit LabVIEW. Socket connection broken.")
#end socket sessions
self.rSock.shutdown(1)
self.tSock.shutdown(1)
#close sockets
self.rSock.close()
self.tSock.close()
def get(self, options, url):
data = get_http_data(url)
match = re.search("liveStationsRedundancy = ({.*});</script>", data)
parse = urlparse(url)
station = parse.path[1:]
streams = None
if match:
data = json.loads(match.group(1))
for i in data["stations"]:
if station == i["name"].lower().replace(" ", ""):
streams = i["streams"]
break
else:
log.error("Can't find any streams.")
sys.exit(2)
if streams:
if options.hls:
try:
m3u8_url = streams["hls"]
base_url = m3u8_url.rsplit("/", 1)[0]
download_hls(options, m3u8_url, base_url)
except KeyError:
log.error("Can't find any streams.")
sys.error(2)
else:
try:
rtmp = streams["rtmp"]
download_rtmp(options, rtmp)
except KeyError:
mp3 = streams["mp3"]
download_http(options, mp3)
else:
log.error("Can't find any streams.")
sys.exit(2)
def plot_volumes(volume_files):
"""
Use fslview to visualize image volume data.
Inputs
------
volume_files : list of strings
names of image volume files
Examples
--------
>>> import os
>>> from mindboggle.utils.plots import plot_volumes
>>> path = os.environ['MINDBOGGLE_DATA']
>>> volume_file1 = os.path.join(path, 'arno', 'mri', 't1weighted.nii.gz')
>>> volume_file2 = os.path.join(path, 'arno', 'mri', 't1weighted_brain.nii.gz')
>>> volume_files = [volume_file1, volume_file2]
>>> plot_volumes(volume_files)
"""
from mindboggle.utils.utils import execute
if isinstance(volume_files, str):
volume_files = [volume_files]
elif not isinstance(volume_files, list):
import sys
sys.error('plot_volumes() requires volume_files to be a list or string.')
cmd = ["fslview"]
cmd.extend(volume_files)
cmd.extend('&')
execute(cmd, 'os')
def main(args):
lvl = _levels[max(0, min(args.verbose, len(_levels)-1))]
logging.basicConfig(level=lvl)
rundir = getrundir(user=args.user)
info = '%s/procserv-%s/info'%(rundir, args.proc)
try:
with open(info) as F:
for L in map(str.strip, F):
if not L.startswith('tcp:'):
continue
_tcp, iface, port = L.split(':', 2)
args = [telnet, iface, port]+args.extra
_log.debug('exec: %s', ' '.join(args))
os.execv(telnet, args)
sys.exit(1) # never reached
sys.error('%s has no tcp control port')
except OSError as e:
if e.errno==errno.ENOENT:
_log.error('%s is not an active %s procServ', args.name, 'user' if args.user else 'system')
else:
_log.exception("Can't open %s"%info)
sys.exit(1)
def p_lAsigna(p): '''lAsigna : LB exp C exp RB PC''' global DT if(not DT): print "Dimension error" sys.error(0) else: DT = False
def readQ(filename):
items, timesteps, c = read(filename)
if not 'q' in items:
sys.error('Error: q is not column in the lammps trajectory %s' %
filename)
index = items.index('q')
cout = c[:, :, index]
return cout
def p_idList(p):
'''idList : ID'''
variables_declaradas(p[1])
dimention = dimension(p[1])
if dimension(p[1]) == -1:
print "Error en cuanto la dimension"
sys.error(0)
avail.OPila_push(dir_var(p[1]))
avail.OPila_push(dimention)
def get_filepath(dirpath, filename):
if(is_valid_dir(dirpath)):
filepath = "%s/%s" %(dirpath, filename)
if(is_valid_file(filepath)):
return filepath
else:
sys.error("File not in directory")
else:
sys.error("Invalid path to file")
def p_idList(p): '''idList : ID''' variables_declaradas(p[1]) dimention = dimension(p[1]) if dimension(p[1]) == -1: print "Error en cuanto la dimension" sys.error(0) avail.OPila_push(dir_var(p[1])) avail.OPila_push(dimention)
def updatePlatform(self, platform):
self.platform = platform
self.printVerbose("get cfg for platform: " + self.platform)
if self.platform in list(self.mirrorCfg.keys()):
self.platformCfg = self.mirrorCfg[self.platform]
else:
pError("Config: platform " + self.platform +
" not found in cfg file " + self.cfgFile)
sys.error(2)
def get_filepath(dirpath, filename):
if (is_valid_dir(dirpath)):
filepath = "%s/%s" % (dirpath, filename)
if (is_valid_file(filepath)):
return filepath
else:
sys.error("File not in directory")
else:
sys.error("Invalid path to file")
def compil():
try:
# cd into the biuld directory
os.chdir('build')
# run make and make install
os.system('make && make install')
except:
sys.error('build directory does not exist. You should \
run ./setup.py -e configure first.')
