import CGData
import CGData.NumpyMatrix
import sys
# matrixProbeRemap.py <matrixFile> <probeFile>
#load the matrix
matrix = CGData.NumpyMatrix.NumpyMatrix()
matrixHandle = open(sys.argv[1])
matrix.read(matrixHandle)
matrixHandle.close()
#load the probeMap
probeMap = CGData.load( sys.argv[2] )
#remove null probes from the matrix
matrix.remove_null_probes()
#remap the matrix using the probe map
valid_map = {}
for alt in probeMap.get_probes():
valid_map[alt.aliases[0]] = True
if alt.name in matrix.get_row_names():
matrix.row_rename(alt.name, alt.aliases[0])
remove_list = []
for name in matrix.get_row_names():
if not name in valid_map:
import CGData
import CGData.NumpyMatrix
import sys
# matrixProbeRemap.py <matrixFile> <probeFile>
#load the matrix
matrix = CGData.NumpyMatrix.NumpyMatrix()
matrixHandle = open(sys.argv[1])
matrix.read(matrixHandle)
matrixHandle.close()
#load the probeMap
probeMap = CGData.load(sys.argv[2])
#remove null probes from the matrix
matrix.remove_null_probes()
#remap the matrix using the probe map
valid_map = {}
for alt in probeMap.get_probes():
valid_map[alt.aliases[0]] = True
if alt.name in matrix.get_row_names():
matrix.row_rename(alt.name, alt.aliases[0])
remove_list = []
for name in matrix.get_row_names():
if not name in valid_map:
#!/usr/bin/env python #note: this script assumes that the first alias in the probeMap aliaslist #is a HUGO gene name... import CGData import sys # matrixProbeRemap.py <matrixFile> <probeFile> #load the matrix matrix = CGData.load( sys.argv[1] ) #load the probeMap probeMap = CGData.load( sys.argv[2] ) #remove null probes from the matrix matrix.remove_null_probes() #remap the matrix using the probe map matrix.remap( probeMap, skip_missing=True ) matrix.add_history( "Transformed from probespace %s to HUGO" % (probeMap.get_name() ) ) matrix.attrs[":probeMap"] = "hugo" #output the matrix matrix.store( sys.argv[3] )
#!/usr/bin/env python
#note: this script assumes that the first alias in the probeMap aliaslist
#is a HUGO gene name...
import CGData
import sys
# matrixProbeRemap.py <matrixFile> <probeFile>
#load the matrix
matrix = CGData.load(sys.argv[1])
#load the probeMap
probeMap = CGData.load(sys.argv[2])
#remove null probes from the matrix
matrix.remove_null_probes()
#remap the matrix using the probe map
matrix.remap(probeMap, skip_missing=True)
matrix.add_history("Transformed from probespace %s to HUGO" %
(probeMap.get_name()))
matrix.attrs[":probeMap"] = "hugo"
#output the matrix
matrix.store(sys.argv[3])
