Can also collapse pybedtools Interval and BedTool.

bam25prime/Python/bam25prime/__init__.py

 from .bam25prime import (
     collapse_ali,
-    collapse_and_sort)
+    collapse_bed,
+    collapse_and_sort,
+    collapse_and_sort_bedtool,
+    )

bam25prime/Python/bam25prime/bam25prime.py

@@ -8,7 +8,8 @@ When executed, this module collapses reads in a bam file to their 5-prime end
 import argparse
 from pybedtools import BedTool, Interval
 from pysam import AlignmentFile
-from .libbam25prime import collapse_ali
+from .libcollapsesam import collapse_ali
+from .libcollapsebed import collapse_bed
 
 # pybedtools.Interval | pysam.AlignedSegment
 # chrom               | reference_name
@@ -114,7 +115,7 @@ from .libbam25prime import collapse_ali
 
 def collapse_and_sort(alis):
     """
-    Collapse elements from *ali* to their 5 prime end.
+    Collapse elements from *alis* to their 5 prime end.
 
     The resulting :class:`pybedtool.BedTool` is sorted.
 
@@ -131,6 +132,23 @@ def collapse_and_sort(alis):
         from_string=True).sort(stream=True)
 
 
+def collapse_and_sort_bedtool(bedtool):
+    """
+    Collapse elements from *bedtool* to their 5 prime end.
+
+    The resulting :class:`pybedtool.BedTool` is sorted.
+
+    :param bedtool: A :class:`pybedtool.BedTool`
+    :rtype: :class:`pybedtool.BedTool`
+
+    :class:`pybedtool.BedTool` is an iterable:
+    It can be iterated over in a for loop, or produce an iterator
+    using :func:`iter` on it
+    (see https://stackoverflow.com/a/28353158/1878788).
+    """
+    return bedtool.each(collapse_bed).sort(stream=True)
+
+
 def main():
     """Main function of the program."""
     parser = argparse.ArgumentParser(

bam25prime/Python/bam25prime/libcollapsebed.pyx

+#!/usr/bin/env python3
+# vim: set fileencoding=<utf-8> :
+# cython: language_level=3
+"""
+This library contains a cythonized version of a function to collapse
+:class:`pybedtools.Interval`s to their 5' end.
+"""
+
+# http://stackoverflow.com/a/23575771/1878788
+# Also works by setting language_level as comment
+# at the top of the file.
+#from __future__ import print_function
+from pybedtools.cbedtools cimport Interval
+
+
+cdef ccollapse_bed(Interval bed):
+    """
+    Return the Interval corresponding to the 5' collapse of Interval *bed*.
+    """
+    if bed.strand == "-":
+        bed.start = bed.stop - 1
+    else:
+        bed.stop = bed.start + 1
+    return bed
+
+
+def collapse_bed(bed):
+    """
+    Return the Interval corresponding to the 5' collapse of Interval *bed*.
+    """
+    return ccollapse_bed(bed)
+
+
+def main():
+    """Example use case."""
+    print("No examples to show here.")
+    return 0
+
+
+if __name__ == "__main__":
+    import sys
+    sys.exit(main())

bam25prime/Python/bam25prime/libbam25prime.pyx → bam25prime/Python/bam25prime/libcollapsesam.pyx

@@ -12,9 +12,8 @@ segments to their 5' end.
 #from __future__ import print_function
 #from pybedtools import Interval
 from pysam.libchtslib cimport BAM_FREVERSE
-from pysam.libcalignedsegment cimport AlignedSegment
-
 #cdef int BAM_FREVERSE = 16
+from pysam.libcalignedsegment cimport AlignedSegment
 
 
 cdef object ccollapse_ali(AlignedSegment ali):
@@ -50,94 +49,6 @@ def collapse_ali(ali):
     return ccollapse_ali(ali)
 
