'''
-import os, sys, glob, shutil
+import os, sys, glob, shutil, hashlib, re, fnmatch
+import platform
name = "pysam"
-version = "0.2"
-samtools_exclude = ( "bamtk.c", "razip.c", "bgzip.c" )
+# 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",)
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")
- samtools_src = os.path.abspath( sys.argv[2] )
- if not os.path.exists( samtools_src ): raise IOError( "samtools src dir `%s` does not exist." % samtools_src )
-
- cfiles = glob.glob( os.path.join( samtools_src, "*.c" ) )
- hfiles = glob.glob( os.path.join( samtools_src, "*.h" ) )
- ncopied = 0
- for p in cfiles + hfiles:
- f = os.path.basename(p)
- if f in samtools_exclude: continue
- if os.path.exists( os.path.join( samtools_dest, f )): continue
- shutil.copy( p, samtools_dest )
- ncopied += 1
- print "installed latest source code from %s: %i files copied" % (samtools_src, ncopied)
+ 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)
-from distutils.core import setup, Extension
-from Pyrex.Distutils import build_ext
+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)
+
+
+
+from distribute_setup import use_setuptools
+use_setuptools()
+
+from setuptools import Extension, setup
+from Cython.Distutils import build_ext
classifiers = """
Development Status :: 2 - Alpha
Topic :: Scientific/Engineering :: Bioinformatics
"""
-pysam = Extension(
- "pysam/csamtools", # name of extension
+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", ],
+ include_dirs=[ "samtools", "pysam" ] + include_os,
+ libraries=[ "z", ],
+ language="c",
+ define_macros = [('_FILE_OFFSET_BITS','64'),
+ ('_USE_KNETFILE','')],
+ )
+
+tabix = Extension(
+ "ctabix", # name of extension
+ [ "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",
+ define_macros = [('_FILE_OFFSET_BITS','64'),
+ ('_USE_KNETFILE','')],
+ )
+
+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",] + include_os,
libraries=[ "z", ],
language="c",
)
'platforms': "ALL",
'url': "http://code.google.com/p/pysam/",
'py_modules': [
- "pysam/__init__", "pysam/Pileup", "pysam/namedtuple" ],
- 'ext_modules': [pysam,],
- 'cmdclass' : {'build_ext': build_ext} }
+ "pysam/__init__",
+ "pysam/Pileup",
+ "pysam/version" ],
+ # cython larger that 0.16 for yield support
+ 'requires' : ['cython (>=0.16)'],
+ '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,
+ 'use_2to3': True,
+ }
+
+if sys.version_info[0] < 3:
+ metadata['py_modules'].append("pysam/namedtuple")
if __name__=='__main__':
dist = setup(**metadata)
projects / pysam.git / blobdiff