fixes compilation issues more testing needs to be done #18

jeffhsu3 · Jan 20, 2015 · adc182d · adc182d
1 parent 62d9d4a
commit adc182d
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Showing 5 changed files with 4 additions and 519 deletions.
diff --git a/genda/pysam_callbacks/allele_counter.pyx b/genda/pysam_callbacks/allele_counter.pyx
@@ -5,7 +5,7 @@ from cpython cimport bool
 #from multiprocessing import Process
 #import cython
 cimport pysam.csamtools as csam
-from pysam.csamtools cimport AlignedRead, bam1_t, bam_pileup1_t
+from pysam.calignmentfile cimport AlignedSegment
 from libc.stdlib cimport malloc, free
 from cpython cimport PyObject
 #cimport csamtools
@@ -15,13 +15,6 @@ ctypedef np.float64_t dtype_t
 
 cdef inline int int_max(int i , int j): return i if i >= j else j
 
-'''
-cpdef object construct_known_var(csam.Samfile samfile, PileupProxy col):
-    """ Counts the various alleles at a given position.
-    """
-
-    cdef int i # loop index
-'''
 
 cdef class AlleleCounter:
     """ Counts the various alleles at a given position.
@@ -52,12 +45,11 @@ cdef class AlleleCounter:
         self.region = region
         self.position = int(position)
         self.phredThreshold = phredThreshold
-        print('hi_c')
         #self.counts = np.zeros(4, dtype=np.uint16)
 
 
 
-    def  __call__(self, AlignedRead alignment, int position = 0,
+    def  __call__(self, AlignedSegment alignment, int position = 0,
                  int phredThreshold = 0,
                  bool isIndel = False):
         cdef int index

diff --git a/genda/stats/aei_count_samples.pyx b/genda/stats/aei_count_samples.pyx
@@ -4,7 +4,7 @@ ctypedef np.float64_t dtype_t
 ctypedef np.uint16_t DTYPE_t
 from genda.pysam_callbacks.allele_counter cimport AlleleCounter
 from cpython cimport bool
-from pysam.csamtools cimport Samfile, IteratorRowRegion, AlignedRead
+from pysam.calignmentfile cimport AlignmentFile, IteratorRowRegion, AlignedSegment
 import cython
 from cython.parallel import prange
 from . import *
@@ -22,7 +22,7 @@ cpdef aei_count_samples(np.ndarray[dtype_t, ndim=2] geno,
     """
     cdef int n_samples
     cdef int counter
-    cdef Samfile bamfile
+    cdef AlignmentFile bamfile
     cdef int n_markers
     cdef int j 
     cdef int i

diff --git a/scripts/AEI/AEI.py b/scripts/AEI/AEI.py
diff --git a/scripts/AEI/AEI_2.py → scripts/AEI/aei_count.py b/scripts/AEI/AEI_2.py → scripts/AEI/aei_count.py
@@ -240,7 +240,6 @@ def main():
         subset_geno.apply(counts_fixed)
     reget_fixed = functools.partial(reget_sample_names, mapping = file_to_sample)
     counts_matrix.rename(columns=file_to_sample, inplace=True)
-    print(counts_matrix)
 
     counts_matrix.to_pickle(options.filename)