def query_depth_ontology(net, node, root='cl:0000000'):
depth = 0
while node != root:
if len(net[node]) == 0:
print(node)
node = sorted(list(net[node].keys()))[0]
depth += 1
if depth > 100:
sys.error('root not found')
return depth
def openCustomCfg(self):
# test that the file exists
if not os.path.isfile(self.optCfg):
pError("Config: custom cfg file " + self.optCfg + " does not exist.")
sys.error(2)
# open
with open(self.optCfg) as cfgFileHandle:
mirrorCfg = json.load(cfgFileHandle)
# update mirror's cfg
self.mirrorCfg = update(self.mirrorCfg, mirrorCfg)
def print_arguments(program, args):
""" Run program specified by user (species, genes, or snps) """
if program == 'species':
print_species_arguments(args)
elif program == 'genes':
print_gene_arguments(args)
elif program == 'snps':
print_snp_arguments(args)
else:
sys.error("Unrecognized program: '%s'" % program)
def addFromFileNames(cls, filenames):
"""The method, given a list of file names, creates an array of dataset objects."""
if len(filenames) == 0:
sys.error(
"Trying to create a Datasets object from an empty list of filenames"
)
datasets = []
for filename in filenames:
datasets.append(self.datasetFromFileName(filename))
return cls(Datasets.__init__(datasets))
def print_arguments(program, args):
""" Run program specified by user (species, genes, or snps) """
if program == 'species':
print_species_arguments(args)
elif program == 'genes':
print_genes_arguments(args)
elif program == 'snps':
print_snps_arguments(args)
else:
sys.error("Unrecognized program: '%s'" % program)
def openCfg(self):
# get the standard cluster cfg
self.stdCfg = os.path.join(self.commandPath, self.stdCfg)
self.printVerbose("reading std cfg file: " + self.stdCfg)
if not os.path.isfile(self.stdCfg):
pError("Config: mirror cfg file " + self.stdCfg + " does not exist.")
sys.error(2)
with open(self.stdCfg) as cfgFileHandle:
self.mirrorCfg = json.load(cfgFileHandle)
def readXYZ(filename):
items, timesteps, c = read(filename)
if (not 'x' in items) or (not 'y' in items) or (not 'z' in items):
sys.error(
'Error: x,y,z are not columns in the lammps trajectory %s (only %s)'
% (filename, items))
indices = [items.index('x'), items.index('y'), items.index('z')]
cout = c[:, :, indices]
return cout
def condicion(self):
estCondic = self.OPila.pop()
tipoCondicion = self.TPila.pop()
if (tipoCondicion != "bool"):
print "Error, el tipo no coincide"
sys.error(0)
else:
cuads = ['GOTOF', estCondic, -1, -1]
self.cuad.append(cuads)
self.numCuad += 1
self.salto.push(self.numCuad)
def plotVertLine(self,Name='Curv', vCent=1, vY=[] ,Color=kBlack,Style=0,Width=2,Legend='None'):
nP = len(vY)
if nP == 0 : sys.error("plotHorizBand: ZERO size")
obj = TGraph( nP , array('d',[vCent]*nP) , array('d',vY) )
obj.SetLineColor(Color)
obj.SetMarkerColor(Color)
obj.SetLineWidth(2)
obj.SetLineStyle(Style)
obj.SetMarkerStyle(0)
obj.SetMarkerSize(0)
self.Obj2Plot[Name] = { 'Obj' : obj , 'Type' : 'Curve' , 'Legend' : Legend }
def condicion(self): estCondic = self.OPila.pop() tipoCondicion = self.TPila.pop() if(tipoCondicion != "bool"): print "Error, el tipo no coincide" sys.error(0) else: cuads = ['GOTOF', estCondic, -1, -1] self.cuad.append(cuads) self.numCuad += 1 self.salto.push(self.numCuad)
def plotHorizCurve(self,Name='Curv',vX=[],vCent=[],Color=kBlack,Style=0,Width=2,Legend='None'):
nP = len(vX)
if nP == 0 : sys.error("plotHorizBand: ZERO size")
if len(vCent) != nP : sys.error("plotHorizBand: size mismatch")
obj = TGraph( nP , array('d',vX) ,array('d',vCent) )
obj.SetLineColor(Color)
obj.SetMarkerColor(Color)
obj.SetLineWidth(Width)
obj.SetLineStyle(Style)
obj.SetMarkerStyle(0)
obj.SetMarkerSize(0)
self.Obj2Plot[Name] = { 'Obj' : obj , 'Type' : 'Curve' , 'Legend' : Legend }
def check_arguments(program, args):
""" Run program specified by user (species, genes, or snps) """
