#!/usr/bin/python ''' pysam ***** ''' import os, sys, glob, shutil, hashlib, re, fnmatch import platform name = "pysam" IS_PYTHON3 = sys.version_info[0] >= 3 # collect pysam version sys.path.insert( 0, "pysam") import version version = version.__version__ samtools_exclude = ( "bamtk.c", "razip.c", "bgzip.c", "main.c", "calDepth.c", "bam2bed.c", "wgsim.c", "md5fa.c", "maq2sam.c", "bamcheck.c", "chk_indel.c" ) samtools_dest = os.path.abspath( "samtools" ) tabix_exclude = ( "main.c", ) tabix_dest = os.path.abspath( "tabix" ) def locate(pattern, root=os.curdir): '''Locate all files matching supplied filename pattern in and below supplied root directory.''' for path, dirs, files in os.walk(os.path.abspath(root)): for filename in fnmatch.filter(files, pattern): yield os.path.join(path, filename) def _update_pysam_files(cf, destdir): '''update pysam files applying redirection of ouput''' for filename in cf: if not filename: continue dest = filename + ".pysam.c" with open( filename ) as infile: with open( dest, "w" ) as outfile: outfile.write( '#include "pysam.h"\n\n' ) outfile.write( re.sub( "stderr", "pysamerr", "".join(infile.readlines()) ) ) with open( os.path.join( destdir, "pysam.h" ), "w" )as outfile: outfile.write ("""#ifndef PYSAM_H #define PYSAM_H #include "stdio.h" extern FILE * pysamerr; #endif """) # copy samtools source if len(sys.argv) >= 2 and sys.argv[1] == "import": if len(sys.argv) < 3: raise ValueError("missing PATH to samtools source directory") if len(sys.argv) < 4: raise ValueError("missing PATH to tabix source directory") for destdir, srcdir, exclude in zip( (samtools_dest, tabix_dest), sys.argv[2:4], (samtools_exclude, tabix_exclude)): srcdir = os.path.abspath( srcdir ) if not os.path.exists( srcdir ): raise IOError( "samtools src dir `%s` does not exist." % srcdir ) cfiles = locate( "*.c", srcdir ) hfiles = locate( "*.h", srcdir ) ncopied = 0 def _compareAndCopy( src, srcdir, destdir, exclude ): d, f = os.path.split(src) if f in exclude: return None common_prefix = os.path.commonprefix( (d, srcdir ) ) subdir = re.sub( common_prefix, "", d )[1:] targetdir = os.path.join( destdir, subdir ) if not os.path.exists( targetdir ): os.makedirs( targetdir ) old_file = os.path.join( targetdir, f ) if os.path.exists( old_file ): md5_old = hashlib.md5("".join(open(old_file,"r").readlines())).digest() md5_new = hashlib.md5("".join(open(src,"r").readlines())).digest() if md5_old != md5_new: raise ValueError( "incompatible files for %s and %s" % (old_file, src )) shutil.copy( src, targetdir ) return old_file for src_file in hfiles: _compareAndCopy( src_file, srcdir,destdir, exclude ) ncopied += 1 cf = [] for src_file in cfiles: cf.append( _compareAndCopy( src_file, srcdir, destdir, exclude ) ) ncopied += 1 sys.stdout.write("installed latest source code from %s: %i files copied" % (srcdir, ncopied)) # redirect stderr to pysamerr and replace bam.h with a stub. sys.stdout.write("applying stderr redirection") _update_pysam_files(cf, destdir) sys.exit(0) if len(sys.argv) >= 2 and sys.argv[1] == "refresh": sys.stdout.write("refreshing latest source code from .c to .pysam.c") # redirect stderr to pysamerr and replace bam.h with a stub. sys.stdout.write("applying stderr redirection") for destdir in ('samtools', 'tabix'): pysamcfiles = locate( "*.pysam.c", destdir ) for f in pysamcfiles: os.remove(f) cfiles = locate( "*.c", destdir ) _update_pysam_files(cfiles, destdir) sys.exit(0) ################### # populate headers # mkdir pysam/include pysam/include/win32 # touch pysam/include/__init__.py pysam/include/win32/__init__.py # cp samtools/*.h pysam/*.h pysam/include # cp samtools/win32/*.h