[med-svn] [python-pysam] 01/06: Imported Upstream version 0.9.1.4+ds
Afif Elghraoui
afif at moszumanska.debian.org
Sun Jul 24 01:51:05 UTC 2016
This is an automated email from the git hooks/post-receive script.
afif pushed a commit to branch master
in repository python-pysam.
commit 6528922f1d45d0364eefc4c80ad2fce35f885570
Author: Afif Elghraoui <afif at debian.org>
Date: Sat Jul 23 15:39:14 2016 -0700
Imported Upstream version 0.9.1.4+ds
---
INSTALL | 12 +---
MANIFEST.in | 4 ++
README.rst | 12 +++-
cy_build.py | 7 +-
pysam/calignmentfile.pyx | 13 ++--
pysam/version.py | 2 +-
run_tests_travis.sh | 46 ++++++++++--
setup.py | 169 +++++++++++++++++++++++++-------------------
tests/AlignmentFile_test.py | 71 ++++++++++++++++++-
9 files changed, 241 insertions(+), 95 deletions(-)
diff --git a/INSTALL b/INSTALL
index 5ddff7f..a1edd45 100644
--- a/INSTALL
+++ b/INSTALL
@@ -18,6 +18,8 @@ curl
Pysam requires Python (2.7 or greater) and Cython (0.22 or greater).
It has not been tested on many other platforms.
+Windows support does not work yet.
+
Compilation
===========
@@ -53,13 +55,3 @@ or
python3 setup.py build_sphinx
The documentation will be put into build/sphinx.
-
-Architecture specific options
-=============================
-
-Pysam has been compiled on various Linux systems and works
-with python 2.6 and python 2.5.
-
-Python 2.7 and Python 3 have not been tested.
-
-Windows support does not work yet.
diff --git a/MANIFEST.in b/MANIFEST.in
index 7b1cbda..be43691 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -19,9 +19,13 @@ include samtools/configure
include samtools/config.mk.in
include samtools/config.h.in
include samtools/*.h
+exclude samtools/config.h
include samtools/*/*.h
include htslib/*.c
include htslib/*.h
+exclude htslib/config.h
+include htslib/Makefile
+include htslib/htslib_vars.mk
include htslib/configure
include htslib/config.mk.in
include htslib/config.h.in
diff --git a/README.rst b/README.rst
index ab9e612..5e37be5 100644
--- a/README.rst
+++ b/README.rst
@@ -14,9 +14,19 @@ includes an interface for tabix_.
The latest version is available through `pypi
<https://pypi.python.org/pypi/pysam>`_. To install, simply type::
-
+
pip install pysam
+If you are using the conda packaging manager (e.g. miniconda or anaconda),
+you can install pysam from the `bioconda channel <https://bioconda.github.io/>`_:
+
+ conda config --add channels r
+
+ conda config --add channels bioconda
+
+ conda install pysam
+
+
Pysam documentation is available through https://readthedocs.org/ from
`here <http://pysam.readthedocs.org/en/latest/>`_
diff --git a/cy_build.py b/cy_build.py
index e052ddb..880b5cc 100644
--- a/cy_build.py
+++ b/cy_build.py
@@ -2,7 +2,11 @@ import os
import re
import sys
-from Cython.Distutils import build_ext
+try:
+ from Cython.Distutils import build_ext
+except ImportError:
+ from setuptools.command.build_ext import build_ext
+
from distutils.extension import Extension
from distutils.sysconfig import get_config_vars, get_python_lib, get_python_version
from pkg_resources import Distribution
@@ -49,6 +53,7 @@ class cy_build_ext(build_ext):
self.distribution.has_ext_modules() and self.plat_name).egg_name()
def build_extension(self, ext):
+
if isinstance(ext, CyExtension) and ext._init_func:
ext._init_func(ext)
diff --git a/pysam/calignmentfile.pyx b/pysam/calignmentfile.pyx
index 6473220..ed5e584 100644
--- a/pysam/calignmentfile.pyx
+++ b/pysam/calignmentfile.pyx
@@ -106,16 +106,17 @@ KNOWN_HEADER_FIELDS = {"HD" : {"VN" : str, "SO" : str, "GO" : str},
"PG" : {"ID" : str, "PN" : str, "CL" : str,
"PP" : str, "DS" : str, "VN" : str,},}
-# output order of fields within records
+# output order of fields within records. Ensure that CL is at
+# the end as parsing a CL will ignore any subsequent records.
