diff --git a/bam25prime/Python/bam25prime/__init__.py b/bam25prime/Python/bam25prime/__init__.py
index f3ac9f63620cc5930d7bece50349a7b966975639..9c979ee4d31bca39c8c2c27598fb5f7c94e39ddf 100644
--- a/bam25prime/Python/bam25prime/__init__.py
+++ b/bam25prime/Python/bam25prime/__init__.py
@@ -1,3 +1,6 @@
from .bam25prime import (
collapse_ali,
- collapse_and_sort)
+ collapse_bed,
+ collapse_and_sort,
+ collapse_and_sort_bedtool,
+ )
diff --git a/bam25prime/Python/bam25prime/bam25prime.py b/bam25prime/Python/bam25prime/bam25prime.py
index 60017112f21a3be36f241207f425a80e842fa2eb..0c9e84879ace2da5a5db8509ea39bc3b278c9c97 100755
--- a/bam25prime/Python/bam25prime/bam25prime.py
+++ b/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(
diff --git a/bam25prime/Python/bam25prime/libbam25prime.pyx b/bam25prime/Python/bam25prime/libbam25prime.pyx
deleted file mode 100755
index d91e4435564485b84c4d9aa585fb997c858bdef3..0000000000000000000000000000000000000000
--- a/bam25prime/Python/bam25prime/libbam25prime.pyx
+++ /dev/null
@@ -1,149 +0,0 @@
-#!/usr/bin/env python3
-# vim: set fileencoding=<utf-8> :
-# cython: language_level=3
-"""
-This library contains a cythonized version of a function to collapse aligned
-segments 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 import Interval
-from pysam.libchtslib cimport BAM_FREVERSE
-from pysam.libcalignedsegment cimport AlignedSegment
-
-#cdef int BAM_FREVERSE = 16
-
-
-cdef object ccollapse_ali(AlignedSegment ali):
- """
- Return the bed information corresponding to the 5' collapse
- of AlignedSegment *ali*.
- """
- if (ali.flag & BAM_FREVERSE) != 0:
- return "\t".join([
- ali.reference_name,
- # five prime position
- str(ali.reference_end - 1),
- str(ali.reference_end),
- ".",
- ".",
- "-"])
- else:
- return "\t".join([
- ali.reference_name,
- # five prime position
- str(ali.reference_start),
- str(ali.reference_start + 1),
- ".",
- ".",
- "+"])
-
-
-def collapse_ali(ali):
- """
- Return the bed information corresponding to the 5' collapse
- of AlignedSegment *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.")
- return 0
-
-
-if __name__ == "__main__":
- import sys
- sys.exit(main())
diff --git a/bam25prime/Python/bam25prime/libcollapsebed.pyx b/bam25prime/Python/bam25prime/libcollapsebed.pyx
new file mode 100644
index 0000000000000000000000000000000000000000..ba2aa8d42db4f6880ffa2c03a020961d90790fcf
--- /dev/null
+++ b/bam25prime/Python/bam25prime/libcollapsebed.pyx
@@ -0,0 +1,42 @@
+#!/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())
diff --git a/bam25prime/Python/bam25prime/libcollapsesam.pyx b/bam25prime/Python/bam25prime/libcollapsesam.pyx
new file mode 100755
index 0000000000000000000000000000000000000000..4d7879a480f5875860cf3bb0e6ebe916c0ce24cc
--- /dev/null
+++ b/bam25prime/Python/bam25prime/libcollapsesam.pyx
@@ -0,0 +1,60 @@
+#!/usr/bin/env python3
+# vim: set fileencoding=<utf-8> :
+# cython: language_level=3
+"""
+This library contains a cythonized version of a function to collapse aligned
+segments 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 import Interval
+from pysam.libchtslib cimport BAM_FREVERSE
+#cdef int BAM_FREVERSE = 16
+from pysam.libcalignedsegment cimport AlignedSegment
+
+
+cdef object ccollapse_ali(AlignedSegment ali):
+ """
+ Return the bed information corresponding to the 5' collapse
+ of AlignedSegment *ali*.
+ """
+ if (ali.flag & BAM_FREVERSE) != 0:
+ return "\t".join([
+ ali.reference_name,
+ # five prime position
+ str(ali.reference_end - 1),
+ str(ali.reference_end),
+ ".",
+ ".",
+ "-"])
+ else:
+ return "\t".join([
+ ali.reference_name,
+ # five prime position
+ str(ali.reference_start),
+ str(ali.reference_start + 1),
+ ".",
+ ".",
+ "+"])
+
+
+def collapse_ali(ali):
+ """
+ Return the bed information corresponding to the 5' collapse
+ of AlignedSegment *ali*.
+ """
+ return ccollapse_ali(ali)
+
+
+def main():
+ """Example use case."""
+ print("No examples to show here.")
+ return 0
+
+
+if __name__ == "__main__":
+ import sys
+ sys.exit(main())
diff --git a/bam25prime/Python/setup.py b/bam25prime/Python/setup.py
index e89db1d7cdc2bd46b17fdca58cfaecb7f215de6a..0f716255bffc30a79efd45beaeba2162d61bf9d4 100644
--- a/bam25prime/Python/setup.py
+++ b/bam25prime/Python/setup.py
@@ -1,4 +1,5 @@
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(