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

introduce normal_CNV parameter

import ctypes
import os

base = os.path.dirname(os.path.abspath(__file__))
libFile = base + "/CsegToMatrix.so"

os.system("rm -f "+ base+"/CsegToMatrix.so")
os.system("g++ -fPIC --shared "+ base +"/CsegToMatrix.cc -o "+ base +"/CsegToMatrix.so")

if os.path.exists(libFile):
    segLib = ctypes.cdll.LoadLibrary(libFile)

def seg_to_matrix(seg_handle, out_handle, NORMAL_CNV):
    """
    Turn a segment file into a segmented matrix.
    
    seg_handle -- CGData.GenomicSegment object
    out_handle -- File handle to write to
    """
    s = segLib.new_segment()
    t = segLib.new_target_set()
    for target in seg_handle.get_key_list():
        for seg in seg_handle.get_by(target):
            segLib.add_segment(s, t, target, seg.chrom, seg.chrom_start, seg.chrom_end, ctypes.c_float(seg.value))

    def printback(s):
        out_handle.write(s)
        return 0

    printbackTYPE = ctypes.CFUNCTYPE(ctypes.c_int, ctypes.c_char_p)
    segLib.print_matrix(s, t, printbackTYPE(printback), NORMAL_CNV)