if program == 'species':
check_species(args)
elif program == 'genes':
check_genes(args)
elif program == 'snps':
check_snps(args)
else:
sys.error("Unrecognized program: '%s'" % program)
if platform.system() not in ['Linux', 'Darwin']:
sys.exit("Operating system '%s' not supported" % system())
def get_arguments(program):
""" Get arguments for specified program """
if program == 'species':
args = species_arguments()
elif program == 'genes':
args = gene_arguments()
elif program == 'snps':
args = snp_arguments()
else:
sys.error("Unrecognized program: '%s'" % program)
args = add_ref_db(args)
return args
def check_arguments(program, args):
""" Run program specified by user (species, genes, or snps) """
if program == 'species':
check_species(args)
elif program == 'genes':
check_genes(args)
elif program == 'snps':
check_snps(args)
else:
sys.error("Unrecognized program: '%s'" % program)
if platform.system() not in ['Linux', 'Darwin']:
sys.exit("Operating system '%s' not supported" % system())
def estimateGaussianParametersCOM(self):
#try to estimate first guess for fitting a Gaussian based on center of mass
if self.__ip != []:
bla = self.__ip.getStatistics()
return [
bla.xCenterOfMass, bla.yCenterOfMass, self.__objSigma,
self.__objSigma, bla.max, bla.min
]
else:
sys.error(
'Could not estimate centroid, ImageProcessor not defined!')
def get_arguments(program):
""" Get arguments for specified program """
if program == 'species':
args = species_arguments()
elif program == 'genes':
args = genes_arguments()
elif program == 'snps':
args = snps_arguments()
else:
sys.error("Unrecognized program: '%s'" % program)
utility.add_ref_db(args)
return args
def run_program(program, args):
""" Run program specified by user (species, genes, or snps) """
if program == 'species':
from midas.run import species
species.estimate_abundance(args)
elif program == 'genes':
from midas.run import genes
genes.run_pipeline(args)
elif program == 'snps':
from midas.run import snps
snps.run_pipeline(args)
else:
sys.error("Unrecognized program: '%s'" % program)
def run_program(program, args):
""" Run program specified by user (species, genes, or snps) """
if program == 'species':
from phylo_cnv import species
species.estimate_abundance(args)
elif program == 'genes':
from phylo_cnv import genes
genes.run_pipeline(args)
elif program == 'snps':
from phylo_cnv import snps
snps.run_pipeline(args)
else:
sys.error("Unrecognized program: '%s'" % program)
def run_program(program, args):
""" Run program specified by user (species, genes, or snps) """
if program == 'species':
from midas.merge import merge_species
merge_species.run_pipeline(args)
elif program == 'genes':
from midas.merge import merge_genes
merge_genes.run_pipeline(args)
elif program == 'snps':
from midas.merge import merge_snps
merge_snps.run_pipeline(args)
else:
sys.error("Unrecognized program: '%s'" % program)
def run_program(program, args):
""" Run program specified by user (species, genes, or snps) """
if program == 'species':
from midas.merge import merge_species
merge_species.run_pipeline(args)
elif program == 'genes':
from midas.merge import merge_genes
merge_genes.run_pipeline(args)
elif program == 'snps':
from midas.merge import merge_snps
merge_snps.run_pipeline(args)
else:
sys.error("Unrecognized program: '%s'" % program)
def correctPath(thepath,linesDeletedInCurrentId):
s=thepath
if s[-4:-3]=="#":
n=int(s[-3:])
j=3
elif s[-3:-2]=="#":
n=int(s[-2:])
j=2
elif s[-2:-1]=="#":
n=int(s[-1:])
j=1
else:
sys.error('this should not happen')
return s[:-j]+str(n-linesDeletedInCurrentId)
def create_transformation(t, v):
if t == 'rotation': # [0, 180]
return {'rotation_range': int(v * 180)}
if t == 'shift': # [0, 1]
return {'width_shift_range': v, 'height_shift_range': v}
if t == 'brightness': # [0.5, 2]
