Mercurial > repos > melissacline > ucsc_cancer_utilities

comparison seg2matrix/CGData/SegToMatrix.py @ 54:59dbe857f5d4

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introduce normal_CNV parameter
author jingchunzhu
date Thu, 17 Sep 2015 22:03:04 -0700
parents 8ef79bd0be9a
children
comparison
equal deleted inserted replaced
53:7de3db823f90 54:59dbe857f5d4
8 os.system("g++ -fPIC --shared "+ base +"/CsegToMatrix.cc -o "+ base +"/CsegToMatrix.so") 8 os.system("g++ -fPIC --shared "+ base +"/CsegToMatrix.cc -o "+ base +"/CsegToMatrix.so")
9 9
10 if os.path.exists(libFile): 10 if os.path.exists(libFile):
11 segLib = ctypes.cdll.LoadLibrary(libFile) 11 segLib = ctypes.cdll.LoadLibrary(libFile)
12 12
13 13 def seg_to_matrix(seg_handle, out_handle, NORMAL_CNV):
14 def seg_to_matrix(seg_handle, out_handle):
15 """ 14 """
16 Turn a segment file into a segmented matrix. 15 Turn a segment file into a segmented matrix.
17 16
18 seg_handle -- CGData.GenomicSegment object 17 seg_handle -- CGData.GenomicSegment object
19 out_handle -- File handle to write to 18 out_handle -- File handle to write to
27 def printback(s): 26 def printback(s):
28 out_handle.write(s) 27 out_handle.write(s)
29 return 0 28 return 0
30 29
31 printbackTYPE = ctypes.CFUNCTYPE(ctypes.c_int, ctypes.c_char_p) 30 printbackTYPE = ctypes.CFUNCTYPE(ctypes.c_int, ctypes.c_char_p)
32 segLib.print_matrix(s, t, printbackTYPE(printback)) 31 segLib.print_matrix(s, t, printbackTYPE(printback), NORMAL_CNV)