Commit f4801501 authored by Steffen Möller's avatar Steffen Möller
Browse files

New upstream version 0.8.5

parent d00e2e62

lib/bx/bbi/bigwig_file.pyx

+41 −2
Original line number Diff line number Diff line
@@ -123,6 +123,36 @@ cdef class ArrayAccumulatingBlockHandler( BigWigBlockHandler ): 
        for i from s - self.start <= i < e - self.start:

            array[ i ] = val



cdef class BigWigHeaderBlockHandler( BigWigBlockHandler ):

    "Reads and returns headers"

    cdef list headers



    def __init__( self, bits32 start, bits32 end ):

        BigWigBlockHandler.__init__( self, start, end )

        self.headers = []



    cdef handle_block( self, bytes block_data, BBIFile bbi_file ):

        cdef bits32 b_chrom_id, b_start, b_end, b_valid_count

        cdef bits32 b_item_step, b_item_span

        cdef bits16 b_item_count

        cdef UBYTE b_type

        cdef int s, e

        cdef float val

        # parse the block header

        block_reader = BinaryFileReader( BytesIO( block_data ), is_little_endian=bbi_file.reader.is_little_endian )

        b_chrom_id = block_reader.read_uint32()

        b_start = block_reader.read_uint32()

        b_end = block_reader.read_uint32()

        b_item_step = block_reader.read_uint32()

        b_item_span = block_reader.read_uint32()

        b_type = block_reader.read_uint8()

        block_reader.skip(1)

        b_item_count = block_reader.read_uint16()

        self.handle_header( b_start, b_end,  b_item_step, b_item_span, b_type, b_item_count )



    cdef handle_header( self, bits32 start, bits32 end, bits32 step, bits32 span, bits8 type, bits16 itemCount ):

        self.headers.append( ( start, end, step, span, type, itemCount ) )



cdef class BigWigFile( BBIFile ):

    """

    A "big binary indexed" file whose raw data is in wiggle format.
@@ -167,6 +197,15 @@ cdef class BigWigFile( BBIFile ): 
        self.visit_blocks_in_region( chrom_id, start, end, v )

        return v.array



    cpdef get_headers( self, char * chrom, bits32 start, bits32 end ):

        if start >= end:

            return None

        chrom_id, chrom_size = self._get_chrom_id_and_size( chrom )

        if chrom_id is None:

            return None

        v = BigWigHeaderBlockHandler( start, end )

        self.visit_blocks_in_region( chrom_id, start, end, v )

        return v.headers

lib/bx/bbi/bpt_file.pyx

+15 −15
Original line number Diff line number Diff line
@@ -71,6 +71,6 @@ cdef class BPTFile: 
            return None

        # Key is less than key_size, right pad with 0 bytes

        if len(key) < self.key_size:

            key += ( '\0' * ( self.key_size - len(key) ) )

            key += b'\0' * (self.key_size - len(key))

        # Call the recursive finder

        return self.r_find(self.root_offset, key)

setup.py

+118 −114
Original line number Diff line number Diff line 
import platform

import sys

from distutils.core import Command

from glob import glob



if sys.version_info < (2, 6):

    sys.exit("ERROR: bx-python requires Python 2.6 or greater")
@@ -12,14 +14,14 @@ except ImportError: 
    from ez_setup import use_setuptools

    use_setuptools()



from setuptools import *

from glob import glob

from setuptools import Extension  # noqa: E402





def main():



    metadata = \

      dict( name = "bx-python",

            version = "0.8.4",

    metadata = dict(

        name="bx-python",

        version="0.8.5",

        setup_requires=['numpy', 'cython'],

        install_requires=['numpy', 'six'],

        py_modules=['psyco_full'],
@@ -40,15 +42,14 @@ def main(): 
            "License :: OSI Approved :: MIT License",

