#use a sample map to check for sample overlaps between matrix files
import sys
from cgData.matrix import GeneMatrix
from cgData.sampleMap import SampleMap
handle = open( sys.argv[1] )
sm = SampleMap()
sm.read( handle )
handle.close()
gmList = []
sampleHash = {}
for path in sys.argv[2:]:
gm = GeneMatrix()
handle = open( path )
gm.readTSV( handle, skipVals=True )
handle.close()
gmList.append( gm )
for sample in gm.getSampleList():
if sample not in sampleHash:
sampleHash[ sample ] = []
sampleHash[ sample ].append( path )
sampleRemap = {}
for sample in sampleHash:
children = sm.getChildren( sample )
for c in children:
if c in sampleHash:
sampleRemap[ c ] = sample
#!/usr/bin/env python from cgData.matrix import GeneMatrix import sys handle = open(sys.argv[1]) gm = GeneMatrix() gm.readTSV(handle) gm.writeGCT(sys.stdout, missing="0")
#!/usr/bin/env python from cgData.matrix import GeneMatrix import sys handle = open( sys.argv[1] ) gm = GeneMatrix() gm.readTSV( handle ) gm.writeGCT( sys.stdout, missing="0" )