VALID_HEADER_ORDER = {"HD" : ("VN", "SO", "GO"),
"SQ" : ("SN", "LN", "AS", "M5",
"UR", "SP"),
- "RG" : ("ID", "SM", "LB", "DS",
- "PU", "PI", "CN", "DT",
+ "RG" : ("ID", "CN", "SM", "LB",
+ "PU", "PI", "DT", "DS",
"PL", "FO", "KS", "PG",
"PM"),
- "PG" : ("PN", "ID", "VN", "CL",
- "PP"),}
+ "PG" : ("PN", "ID", "VN", "PP",
+ "DS", "CL"),}
def build_header_line(fields, record):
@@ -589,7 +590,7 @@ cdef class AlignmentFile:
raise ValueError(
("file has no sequences defined (mode='%s') - "
"is it SAM/BAM format? Consider opening with "
- "check_seq=True") % mode)
+ "check_sq=False") % mode)
if self.htsfile == NULL:
raise IOError("could not open file `%s`" % filename )
diff --git a/pysam/version.py b/pysam/version.py
index 15cefc4..0a985de 100644
--- a/pysam/version.py
+++ b/pysam/version.py
@@ -1,6 +1,6 @@
# pysam versioning information
-__version__ = "0.9.1"
+__version__ = "0.9.1.4"
__samtools_version__ = "1.3.1"
diff --git a/run_tests_travis.sh b/run_tests_travis.sh
index f1fcdce..414043e 100755
--- a/run_tests_travis.sh
+++ b/run_tests_travis.sh
@@ -105,9 +105,47 @@ if [ $? != 0 ]; then
exit 1
fi
-# build source tar-ball and test installation from tar-ball
+# build source tar-ball
cd ..
python setup.py sdist
-tar -xvzf dist/pysam-*.tar.gz
-cd pysam-*
-python setup.py install
+
+if [ $? != 0 ]; then
+ exit 1
+fi
+
+# check for presence of config.h files
+echo "checking for presence of config.h files in tar-ball"
+tar -tvzf dist/pysam-*.tar.gz | grep "config.h$"
+
+if [ $? != 1 ]; then
+ exit 1
+fi
+
+# test pip installation from tar-ball with cython
+echo "pip installing with cython"
+pip install --verbose --no-deps --no-use-wheel dist/pysam-*.tar.gz
+
+if [ $? != 0 ]; then
+ exit 1
+fi
+
+# attempt pip installation without cython
+echo "pip installing without cython"
+~/miniconda3/bin/conda remove cython
+~/miniconda3/bin/conda list
+echo "pthyon is" `which python`
+pip install --verbose --no-deps --no-use-wheel --force-reinstall --upgrade dist/pysam-*.tar.gz
+
+if [ $? != 0 ]; then
+ exit 1
+fi
+
+# attempt pip installation without cython and without
+# command line options
+echo "pip installing without cython and no configure options"
+export HTSLIB_CONFIGURE_OPTIONS=""
+pip install --verbose --no-deps --no-use-wheel --force-reinstall --upgrade dist/pysam-*.tar.gz
+
+if [ $? != 0 ]; then
+ exit 1
+fi
diff --git a/setup.py b/setup.py
index 080bc24..e301f11 100644
--- a/setup.py
+++ b/setup.py
@@ -29,6 +29,7 @@ import platform
import re
import subprocess
import sys
+import sysconfig
from contextlib import contextmanager
from setuptools import Extension, setup
@@ -45,6 +46,29 @@ def changedir(path):
os.chdir(save_dir)
+def run_configure(option):
+ try:
+ retcode = subprocess.call(
+ " ".join(("./configure", option)),
+ shell=True)
+ if retcode != 0:
+ return False
+ else:
+ return True
+ except OSError as e:
+ return False
+
+
+def run_make_print_config():
+ stdout = subprocess.check_output(["make", "print-config"])
+ if IS_PYTHON3:
+ stdout = stdout.decode("ascii")
+