if v == 0:
return {'brightness_range': None}
return {'brightness_range': (1 - v * 0.5, 1 + v * 1)}
if t == 'shear': # [0, 60]
return {'shear_range': v * 60}
if t == 'channel': # [0, 50]
return {'channel_shift_range': v * 50}
sys.error('Unknown transformation: %s' % t)
def plotHorizBand(self,
Name='Band',
vX=[],
vCent=[],
vUp=[],
vDown=[],
Color=90,
Style=1001,
Legend='None'):
nP = len(vX)
if nP == 0: sys.error("plotHorizBand: ZERO size")
if len(vCent) != nP: sys.error("plotHorizBand: size mismatch")
if len(vUp) != nP: sys.error("plotHorizBand: size mismatch")
if len(vDown) != nP: sys.error("plotHorizBand: size mismatch")
obj = TGraphAsymmErrors(
nP, array('d', vX), array('d', vCent), array('d', [0.] * nP),
array('d', [0.] * nP),
array('d', [vCent[i] - vDown[i] for i in range(nP)]),
array('d', [vUp[i] - vCent[i] for i in range(nP)]))
print obj.GetFillStyle()
obj.SetFillStyle(Style)
obj.SetFillColor(Color)
obj.SetLineColor(Color)
obj.SetLineWidth(2)
self.Obj2Plot[Name] = {'Obj': obj, 'Type': 'Band', 'Legend': Legend}
def main(prog_args):
parser = optparse.OptionParser(version=meta.__version__)
extract_group = optparse.OptionGroup(parser, 'Extract Queries from psql log')
extract_group.add_option('--extract-queries', action='store_true', help='extract queries from a log file')
extract_group.add_option('--log-file', help='specify log file')
parser.add_option_group(extract_group)
analyze_group = optparse.OptionGroup(parser, 'Analyze extracted queries')
analyze_group.add_option('--analyze-queries', action='store_true', help='analyze query file (or stdin)')
analyze_group.add_option('--query-file', help='specify query file (file with queries delimited by %s or stdin)' % SEP)
analyze_group.add_option('--dburl', help='sqlalchemy connection string (we do not use sa, just the style of it ie postgres://postgres:password@localhost:port/dbname)')
analyze_group.add_option('--config-file', help='specify config file containing parameters for analyzing')
parser.add_option_group(analyze_group)
parser.add_option('--gen-config', action='store_true', help='generate a config file writeing work_mem and maintenance_work_mem')
parser.add_option('--test', action='store_true', help='run doctests')
opt, args = parser.parse_args(prog_args)
if opt.extract_queries:
if not opt.log_file:
sys.error('Specify --log-file')
return 1
fin = open(opt.log_file)
fout = sys.stdout
get_log_queries(fin, fout)
fout.close()
if opt.analyze_queries:
if not opt.query_file:
fin = sys.stdin
else:
fin = open(opt.query_file)
if not opt.config_file:
sys.error('Specify --config-file (--gen-config to generate sample)')
analyze_queries(_get_qf_queries(fin), opt.dburl, open(opt.config_file), sys.stdout)
if opt.gen_config:
c = Config()
c.add_setting('work_mem', ['1MB', '512MB'])
c.add_setting('maintenance_work_mem', ['1MB', '512MB'])
c.write(sys.stdout)
if opt.test:
import doctest
doctest.testmod()
def fromString(s):
line = s.split("\n")
style = line[0][line[0].find("<BG"):line[0].find(">")]
G = nx.DiGraph()
attr = line[0][line[0].find(">")+2:].rstrip()
if len(attr)>0:
for k in attr.split(" "):
kk,v = k.split("=")
G.graph[kk] = v
row = 1
numrows = len(line)
while row < numrows and line[row][0]=="N":
r = line[row].rstrip().split(" ")
if len(r) < 2:
sys.exit("ERROR: graph node index not found on line " + line[row])
G.add_node(int(r[1])+1)
G.node[int(r[1])+1]['ind'] = int(r[1])+1
G.node[int(r[1])+1]['viewpoint'] = True
G.node[int(r[1])+1]['childrenOrder']=[]
if len(r) > 2:
G.node[int(r[1])+1]['label'] = ("".join(r[2:]).encode('utf-8'))
row += 1
while row < numrows and line[row][0]=="E":
r = line[row].rstrip().split(" ")
if len(r) < 3:
sys.exit("ERROR: graph edge index not found on line " + line[row])
G.add_edge(int(r[1])+1, int(r[2])+1)
if len(r) == 3:
print "Error unordered edge!"