pysam/include/win32 try: from setuptools import Extension, setup, find_packages except ImportError: #from ez_setup import use_setuptools #use_setuptools() from setuptools import Extension, setup, find_packages ####################################################### ####################################################### try: from Cython.Distutils import build_ext except ImportError: # no Cython available - use existing C code cmdclass = { } csamtools_sources = [ "pysam/csamtools.c" ] tabix_sources = [ "pysam/ctabix.c" ] tabproxies_sources = ["pysam/TabProxies.c" ] cvcf_sources = ["pysam/cvcf.c" ] else: # remove existing files to recompute # necessary to be both compatible for python 2.7 and 3.3 if IS_PYTHON3: for f in ( "pysam/csamtools.c", "pysam/ctabix.c", "pysam/TabProxies.c", "pysam/cvcf.c" ): try: os.unlink( f ) except: pass cmdclass = { 'build_ext' : build_ext } csamtools_sources = [ "pysam/csamtools.pyx" ] tabix_sources = [ "pysam/ctabix.pyx" ] tabproxies_sources = ["pysam/TabProxies.pyx" ] cvcf_sources = ["pysam/cvcf.pyx" ] ####################################################### classifiers = """ Development Status :: 2 - Alpha Operating System :: MacOS :: MacOS X Operating System :: Microsoft :: Windows :: Windows NT/2000 Operating System :: OS Independent Operating System :: POSIX Operating System :: POSIX :: Linux Operating System :: Unix Programming Language :: Python Topic :: Scientific/Engineering Topic :: Scientific/Engineering :: Bioinformatics """ ####################################################### ## Windows compatibility if platform.system()=='Windows': include_os = ['win32'] os_c_files = ['win32/getopt.c'] else: include_os = [] os_c_files = [] ####################################################### samtools = Extension( "pysam.csamtools", csamtools_sources +\ [ "pysam/%s" % x for x in ( "pysam_util.c", )] +\ glob.glob( os.path.join( "samtools", "*.pysam.c" )) +\ os_c_files + \ glob.glob( os.path.join( "samtools", "*", "*.pysam.c" ) ), library_dirs=[], include_dirs=[ "samtools", "pysam" ] + include_os, libraries=[ "z", ], language="c", define_macros = [('_FILE_OFFSET_BITS','64'), ('_USE_KNETFILE','')], ) tabix = Extension( "pysam.ctabix", tabix_sources +\ [ "pysam/%s" % x for x in ( "tabix_util.c", )] +\ os_c_files + \ glob.glob( os.path.join( "tabix", "*.pysam.c" ) ), library_dirs=[], include_dirs=[ "tabix", "pysam" ] + include_os, libraries=[ "z", ], language="c", define_macros = [('_FILE_OFFSET_BITS','64'), ('_USE_KNETFILE','')], ) tabproxies = Extension( "pysam.TabProxies", tabproxies_sources + os_c_files, library_dirs=[], include_dirs= include_os, libraries=[ "z", ], language="c", ) cvcf = Extension( "pysam.cvcf", cvcf_sources + os_c_files, library_dirs=[], include_dirs= ["tabix",] + include_os, libraries=[ "z", ], language="c", ) metadata = { 'name': name, 'version': version, 'description': "pysam", 'long_description': __doc__, 'author': "Andreas Heger", 'author_email': "andreas.heger@gmail.com", 'license': "MIT", 'platforms': "ALL", 'url': "http://code.google.com/p/pysam/", 'packages' : ['pysam', 'pysam.include', 'pysam.include.samtools', 'pysam.include.samtools.bcftools', 'pysam.include.samtools.win32', 'pysam.include.tabix'], 'requires' : ['cython (>=0.17)'], 'ext_modules': [samtools, tabix, tabproxies, cvcf ], 'cmdclass' : cmdclass, 'install_requires' : ['cython>=0.17',], 'package_dir' : { 'pysam' : 'pysam', 'pysam.include.samtools' : 'samtools', 'pysam.include.tabix' : 'tabix' }, 'package_data' : { '' : ['*.pxd', '*.h'], }, # do not pack in order to permit linking to csamtools.so 'zip_safe' :False, 'use_2to3': True, } if __name__=='__main__': dist = setup(**metadata)