def readRefTableSize(reftablefile):
""" @rtype: int
@return: the record number in binary reftable header
"""
if os.path.exists(reftablefile.encode(getFsEncoding(logLevel=False))):
binint = array.array('i')
f = open(reftablefile.encode(getFsEncoding(logLevel=False)),'rb')
binint.read(f,1)
f.close()
rtSize = binint[0]
return rtSize
else:
return None
def readNbRecordsOfScenario(reftablefile,numSc):
""" @rtype: int
@return: record number of a given scenario
in binary reftable header
"""
if os.path.exists(reftablefile.encode(getFsEncoding(logLevel=False))):
binint = array.array('i')
f = open(reftablefile.encode(getFsEncoding(logLevel=False)),'rb')
binint.read(f,numSc+2)
f.close()
nbRec = binint[-1]
return nbRec
else:
return None
def __init__(self,name,cmd_args_list,realtime_output=False,outfile_path=None,progressfile_path=None,
signalnames={"progress":"progress","log":"log","termSuccess":"termSuccess","termProblem":"termProblem","newOutput":"newOutput"}):
""" If progressfile_path is None or not given, no progress scrutation will be performed
If signalnames is not given, signals will have basic names
"""
super(LauncherThread,self).__init__()
self.name = name
self.cmd_args_list = cmd_args_list
self.fsCoding = getFsEncoding(logLevel=False)
self.cmd_args_list_quoted = list(self.cmd_args_list)
for i in range(len(self.cmd_args_list_quoted)):
if ";" in self.cmd_args_list_quoted[i] or " " in self.cmd_args_list_quoted[i] or ":" in self.cmd_args_list_quoted[i]:
self.cmd_args_list_quoted[i] = '"'+self.cmd_args_list_quoted[i]+'"'
self.realtime_output = realtime_output
self.outfile_path = outfile_path
self.progressfile_path = progressfile_path
self.progress_file_content = ""
self.processus = None
try:
self.SIGPROGRESS = signalnames["progress"]
self.SIGLOG = signalnames["log"]
self.SIGTERMSUCCESS = signalnames["termSuccess"]
self.SIGTERMPROBLEM = signalnames["termProblem"]
self.SIGNEWOUTPUT = signalnames["newOutput"]
except Exception as e:
print e
raise Exception("Signal name hashtable malformed")
def isSNPDatafile(name):
if os.path.exists(str(name).encode(getFsEncoding(logLevel=False))):
f=open(str(name).encode(getFsEncoding(logLevel=False)),'rU')
lines=f.readlines()
f.close()
if len(lines) > 0:
l1 = lines[0].strip()
pat = re.compile(r'\s+')
l1compressed = pat.sub(' ',l1)
l1parts = l1compressed.split(' ')
if len(l1parts) > 3 and l1parts[0] == "IND" and (l1parts[1].lower() == "sex") and l1parts[2] == "POP":
return True
l1 = lines[1].strip()
pat = re.compile(r'\s+')
l1compressed = pat.sub(' ',l1)
l1parts = l1compressed.split(' ')
if len(l1parts) > 3 and l1parts[0] == "IND" and (l1parts[1].lower() == "sex") and l1parts[2] == "POP":
return True
return False
def __init__(self,filename):
super(DataSnp, self).__init__()
self.filename = str(filename)
self.fsCoding = getFsEncoding(logLevel=False)
self.nloc = 0
self.nloctot = 0
self.nindtot = 0
self.nsample = 0
self.ntypeloc = {}
# taille des populations
self.nind = []
self.nind_hash = {}
self.commentValuesDict = {'maf' : 'hudson'}
#'nm' : "1.0nf"}
self.__readData(writeMafFile=False)
def handler(req):
req.log_error('handler')
req.content_type = 'text/html'
req.send_http_header()
#req.write('<html><head><title>Testing mod_python</title></head><body>')
#req.write('%s'%util.FieldStorage(req)["file"])
try:
date = datetime.datetime.now().strftime("%Y %m %d %H:%M:%S")
ip = req.connection.remote_ip
name = u"%s/%s %s.tar.gz"%(os.path.dirname(os.path.abspath(__file__)),date,ip)
f = open(name.encode(getFsEncoding(logLevel=False)),"w")
f.write(util.FieldStorage(req)["file"])
f.close()
req.write('OK')
except Exception as e:
req.write('%s'%e)
#req.write('</body></html>')
return apache.OK
def __init__(self,filename):
super(Data, self).__init__()
self.filename = filename # name of the genepop data file (string)
self.fsCoding = getFsEncoding(logLevel=False)
self.message = None # message about the content of the data file if reading is successful or error message if not (string)
self.title = None # title of the data file (string)
self.nloc_mic = 0 # number of microsatellite loci (integer)
self.nloc_seq = 0 # number of sequence loci (integer)
self.nloc = 0 # total number of loci (integer)
self.nsample = 0 # number of samples (integer)
self.nind = [] # number of individuals per [sample] (list of integer)
self.nindtot = 0 # total number of individuals
self.samplesize = [] # number of gene copies per [locus][sample] EXcluding missing data (list of list of integer)
self.locuslist = LocusList() # list of loci (list of Locus)
self.locusgrouplist = LocusGroupList() # list of groups of loci (list of LocusGroup)
self.indivname = [] # list of names of individuals (list of list of string) [sample][individual]
self.indivsexe = [] # list of sexes of individuals (list of list of integer) (male=1,female=2) [sample][individual]
self.haplo = [] # values of gene copies per [locus][sample][gene copy] : list of list of list of (integer,string)
self.nhaplo = [] # number of gene copies per [locus][sample] including missing data (list of list of integer)
self.missdat = [] # list of missing data in microsatellite loci (list of Missingdata)
self.missnuc = [] # list of missing nucleotide in sequence loci (list of MissingNucleotide)
self.sexratio = 0.5 # NM/(NF+NM)
self.commentValuesDict = {} #'nm' : "1.0nf"}