if len(r) > 3:
index=int(r[3])-2
#extend list if it is not long enough for the index
G.node[int(r[1])+1]['childrenOrder'].extend([-1 for i in xrange(len(G.node[int(r[1])+1]['childrenOrder']),index+1)])
G.node[int(r[1])+1]['childrenOrder'][index]=int(r[2])+1
#print G.node[int(r[1])]['childrenOrder']
#childrenOrder sould be correct
G.edge[int(r[1])+1][int(r[2])+1]['childindex'] = r[3]
#G.edge[int(r[1])][r[2]]['label'] = r[3:]
row += 1
#integrity check
for i in G.nodes():
#print i,DAG.node[i]['childrenOrder'],DAG.out_degree(i)
assert len(G.node[i]['childrenOrder'])==G.out_degree(i)
if not line[row]=="<EG>":
sys.error("ERROR: cannot find expected <EG> marker at the end of the graph")
return G
def readGenes(fname):
"""
Take a file name that is bed-like (needs at least 3 columns) - will conserve strand and name if they exist
Name will be the dictionary key for the output coverages
"""
genes = {}
i = 1
fieldsep = getsep(fname)
patt = re.compile(r'^chr$')
with open(fname) as fn:
for line in fn:
if line.startswith('#'):
continue
try:
chrom, start, end, name, score, strand = line.strip().split(
fieldsep)[:6]
except:
try:
a = line.strip().split(fieldsep)
length = len(a)
ext = 6 - length
a.extend(['.'] * ext)
chrom, start, end, name, score, strand = a
except:
sys.error(fname, 'Not a valid bed')
if name == '.':
name = 'peak' + str(i)
else:
name = os.path.basename(
name
) #macs puts the full path in this name field, if it hasn't been cleaned up yet this will
if strand not in ('+', '-', '.'):
strand = '.'
if args.m:
try:
start = (int(start) + int(end)) / 2
end = int(start + 1)
except:
continue
else:
#this should be used to deal with TSS
start = int(start)
end = int(start) + 1
iv = HTSeq.GenomicInterval(chrom.replace('"', ''), int(start),
int(end), strand)
genes[str(name)] = iv
i += 1
return (genes)
def get_concat_contigs(dirpath, filename):
filepath = get_filepath(dirpath, filename)
if (is_valid_file(filepath)):
count_contig = get_contig_count(filepath)
if (count_contig > 1):
file_org = open("%s" % filepath, "r")
file_new = open("%s/concat-%s" % (dirpath, filename), "a")
file_new.write(">%s\n" % (filename))
for line in file_org:
if (line[0] != ">"):
line = line.rstrip()
file_new.write(line)
file_org.close()
file_new.close()
else:
sys.error("Invalid path")
def get_concat_contigs(dirpath, filename):
filepath = get_filepath(dirpath, filename)
if(is_valid_file(filepath)):
count_contig = get_contig_count(filepath)
if(count_contig > 1):
file_org = open("%s" %filepath, "r")
file_new = open("%s/concat-%s" %(dirpath, filename), "a")
file_new.write(">%s\n" %(filename))
for line in file_org:
if(line[0] != ">"):
line = line.rstrip()
file_new.write(line)
file_org.close()
file_new.close()
else:
sys.error("Invalid path")
def estimateGaussianParametersBinary(self):
#try to estimate first guess for fitting a Gaussian based on largest binary particle
if self.__ip != []:
ip_binary = self.__ip.duplicate()
ip_binary.setAutoThreshold(
ij.process.AutoThresholder.Method.IsoData, True)
#ip_binary.setAutoThreshold(ImageProcessor.ISODATA2, True)
ip_binary.threshold(int(ip_binary.getMinThreshold()))
imp = ImagePlus('temp', ip_binary)
#not finished yet
print 'Threshold: ', int(ip_binary.getMinThreshold())
#return [bla.xCenterOfMass, bla.yCenterOfMass, self.__objSigma, self.__objSigma, bla.max, bla.min]
else:
sys.error(
'Could not estimate centroid, ImageProcessor not defined!')
