Mercurial > repos > melissacline > ucsc_cancer_utilities

annotate seg2matrix/CGData/SegToMatrix.py @ 60:bf57076e27b9 default tip

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change genomicSegment input data
author jingchunzhu@gmail.com
date Tue, 27 Oct 2015 16:07:09 -0700
parents 59dbe857f5d4
children
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1 import ctypes
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2 import os
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4 base = os.path.dirname(os.path.abspath(__file__))
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5 libFile = base + "/CsegToMatrix.so"
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7 os.system("rm -f "+ base+"/CsegToMatrix.so")
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8 os.system("g++ -fPIC --shared "+ base +"/CsegToMatrix.cc -o "+ base +"/CsegToMatrix.so")
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10 if os.path.exists(libFile):
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11 segLib = ctypes.cdll.LoadLibrary(libFile)
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12
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13 def seg_to_matrix(seg_handle, out_handle, NORMAL_CNV):
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14 """
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15 Turn a segment file into a segmented matrix.
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17 seg_handle -- CGData.GenomicSegment object
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18 out_handle -- File handle to write to
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19 """
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20 s = segLib.new_segment()
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21 t = segLib.new_target_set()
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22 for target in seg_handle.get_key_list():
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23 for seg in seg_handle.get_by(target):
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24 segLib.add_segment(s, t, target, seg.chrom, seg.chrom_start, seg.chrom_end, ctypes.c_float(seg.value))
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26 def printback(s):
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27 out_handle.write(s)
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28 return 0
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30 printbackTYPE = ctypes.CFUNCTYPE(ctypes.c_int, ctypes.c_char_p)
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31 segLib.print_matrix(s, t, printbackTYPE(printback), NORMAL_CNV)