+ result = dict([[x.strip() for x in line.split("=")]
+ for line in stdout.splitlines()])
+ return result
+
+
def configure_library(library_dir, env_options=None, options=[]):
configure_script = os.path.join(library_dir, "configure")
@@ -53,18 +77,6 @@ def configure_library(library_dir, env_options=None, options=[]):
raise ValueError(
"configure script {} does not exist".format(configure_script))
- def run_configure(option):
- try:
- retcode = subprocess.call(
- " ".join(("./configure", option)),
- shell=True)
- if retcode != 0:
- return False
- else:
- return True
- except OSError as e:
- return False
-
with changedir(library_dir):
if env_options is not None:
if run_configure(env_options):
@@ -73,9 +85,20 @@ def configure_library(library_dir, env_options=None, options=[]):
for option in options:
if run_configure(option):
return option
+
return None
+def distutils_dir_name(dname):
+ """Returns the name of a distutils build directory
+ see: http://stackoverflow.com/questions/14320220/
+ testing-python-c-libraries-get-build-path
+ """
+ f = "{dirname}.{platform}-{version[0]}.{version[1]}"
+ return f.format(dirname=dname,
+ platform=sysconfig.get_platform(),
+ version=sys.version_info)
+
# How to link against HTSLIB
# separate: use included htslib and include in each extension
# module. No dependencies between modules and works
@@ -87,10 +110,25 @@ def configure_library(library_dir, env_options=None, options=[]):
# pysam.
# external: use shared libhts.so compiled outside of
# pysam
-HTSLIB_MODE = "shared"
+HTSLIB_MODE = os.environ.get("HTSLIB_MODE", "shared")
HTSLIB_LIBRARY_DIR = os.environ.get("HTSLIB_LIBRARY_DIR", None)
HTSLIB_INCLUDE_DIR = os.environ.get("HTSLIB_INCLUDE_DIR", None)
HTSLIB_CONFIGURE_OPTIONS = os.environ.get("HTSLIB_CONFIGURE_OPTIONS", None)
+HTSLIB_SOURCE = None
+
+package_list = ['pysam',
+ 'pysam.include',
+ 'pysam.include.samtools',
+ 'pysam.include.bcftools',
+ 'pysam.include.samtools.win32']
+package_dirs = {'pysam': 'pysam',
+ 'pysam.include.samtools': 'samtools',
+ 'pysam.include.bcftools': 'bcftools'}
+config_headers = ["samtools/config.h"]
+
+from cy_build import CyExtension as Extension, cy_build_ext as build_ext
+
+cmdclass = {'build_ext': build_ext}
# Check if cython is available
#
@@ -98,16 +136,19 @@ HTSLIB_CONFIGURE_OPTIONS = os.environ.get("HTSLIB_CONFIGURE_OPTIONS", None)
# the .pyx files. If no cython is available, the C-files included in the
# distribution will be used.
try:
- from cy_build import CyExtension as Extension, cy_build_ext as build_ext
+ import cython
+ HAVE_CYTHON = True
+ print ("# pysam: cython is available - using cythonize if necessary")
source_pattern = "pysam/c%s.pyx"
- cmdclass = {'build_ext': build_ext}
- HTSLIB_MODE = "shared"
+ if HTSLIB_MODE != "external":
+ HTSLIB_MODE = "shared"
except ImportError:
+ HAVE_CYTHON = False
+ print ("# pysam: no cython available - using pre-compiled C")
# no Cython available - use existing C code
- cmdclass = {}
source_pattern = "pysam/c%s.c"
- # Set mode to separate, as "shared" not fully tested yet.
