Mercurial > repos > melissacline > ucsc_cancer_utilities
view seg2matrix/CGData/SegToMatrix.py @ 34:d8e98030eca9
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author | jingchunzhu <jingchunzhu@gmail.com> |
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date | Fri, 24 Jul 2015 14:56:37 -0700 |
parents | ab20c0d04f4a |
children | 8ef79bd0be9a |
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import ctypes import os base = os.path.dirname(os.path.abspath(__file__)) libFile = base + "/CsegToMatrix.so" if os.path.exists(libFile): segLib = ctypes.cdll.LoadLibrary(libFile) def seg_to_matrix(seg_handle, out_handle): """ 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))