def readRates( infile ):
"""read rates and G+C from a tab-separated file."""
from rpy import r as R
import rpy
handle, name = tempfile.mkstemp()
os.close(handle)
outfile = open(name, "w")
first = True
headers = []
for line in infile:
if line[0] == "#": continue
data = line[:-1].split("\t")
if first:
headers = data
first = False
continue
outfile.write( line )
outfile.close()
assert len(headers) == 3, "malformatted file of rates, please supply id, g+c, rate"
rpy.set_default_mode(rpy.NO_CONVERSION)
matrix = R.read_table( name, na_string = ("NA", "na"), col_names=headers )
rpy.set_default_mode(rpy.BASIC_CONVERSION)
os.remove( name )
return matrix, headers
def readRates(infile):
"""read rates and G+C from a tab-separated file."""
from rpy import r as R
import rpy
handle, name = tempfile.mkstemp()
os.close(handle)
outfile = open(name, "w")
first = True
headers = []
for line in infile:
if line[0] == "#":
continue
data = line[:-1].split("\t")
if first:
headers = data
first = False
continue
outfile.write(line)
outfile.close()
assert len(
headers) == 3, "malformatted file of rates, please supply id, g+c, rate"
rpy.set_default_mode(rpy.NO_CONVERSION)
matrix = R.read_table(name, na_string=("NA", "na"), col_names=headers)
rpy.set_default_mode(rpy.BASIC_CONVERSION)
os.remove(name)
return matrix, headers
def cargar_texto(self, fichero, **opciones):
"""Carga los datos de un fichero de texto"""
import os
if not os.path.exists(fichero):
from pyrqt.excepciones import FicheroNoExisteException
raise FicheroNoExisteException(fichero)
from rpy import r #pylint: disable=import-error
datos = r.read_table(fichero, sep = opciones["delimitadoratrib"], \
header = opciones["cabeceras"], na_strings="NA", dec=".", \
strip_white = False)
for nombre, columna in datos.items():
import types
milista = []
if type(columna[0]) == types.IntType:
self.ana_var(nombre, "Entero")
for registro in columna:
if registro == -2147483648: #Valor nulo
resultado = None
else:
resultado = int(registro)
milista.append(resultado)
elif type(columna[0]) == types.StringType:
#Es un Factor
self.ana_var(nombre, "Factor")
milista = columna
elif type(columna[0]) == types.FloatType:
self.ana_var(nombre, "Real")
milista = columna
else:
raise TypeError #R Devuelve un tipo desconocido
for i in range(self.n_reg(), len(milista)):
self.ana_reg()
for i in range(self.n_reg()):
self._portero.actual().registros()[i][nombre] = milista[i]