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1
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2
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3 import ctypes
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4 import os
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5
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6 base = os.path.dirname(os.path.abspath(__file__))
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7 libFile = base + "/CsegToMatrix.so"
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8 if os.path.exists(libFile):
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9 segLib = ctypes.cdll.LoadLibrary(libFile)
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10
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11
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12 def seg_to_matrix(seg_handle, out_handle):
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13 """
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14 Turn a segment file into a segmented matrix.
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15
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16 seg_handle -- CGData.GenomicSegment object
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17 out_handle -- File handle to write to
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18 """
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19 s = segLib.new_segment()
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20 t = segLib.new_target_set()
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21 for target in seg_handle.get_key_list():
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22 for seg in seg_handle.get_by(target):
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23 segLib.add_segment(s, t, target, seg.chrom, seg.chrom_start, seg.chrom_end, ctypes.c_float(seg.value))
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24
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25 def printback(s):
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26 out_handle.write(s)
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27 return 0
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28
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29 printbackTYPE = ctypes.CFUNCTYPE(ctypes.c_int, ctypes.c_char_p)
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30 segLib.print_matrix(s, t, printbackTYPE(printback))
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