def p_Asignacion(p): '''Asignacion : faID Factor5 Asignacion2''' ID = avail.IDPila_pop() if(idF == "asig"): TDim = avail.DPila_pop() variables_declaradas(ID) if(avail.DPila_pop()): if(TDim): par = avail.OPila_pop() par2 = avail.OPila_pop() avail.OPila_push(par) avail.TPila_push(tipo_variable(ID, "var")) avail.OPila_push(dir_var(ID)) avail.OPila_push(par2) avail.dim(dimension(ID), avail.OPila_pop()) avail.asign(avail.OPila_pop()) else: par = avail.OPila_pop() par2 = avail.OPila_pop() par3 = avail.OPila_pop() avail.OPila_push(par) avail.OPila_push(par2) avail.TPila_push(tipo_variable(ID, "var")) avail.OPila_push(dir_var(ID)) avail.OPila_push(par3) avail.dmT(dimension(ID), avail.OPila_pop()) avail.asign(avail.OPila_pop()) avail.asign(avail.OPila_pop()) else: avail.asign(dir_var(ID)) else: if(ID not in direc): print "Funcion no declarada", ID sys.exit(0) else: if((len(direc[ID][0])) != len(CHF)): print "Error de llamada de funcion, ", ID sys.error(0) else: cont = 0 for key in direc[ID][0]: if(direc[ID][0][key][0] != CHF[cont]): print "Error de tipo de llamada de funcion" sys.error(0) cont += 1 CHF[:] = []
def p_Asignacion(p):
'''Asignacion : faID Factor5 Asignacion2'''
ID = avail.IDPila_pop()
if (idF == "asig"):
TDim = avail.DPila_pop()
variables_declaradas(ID)
if (avail.DPila_pop()):
if (TDim):
par = avail.OPila_pop()
par2 = avail.OPila_pop()
avail.OPila_push(par)
avail.TPila_push(tipo_variable(ID, "var"))
avail.OPila_push(dir_var(ID))
avail.OPila_push(par2)
avail.dim(dimension(ID), avail.OPila_pop())
avail.asign(avail.OPila_pop())
else:
par = avail.OPila_pop()
par2 = avail.OPila_pop()
par3 = avail.OPila_pop()
avail.OPila_push(par)
avail.OPila_push(par2)
avail.TPila_push(tipo_variable(ID, "var"))
avail.OPila_push(dir_var(ID))
avail.OPila_push(par3)
avail.dmT(dimension(ID), avail.OPila_pop())
avail.asign(avail.OPila_pop())
avail.asign(avail.OPila_pop())
else:
avail.asign(dir_var(ID))
else:
if (ID not in direc):
print "Funcion no declarada", ID
sys.exit(0)
else:
if ((len(direc[ID][0])) != len(CHF)):
print "Error de llamada de funcion, ", ID
sys.error(0)
else:
cont = 0
for key in direc[ID][0]:
if (direc[ID][0][key][0] != CHF[cont]):
print "Error de tipo de llamada de funcion"
sys.error(0)
cont += 1
CHF[:] = []
def main(folder_input, type_input, output=None):
folder_input = realpath(folder_input)
if not isdir(folder_input):
logger.error('Input is not a folder: %s' % folder_input)
sys.error(0)
if not output:
fname = basename(normpath(folder_input))
output = join(folder_input, fname + '.json')
if type_input.lower() == 'xml':
convert_xml(folder_input, output)
elif type_input.lower() == 'txt':
convert_txt(folder_input, output)
else:
logger.error('Type of files is not correct: %s' % type_input)
sys.error(0)
def main():
if not os.path.exists('poker.jpg'):
print 'ERROR: This is a simple test meant to be run on local files. Please run from the subimage/test directory.'
sys.exit(-1)
img = cv2.imread('poker.jpg', cv2.CV_LOAD_IMAGE_GRAYSCALE)
cards = ar.find_by_ar(img, 0.7, 0.02,min_height=100,min_width=50)
if not cards:
print 'Sorry, couldn\'t find any cards in the provided image.'
sys.error(-1)
for card in cards:
#try to find what suit this card is
subsection = img[card.box]
subsection = subsection * card.mask
suit = get_suit(subsection)
value = get_value(subsection)
print 'Card found at ' + str(card.x) +','+ str(card.y)+': ' + suit + ' ' + value
def mov_average(self, n=3, win='tri'):
"""
Apply moving average with specified window.
