'''
-import os, sys, glob, shutil, hashlib
+import os, sys, glob, shutil, hashlib, re, fnmatch
+import platform
name = "pysam"
version = version.__version__
-samtools_exclude = ( "bamtk.c", "razip.c", "bgzip.c", "errmod.c", "bam_reheader.c", "bam2bcf.c" )
+samtools_exclude = ( "bamtk.c", "razip.c", "bgzip.c",
+ "bam_reheader.c",
+ "main.c", "calDepth.c", "bam2bed.c",
+ "wgsim.c", "md5fa.c", "maq2sam.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):
+ 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")
srcdir = os.path.abspath( srcdir )
if not os.path.exists( srcdir ): raise IOError( "samtools src dir `%s` does not exist." % srcdir )
- cfiles = glob.glob( os.path.join( srcdir, "*.c" ) )
- hfiles = glob.glob( os.path.join( srcdir, "*.h" ) )
+ cfiles = locate( "*.c", srcdir )
+ hfiles = locate( "*.h", srcdir )
ncopied = 0
- for new_file in cfiles + hfiles:
- f = os.path.basename(new_file)
- if f in exclude: continue
- old_file = os.path.join( destdir, f )
+
+ 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(new_file,"r").readlines())).digest()
- if md5_old == md5_new: continue
- raise ValueError( "incompatible files for %s and %s" % (old_file, new_file ))
+ 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
- shutil.copy( new_file, destdir )
+ cf = []
+ for src_file in cfiles:
+ cf.append( _compareAndCopy( src_file, srcdir, destdir, exclude ) )
ncopied += 1
+
print "installed latest source code from %s: %i files copied" % (srcdir, ncopied)
+ # redirect stderr to pysamerr and replace bam.h with a stub.
+ print "applying stderr redirection"
+
+ _update_pysam_files(cf, destdir)
+
+
sys.exit(0)
-from distutils.core import setup, Extension
-from Cython.Distutils import build_ext
+if len(sys.argv) >= 2 and sys.argv[1] == "refresh":
+ print "refreshing latest source code from .c to .pysam.c"
+# redirect stderr to pysamerr and replace bam.h with a stub.
+ print "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)
+
+
+
+from ez_setup import use_setuptools
+use_setuptools()
+
+from setuptools import Extension, setup
+
+## note that for automatic cythoning,
+## both pyrex and cython need to be installed.
+## see http://mail.python.org/pipermail/distutils-sig/2007-September/008204.html
+
+try:
+ from Cython.Distutils import build_ext
+except:
+ from setuptools.command.build_ext import build_ext
classifiers = """
Development Status :: 2 - Alpha
Topic :: Scientific/Engineering :: Bioinformatics
"""
+if platform.system()=='Windows':
+ include_os = ['win32']
+ os_c_files = ['win32/getopt.c']
+else:
+ include_os = []
+ os_c_files = []
+
samtools = Extension(
"csamtools", # name of extension
[ "pysam/csamtools.pyx" ] +\
- [ "pysam/%s" % x for x in (
- "pysam_util.c", )] +\
- glob.glob( os.path.join( "samtools", "*.c" ) ),
+ [ "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_dirs=[ "samtools", "pysam" ] + include_os,
libraries=[ "z", ],
language="c",
- define_macros = [('FILE_OFFSET_BITS','64'),
+ define_macros = [('_FILE_OFFSET_BITS','64'),
('_USE_KNETFILE','')],
)
tabix = Extension(
"ctabix", # name of extension
- [ "pysam/ctabix.pyx" ] +\
- [ "pysam/%s" % x for x in ()] +\
- glob.glob( os.path.join( "tabix", "*.c" ) ),
+ [ "pysam/ctabix.pyx", ] +\
+ [ "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",
+ )
+
+tabproxies = Extension(
+ "TabProxies", # name of extension
+ [ "pysam/TabProxies.pyx", ] + os_c_files,
+ library_dirs=[],
+ include_dirs= include_os,
+ libraries=[ "z", ],
+ language="c",
+ )
+
+cvcf = Extension(
+ "cvcf", # name of extension
+ [ "pysam/cvcf.pyx", ] + os_c_files,
library_dirs=[],
- include_dirs=[ "tabix", "pysam" ],
+ include_dirs= ["tabix",] + include_os,
libraries=[ "z", ],
language="c",
)
"pysam/Pileup",
"pysam/namedtuple",
"pysam/version" ],
- 'ext_modules': [samtools, tabix],
+ 'requires' : ['cython (>=0.12)'],
+ 'ext_modules': [samtools, tabix, tabproxies, cvcf ],
'cmdclass' : {'build_ext': build_ext},
+ 'install_requires' : ['cython>=0.12.1',],
+ # do not pack in order to permit linking to csamtools.so
+ 'zip_safe' :False,
}
if __name__=='__main__':
projects / pysam.git / blobdiff