- HTSLIB_MODE = "separate"
+ if HTSLIB_MODE != "external":
+ HTSLIB_MODE = "shared"
# collect pysam version
sys.path.insert(0, "pysam")
@@ -136,19 +177,26 @@ EXCLUDE = {
}
print ("# pysam: htslib mode is {}".format(HTSLIB_MODE))
-
+print ("# pysam: HTSLIB_CONFIGURE_OPTIONS={}".format(
+ HTSLIB_CONFIGURE_OPTIONS))
htslib_configure_options = None
if HTSLIB_MODE in ['shared', 'separate']:
+ package_list += ['pysam.include.htslib',
+ 'pysam.include.htslib.htslib']
+ package_dirs.update({'pysam.include.htslib':'htslib'})
+
htslib_configure_options = configure_library(
"htslib",
HTSLIB_CONFIGURE_OPTIONS,
- ["--enable-libcurl"])
+ ["--enable-libcurl",
+ "--disable-libcurl"])
HTSLIB_SOURCE = "builtin"
print ("# pysam: htslib configure options: {}".format(
str(htslib_configure_options)))
+ config_headers += ["htslib/config.h"]
if htslib_configure_options is None:
# create empty config.h file
with open("htslib/config.h", "w") as outf:
@@ -157,6 +205,23 @@ if HTSLIB_MODE in ['shared', 'separate']:
outf.write(
"/* conservative compilation options */\n")
+ with changedir("htslib"):
+ htslib_make_options = run_make_print_config()
+
+ for key, value in htslib_make_options.items():
+ print ("# pysam: htslib_config {}={}".format(key, value))
+
+ external_htslib_libraries = ['z']
+ if "LIBS" in htslib_make_options:
+ external_htslib_libraries.extend(
+ [re.sub("^-l", "", x) for x in htslib_make_options["LIBS"].split(" ") if x.strip()])
+
+ shared_htslib_sources = [re.sub("\.o", ".c", os.path.join("htslib", x))
+ for x in
+ htslib_make_options["LIBHTS_OBJS"].split(" ")]
+
+ htslib_sources = []
+
if HTSLIB_LIBRARY_DIR:
# linking against a shared, externally installed htslib version, no
# sources required for htslib
@@ -171,34 +236,26 @@ if HTSLIB_LIBRARY_DIR:
elif HTSLIB_MODE == 'separate':
# add to each pysam component a separately compiled
# htslib
- htslib_sources = [
- x for x in
- glob.glob(os.path.join("htslib", "*.c")) +
- glob.glob(os.path.join("htslib", "cram", "*.c"))
- if x not in EXCLUDE["htslib"]]
+ htslib_sources = shared_htslib_sources
shared_htslib_sources = htslib_sources
htslib_library_dirs = []
htslib_include_dirs = ['htslib']
internal_htslib_libraries = []
- external_htslib_libraries = ['z']
elif HTSLIB_MODE == 'shared':
-
# link each pysam component against the same
# htslib built from sources included in the pysam
# package.
- htslib_sources = []
- shared_htslib_sources = [
- x for x in
- glob.glob(os.path.join("htslib", "*.c")) +
- glob.glob(os.path.join("htslib", "cram", "*.c"))
- if x not in EXCLUDE["htslib"]]
- htslib_library_dirs = ['pysam', "."]
