diff --git a/bam25prime/Python/bam25prime/__init__.py b/bam25prime/Python/bam25prime/__init__.py
deleted file mode 100644
index 9c979ee4d31bca39c8c2c27598fb5f7c94e39ddf..0000000000000000000000000000000000000000
--- a/bam25prime/Python/bam25prime/__init__.py
+++ /dev/null
@@ -1,6 +0,0 @@
-from .bam25prime import (
- collapse_ali,
- collapse_bed,
- collapse_and_sort,
- collapse_and_sort_bedtool,
- )
diff --git a/bam25prime/Python/bam25prime/bam25prime.py b/bam25prime/Python/bam25prime/bam25prime.py
deleted file mode 100755
index 3ff2d6ee0edf6336864fd251919a568ad0b0eabe..0000000000000000000000000000000000000000
--- a/bam25prime/Python/bam25prime/bam25prime.py
+++ /dev/null
@@ -1,172 +0,0 @@
-#!/usr/bin/env python3
-# vim: set fileencoding=<utf-8> :
-"""
-When executed, this module collapses reads in a bam file to their 5-prime end
-(reducing them to length 1) and writes the result in bed format.
-"""
-
-import argparse
-from pybedtools import BedTool, Interval
-from pysam import AlignmentFile
-from .libcollapsesam import collapse_ali
-from .libcollapsebed import collapse_bed
-
-# pybedtools.Interval | pysam.AlignedSegment
-# chrom | reference_name
-# start | reference_start
-# end | reference_end
-# bool(int(strand)) | is_reverse
-#
-# Interval(reference_name, reference_start, reference_end, strand=strand)
-
-# filename = "../RNA_Seq_analyses/results_44hph_vs_38hph/hisat2/mapped_C_elegans/WT_44hph_4_polyU_on_C_elegans_sorted.bam"
-# bamfile = pysam.AlignmentFile(filename, "rb")
-# beds_in = pybedtools.BedTool(filename)
-#
-# In [99]: %timeit [int(bed.strand) for bed in beds_in]
-# 2.03 s ± 25.3 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)
-#
-# In [100]: %timeit [ali.is_reverse for ali in bamfile.fetch()]
-# 67 ms ± 1.1 ms per loop (mean ± std. dev. of 7 runs, 10 loops each)
-#
-# In [101]: beds_in = pybedtools.BedTool(filename)
-#
-# In [102]: %timeit [bed.strand for bed in beds_in]
-# 2.05 s ± 5.3 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)
-#
-# In [103]: beds_in = pybedtools.BedTool(filename)
-#
-# In [104]: %timeit [bed.strand == "16" for bed in beds_in]
-# 2 s ± 2.52 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)
-
-
-# TODO: Test if replacing by cythonized version is more efficient
-# 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 collapse_and_sort(alis):
-# """
-# Collapse elements from *ali* to their 5 prime end.
-#
-# The resulting :class:`pybedtool.BedTool` is sorted.
-#
-# :param alis: An iterable of :class:`pysam.AlignedSegment`
-# :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.
-# """
-# return BedTool(map(collapse_ali, alis)).sort()
-#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 "\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_and_sort(alis):
- """
- Collapse elements from *alis* to their 5 prime end.
-
- The resulting :class:`pybedtools.BedTool` is sorted.
-
- :param alis: An iterable of :class:`pysam.AlignedSegment`
- :rtype: :class:`pybedtools.BedTool`
-
- :class:`pybedtools.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(
- "\n".join(map(collapse_ali, 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(
- description=__doc__,
- formatter_class=argparse.ArgumentDefaultsHelpFormatter)
- parser.add_argument(
- "-b", "--bamfile",
- required=True,
- help="Sorted and indexed bam file containing the aligned reads.")
- parser.add_argument(
- "-o", "--out_bed",
- required=True,
- help="Bed file in which the results should be written.")
- args = parser.parse_args()
- with AlignmentFile(args.bamfile, "rb") as bamfile:
- collapse_and_sort(bamfile.fetch()).saveas(args.out_bed)
- return 0
-
-
-if __name__ == "__main__":
- exit(main())
diff --git a/bam25prime/Python/bam25prime/libcollapsebed.pyx b/bam25prime/Python/bam25prime/libcollapsebed.pyx
deleted file mode 100644
index ba2aa8d42db4f6880ffa2c03a020961d90790fcf..0000000000000000000000000000000000000000
--- a/bam25prime/Python/bam25prime/libcollapsebed.pyx
+++ /dev/null
@@ -1,42 +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
-: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
deleted file mode 100755
index 4d7879a480f5875860cf3bb0e6ebe916c0ce24cc..0000000000000000000000000000000000000000
--- a/bam25prime/Python/bam25prime/libcollapsesam.pyx
+++ /dev/null
@@ -1,60 +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
-#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/bin/bam25prime b/bam25prime/Python/bin/bam25prime
deleted file mode 120000
index 2929fb4ac91a82dd63ebbb0b9474ed1b10bc11f0..0000000000000000000000000000000000000000
--- a/bam25prime/Python/bin/bam25prime
+++ /dev/null
@@ -1 +0,0 @@
-../bam25prime/bam25prime.py
\ No newline at end of file
diff --git a/bam25prime/Python/install.sh b/bam25prime/Python/install.sh
deleted file mode 100755
index 5ddc41a80e7fe6839786c8be3efa902015bc1b2a..0000000000000000000000000000000000000000
--- a/bam25prime/Python/install.sh
+++ /dev/null
@@ -1,5 +0,0 @@
-#!/bin/sh
-python3.6 setup.py build_ext
-# .egg-link does not work with PYTHONPATH ?
-python3.6 -m pip install -e .
-python3.6 -m pip install --no-deps --ignore-installed .
diff --git a/bam25prime/Python/setup.py b/bam25prime/Python/setup.py
deleted file mode 100644
index fb09e7f1c1227cf1cbb2b6e9a4cb5f7b33cdc170..0000000000000000000000000000000000000000
--- a/bam25prime/Python/setup.py
+++ /dev/null
@@ -1,40 +0,0 @@
-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
-from pybedtools.helpers import get_includes as pybedtools_get_includes
-from pysam import get_include as pysam_get_include
-
-name = "bam25prime"
-__version__ = "0.1"
-
-# https://github.com/cython/cython/blob/master/docs/src/reference/compilation.rst#configuring-the-c-build
-extensions = [
- Extension(
- "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/*"),
- #include_dirs=pybedtools_get_includes(),
- language="c++"),
- ]
-
-setup(
- name=name,
- version=__version__,
- description="Library providing utilities to collapse aligned segments"
- "in a bam file to their 5-prime end.",
- author="Blaise Li",
- author_email="blaise.li@normalesup.org",
- license="MIT",
- packages=find_packages(),
- scripts=["bin/%s" % name],
- ext_modules = cythonize(extensions),
- #ext_modules = cythonize("bam25prime/libbam25prime.pyx", include_path=pysam_get_include()),
- install_requires=["pysam", "pybedtools"])
-# If you have .pyx things to cythonize
- #ext_modules = cythonize("libsmallrna/libsmallrna.pyx"),
- #install_requires=["cytoolz"],
- #zip_safe=False)