Parameters: n: window width (truncated to be odd integer)
win: window type. Available windows are:
'rec': rectangular
'tri': triangular
"""
n = np.int(n) # truncate to integer
n = n - (1 - np.mod(n, 2)) # n is odd or will be decreased by 1
m = (n - 1) // 2 + 1 # window center
W = np.ones(n) # default rectangular window
if (win.lower() == 'rec'):
pass
elif (win.lower() == 'tri'):
W[:m] = np.linspace(1 / m, 1., m)
W[m - 1:] = np.linspace(1., 1 / m, m)
else:
sys.error('Averaging window type not available!')
m = m - 1
W = W / W.sum()
X = MRPy.copy(self)
for kX in range(self.NX):
for k in range(0, m):
k0 = m - k
W0 = W[k0:] / np.sum(W[k0:])
X[kX, k] = np.sum(W0 * self[kX, :k + m + 1])
for k in range(m, self.N - m - 1):
X[kX, k] = np.sum(W * self[kX, k - m:k + m + 1])
for k in range(self.N - m - 1, self.N):
k0 = m - k + self.N
W0 = W[:k0] / np.sum(W[:k0])
X[kX, k] = np.sum(W0 * self[kX, k - m:])
return X
def main():
if not os.path.exists('poker.jpg'):
print 'ERROR: This is a simple test meant to be run on local files. Please run from the subimage/test directory.'
sys.exit(-1)
img = cv2.imread('poker.jpg', cv2.CV_LOAD_IMAGE_GRAYSCALE)
cards = ar.find_by_ar(img, 0.7, 0.02, min_height=100, min_width=50)
if not cards:
print 'Sorry, couldn\'t find any cards in the provided image.'
sys.error(-1)
for card in cards:
#try to find what suit this card is
subsection = img[card.box]
subsection = subsection * card.mask
suit = get_suit(subsection)
value = get_value(subsection)
print 'Card found at ' + str(card.x) + ',' + str(
card.y) + ': ' + suit + ' ' + value
def plotVertLine(self,
Name='Curv',
vCent=1,
vY=[],
Color=kBlack,
Style=0,
Width=2,
Legend='None'):
nP = len(vY)
if nP == 0: sys.error("plotHorizBand: ZERO size")
obj = TGraph(nP, array('d', [vCent] * nP), array('d', vY))
obj.SetLineColor(Color)
obj.SetMarkerColor(Color)
obj.SetLineWidth(2)
obj.SetLineStyle(Style)
obj.SetMarkerStyle(0)
obj.SetMarkerSize(0)
self.Obj2Plot[Name] = {'Obj': obj, 'Type': 'Curve', 'Legend': Legend}
def readGenes (fname):
"""
Take a file name that is bed-like (needs at least 3 columns) - will conserve strand and name if they exist
Name will be the dictionary key for the output coverages
"""
genes = {}
i = 1
fieldsep = getsep(fname)
patt = re.compile(r'^chr$')
with open(fname) as fn:
for line in fn:
if line.startswith('#'):
continue
try:
chrom,start,end,name,score,strand = line.strip().split(fieldsep)[:6]
except:
try:
a = line.strip().split(fieldsep)
length = len(a)
ext = 6-length
a.extend(['.'] * ext)
chrom, start, end, name, score, strand = a
except:
sys.error(fname, 'Not a valid bed')
if name == '.':
name = 'peak'+str(i)
else:
name = os.path.basename(name) #macs puts the full path in this name field, if it hasn't been cleaned up yet this will
if strand not in ('+', '-', '.'):
strand = '.'
if args.m:
try:
start = (int(start)+int(end)) / 2
end = int(start +1 )
except:
continue
else:
#this should be used to deal with TSS
start = int(start)
end = int(start)+1
iv = HTSeq.GenomicInterval(chrom.replace('"',''), int(start), int(end), strand)
genes[str(name)] = iv
i += 1
return(genes)
def tag_insert(thing_id, tag_name):
sql_i = "INSERT OR IGNORE INTO tag (name) VALUES (?)"
c = conn.cursor()
param = (tag_name,)
c.execute(sql_i, param)
conn.commit()
sql_i = "SELECT id FROM tag WHERE name = ?"
param = (tag_name,)
c.execute(sql_i, param)
tag_id = c.fetchone()[0]
if tag_id:
sql_i = "INSERT OR IGNORE INTO thing_tag (thing_id, tag_id) VALUES (?, ?)"
param = (thing_id, tag_id)
# print param
c.execute(sql_i, param)
conn.commit()
else:
sys.error("tag is not exisitng in database file")
c.close()
def __init__(self, path):
# Regex za <div> poruke.
ri = re.compile(
r'<div\s+class="_3-94 _2lem"\s*>.*?</div>\s*(?=<div\s+class="_3-94 _2lem)',
re.MULTILINE | re.S)
try:
f = open(path, "r", encoding="utf8")
except IOError:
sys.error("Fajl ne postoji.")