 
-## These should have problems mapping because the T-tail is not
-## in the genome sequence
-#cdef bint chas_csr1_endosi_signature(str seq, int read_len):
-#    # if read_len <= 22, t_tail will be the empty string
-#    cdef str t_tail
-#    t_tail = (read_len - SI_MIN) * "T"
-#    if t_tail:
-#        return (seq[0] == "G") and (seq[SI_MIN:] == t_tail)
-#    else:
-#        return False
-#
-#
-#def has_csr1_endosi_signature(str seq, int read_len):
-#    return chas_csr1_endosi_signature(seq, read_len)
-#
-#
-#cdef bint chas_allsi_signature(str seq):
-#    cdef unsigned int read_len = len(seq)
-#    return (seq[0] == "G" and (SI_MIN <= read_len <= SI_MAX)) or chas_csr1_endosi_signature(seq, read_len)
-#
-#
-#cdef class Composition:
-#    cdef readonly int a, c, g, t
-#    def __init__(self, int a=0, int c=0, int g=0, int t=0):
-#        self.a = a
-#        self.c = c
-#        self.g = g
-#        self.t = t
-#    def __add__(self, other):
-#        return Composition(
-#            self.a + other.a,
-#            self.c + other.c,
-#            self.g + other.g,
-#            self.t + other.t)
-#    def __reduce__(self):
-#        d = {}
-#        d["a"] = self.a
-#        d["c"] = self.c
-#        d["g"] = self.g
-#        d["t"] = self.t
-#        return (Composition, (), d)
-#    def __setstate__(self, d):
-#        self.a = d["a"]
-#        self.c = d["c"]
-#        self.g = d["g"]
-#        self.t = d["t"]
-#
-#
-#def count_nucl(int read_len, str nucl):
-#    if nucl == "A":
-#        return {read_len: Composition(a=1)}
-#    elif nucl == "C":
-#        return {read_len: Composition(c=1)}
-#    elif nucl == "G":
-#        return {read_len: Composition(g=1)}
-#    elif nucl == "T":
-#        return {read_len: Composition(t=1)}
-#    else:
-#        return {read_len: Composition()}
-#
-#
-#def collapse_ali(ali):
-#    """
-#    Collapse a :class:`pysam.AlignedSegment` to its 5' position.
-#
-#    The returned object is a :class:`pybedtools.Interval` of length 1,
-#    with minimal location and orientation information.
-#
-#    :param ali: The aligned segment to be collapsed.
-#    :type ali: :class:`pysam.AlignedSegment`
-#    :rtype: :class:`pybedtools.Interval`
-#    """
-#    if ali.is_reverse:
-#        return Interval(
-#            ali.reference_name,
-#            # five prime position
-#            ali.reference_end - 1,
-#            ali.reference_end,
-#            strand="-")
-#    else:
-#        return Interval(
-#            ali.reference_name,
-#            # five prime position
-#            ali.reference_start,
-#            ali.reference_start + 1,
-#            strand="+")
-
-
 def main():
     """Example use case."""
     print("No examples to show here.")

bam25prime/Python/setup.py

 from setuptools import setup, find_packages
+from glob import glob
 # If you have .pyx things to cythonize
 from distutils.extension import Extension
 from Cython.Build import cythonize
@@ -10,8 +11,12 @@ __version__ = "0.1"
 # https://github.com/cython/cython/blob/master/docs/src/reference/compilation.rst#configuring-the-c-build
 extensions = [
     Extension(
-        "bam25prime.libbam25prime", ["bam25prime/libbam25prime.pyx"],
+        "bam25prime.libcollapsesam", ["bam25prime/libcollapsesam.pyx"],
         include_dirs=pysam_get_include()),
+    Extension(
+        "bam25prime.libcollapsebed", ["bam25prime/libcollapsebed.pyx"],
+        include_dirs=glob("/home/bli/src/bedtools2-2.27.1/src/utils/*"),
+        language="c++"),
     ]
 
 setup(