            "Operating System :: POSIX",

            "Programming Language :: Python :: 2",

                "Programming Language :: Python :: 2.6",

            "Programming Language :: Python :: 2.7",

            "Programming Language :: Python :: 3",

                "Programming Language :: Python :: 3.3",

                "Programming Language :: Python :: 3.4",

            "Programming Language :: Python :: 3.5",

            "Programming Language :: Python :: 3.6",

            "Programming Language :: Python :: 3.7",

            "Programming Language :: Python :: 3.8",

            "Topic :: Scientific/Engineering :: Bio-Informatics",

                "Topic :: Software Development :: Libraries :: Python Modules"

            ],

            "Topic :: Software Development :: Libraries :: Python Modules"],

        zip_safe=False,

        dependency_links=[],

        cmdclass=command_classes)
@@ -58,11 +59,11 @@ def main(): 
        import numpy

        # Suppress numpy tests

        numpy.test = None

    except:

    except Exception:

        pass



    if len(sys.argv) >= 2 and ('--help' in sys.argv[1:] or

            sys.argv[1] in ('--help-commands', 'egg_info', '--version', 'clean')):

    if len(sys.argv) >= 2 and \

            ('--help' in sys.argv[1:] or sys.argv[1] in ('--help-commands', 'egg_info', '--version', 'clean')):

        # For these actions, NumPy is not required.

        #

        # They are required to succeed without Numpy for example when
@@ -80,14 +81,12 @@ def main(): 


# ---- Commands -------------------------------------------------------------



from distutils.core import Command



# Use build_ext from Cython if found

command_classes = {}

try:

    import Cython.Distutils

    command_classes['build_ext'] = Cython.Distutils.build_ext

except:

except Exception:

    pass



# Run 2to3 builder if we're on Python 3.x, from
@@ -103,14 +102,20 @@ command_classes['build_py'] = build_py 
try:

    import pkg_resources

    pkg_resources.require("epydoc")

    import epydoc.cli, sys, os, os.path

    import epydoc.cli

    import os

    import os.path



    # Create command class to build API documentation

    class BuildAPIDocs(Command):

        user_options = []



        def initialize_options(self):

            pass



        def finalize_options(self):

            pass



        def run(self):

            # Save working directory and args

            old_argv = sys.argv
@@ -133,7 +138,7 @@ try: 
            os.chdir(old_cwd)

    # Add to extra_commands

    command_classes['build_apidocs'] = BuildAPIDocs

except:

except Exception:

    pass



# ---- Extension Modules ----------------------------------------------------
@@ -143,6 +148,7 @@ except: 
# _Extension = Extension

# Extension = partial(_Extension, extra_compile_args=["-Wno-cpp"])





def get_extension_modules(numpy_include=None):

    extensions = []

    # Bitsets
@@ -168,10 +174,8 @@ def get_extension_modules( numpy_include=None ): 
                                include_dirs=["src/samtools"],

                                libraries=['z']))



    

    # The following extensions won't (currently) compile on windows

    if platform.system() not in ('Microsoft', 'Windows'):

        

        # Interval clustering

        extensions.append(Extension("bx.intervals.cluster",

                                    ["lib/bx/intervals/cluster.pyx",
@@ -202,9 +206,8 @@ def get_extension_modules( numpy_include=None ): 
        extensions.append(Extension("bx.arrays.bed", ["lib/bx/arrays/bed.pyx"]))

        extensions.append(Extension("bx.arrays.wiggle", ["lib/bx/arrays/wiggle.pyx"]))





        # CpG masking

        extensions.append( Extension( "bx.align.sitemask._cpg", \

        extensions.append(Extension("bx.align.sitemask._cpg",

                                    ["lib/bx/align/sitemask/_cpg.pyx",

                                     "lib/bx/align/sitemask/find_cpg.c"]))
@@ -219,5 +222,6 @@ def get_extension_modules( numpy_include=None ): 
                                    include_dirs=["src/bunzip"]))

    return extensions





if __name__ == "__main__":

    main()