# U buf se ucitava cela html stranica, a match je kolekcija svih poruka.
buf = f.read()
match = ri.findall(buf)
if match is None:
sys.exit()
else:
self.msgs = match
def plotHorizCurve(self,
Name='Curv',
vX=[],
vCent=[],
Color=kBlack,
Style=0,
Width=2,
Legend='None'):
nP = len(vX)
if nP == 0: sys.error("plotHorizBand: ZERO size")
if len(vCent) != nP: sys.error("plotHorizBand: size mismatch")
obj = TGraph(nP, array('d', vX), array('d', vCent))
obj.SetLineColor(Color)
obj.SetMarkerColor(Color)
obj.SetLineWidth(Width)
obj.SetLineStyle(Style)
obj.SetMarkerStyle(0)
obj.SetMarkerSize(0)
self.Obj2Plot[Name] = {'Obj': obj, 'Type': 'Curve', 'Legend': Legend}
def license_insert(thing_id, license_url):
sql_i = "INSERT OR IGNORE INTO license (url) VALUES (?)"
c = conn.cursor()
param = (license_url,)
c.execute(sql_i, param)
conn.commit()
sql_i = "SELECT id FROM license WHERE url = ?"
param = (license_url,)
c.execute(sql_i, param)
license_id = c.fetchone()
if license_id and license_id[0]:
license_id = license_id[0]
sql_i = "INSERT OR IGNORE INTO thing_license (thing_id, license_id) VALUES (?,?)"
param = (thing_id, license_id)
# print param
c.execute(sql_i, param)
conn.commit()
else:
sys.error("license error in database")
c.close()
def plotHorizBand(self,Name='Band',vX=[],vCent=[],vUp=[],vDown=[],Color=90,Style=1001,Legend='None'):
nP = len(vX)
if nP == 0 : sys.error("plotHorizBand: ZERO size")
if len(vCent) != nP : sys.error("plotHorizBand: size mismatch")
if len(vUp) != nP : sys.error("plotHorizBand: size mismatch")
if len(vDown) != nP : sys.error("plotHorizBand: size mismatch")
obj = TGraphAsymmErrors( nP , array('d',vX) , array('d',vCent) , array('d',[0.]*nP), array('d',[0.]*nP) , array('d',[vCent[i]-vDown[i] for i in range(nP)]) , array('d',[vUp[i]-vCent[i] for i in range(nP)]) )
print obj.GetFillStyle()
obj.SetFillStyle(Style)
obj.SetFillColor(Color)
obj.SetLineColor(Color)
obj.SetLineWidth(2)
self.Obj2Plot[Name] = { 'Obj' : obj , 'Type' : 'Band' , 'Legend' : Legend }
def file_insert(thing_id, file_type, file_url, file_date, file_name, file_download):
sql_i = "INSERT OR IGNORE INTO file_type (type) VALUES (?)"
c = conn.cursor()
param = (file_type,)
# print param
c.execute(sql_i, param)
conn.commit()
sql_i = "SELECT id FROM file_type WHERE type=?"
param = (file_type,)
c.execute(sql_i, param)
type_id = c.fetchone()[0]
if type_id:
sql_i = "INSERT INTO file (thing_id, date, type_id, download_count, url, name) VALUES (?, ?, ?, ?, ?, ?)"
param = (thing_id, file_date, type_id, file_download, file_url, file_name)
# print param
c.execute(sql_i, param)
conn.commit()
else:
sys.error("file type is not correct in database")
c.close()
def copy_file(in_file):
if 'release' in build_type.lower():
file_list = (in_file)
elif 'debug' in build_type.lower():
base_fn, ext = os.path.splitext(in_file)
file_list = (base_fn+'d'+ext,
base_fn[:(len(base_fn)-1)]+'d'+base_fn[-1]+ext,
in_file)#must be the last
else:
sys.error('unknown build type'+buildtype)
for file in file_list:
src = os.path.join(src_root_path, file)
if os.path.isfile(src):
dst = os.path.join(dst_root_path, file)
dir = os.path.dirname(dst)
if not os.path.exists(dir):
os.makedirs(dir)
sh.copy(src, dst)
return
for file in file_list:
src = os.path.join(src_root_path, file)
sys.stderr.write(src+" does not exist\n")