+ htslib_library_dirs = [
+ 'pysam',
+ ".",
+ os.path.join("build",
+ distutils_dir_name("lib"),
+ "pysam")]
+
htslib_include_dirs = ['htslib']
- external_htslib_libraries = ['z']
if IS_PYTHON3:
- import sysconfig
if sys.version_info.minor >= 5:
internal_htslib_libraries = ["chtslib.{}".format(
sysconfig.get_config_var('SOABI'))]
@@ -216,7 +273,6 @@ elif HTSLIB_MODE == 'shared':
else:
raise ValueError("unknown HTSLIB value '%s'" % HTSLIB_MODE)
-
# build config.py
with open(os.path.join("pysam", "config.py"), "w") as outf:
outf.write('HTSLIB = "{}"\n'.format(HTSLIB_SOURCE))
@@ -237,31 +293,11 @@ with open(os.path.join("pysam", "config.py"), "w") as outf:
"HAVE_LIBCURL",
"HAVE_MMAP"]:
outf.write("{} = {}\n".format(key, config_values[key]))
-
-
-if HTSLIB_SOURCE == "builtin":
- EXCLUDE_HTSLIB = ["htslib/hfile_libcurl.c"]
- if htslib_configure_options is None:
- print ("# pysam: could not configure htslib, choosing "
- "conservative defaults")
- htslib_sources = [x for x in htslib_sources
- if x not in EXCLUDE_HTSLIB]
- shared_htslib_sources = [x for x in shared_htslib_sources
- if x not in EXCLUDE_HTSLIB]
- elif "--disable-libcurl" in htslib_configure_options:
- print ("# pysam: libcurl has been disabled")
- htslib_sources = [x for x in htslib_sources
- if x not in EXCLUDE_HTSLIB]
- shared_htslib_sources = [x for x in shared_htslib_sources
- if x not in EXCLUDE_HTSLIB]
- elif "--enable-libcurl" in htslib_configure_options:
- print ("# pysam: libcurl of builtin htslib has been enabled, "
- "adding shared libcurl and libcrypto")
- external_htslib_libraries.extend(["curl", "crypto"])
+ print ("# pysam: config_option: {}={}".format(key, config_values[key]))
# create empty config.h files if they have not been created automatically
# or created by the user:
-for fn in "samtools/config.h", "htslib/config.h":
+for fn in config_headers:
if not os.path.exists(fn):
with open(fn, "w") as outf:
outf.write(
@@ -493,13 +529,7 @@ metadata = {
'license': "MIT",
'platforms': "ALL",
'url': "https://github.com/pysam-developers/pysam",
- 'packages': ['pysam',
- 'pysam.include',
- 'pysam.include.htslib',
- 'pysam.include.htslib.htslib',
- 'pysam.include.samtools',
- 'pysam.include.bcftools',
- 'pysam.include.samtools.win32'],
+ 'packages': package_list,
'requires': ['cython (>=0.21)'],
'ext_modules': [chtslib,
csamfile,
@@ -512,10 +542,7 @@ metadata = {
cfaidx,
cutils],
'cmdclass': cmdclass,
- 'package_dir': {'pysam': 'pysam',
- 'pysam.include.htslib': 'htslib',
- 'pysam.include.samtools': 'samtools',
- 'pysam.include.bcftools': 'bcftools'},
+ 'package_dir': package_dirs,
'package_data': {'': ['*.pxd', '*.h'], },
# do not pack in order to permit linking to csamtools.so
'zip_safe': False,
diff --git a/tests/AlignmentFile_test.py b/tests/AlignmentFile_test.py
index 9a33722..c042f4f 100644
--- a/tests/AlignmentFile_test.py
+++ b/tests/AlignmentFile_test.py
@@ -9,6 +9,8 @@ import unittest
import os
import shutil
import sys
+import re
+import copy
import collections
import subprocess
import logging
@@ -23,7 +25,8 @@ from functools import partial
import pysam
import pysam.samtools
from TestUtils import checkBinaryEqual, checkURL, \
- check_samtools_view_equal, checkFieldEqual, force_str
+ check_samtools_view_equal, checkFieldEqual, force_str, \
+ get_temp_filename
DATADIR = "pysam_data"
@@ -1395,6 +1398,72 @@ class TestHeader1000Genomes(unittest.TestCase):
self.assertTrue(data)
+class TestHeaderWriteRead(unittest.TestCase):
+ header = {'SQ': [{'LN': 1575, 'SN': 'chr1'},
+ {'LN': 1584, 'SN': 'chr2'}],
+ 'RG': [{'LB': 'SC_1', 'ID': 'L1', 'SM': 'NA12891',
+ 'PU': 'SC_1_10', "CN": "name:with:colon"},
+ {'LB': 'SC_2', 'ID': 'L2', 'SM': 'NA12891',
+ 'PU': 'SC_2_12', "CN": "name:with:colon"}],
+ 'PG': [{'ID': 'P1', 'VN': '1.0', 'CL': 'tool'},
+ {'ID': 'P2', 'VN': '1.1', 'CL': 'tool with in option -R a\tb',
+ 'PP': 'P1'}],
+ 'HD': {'VN': '1.0'},
+ 'CO': ['this is a comment', 'this is another comment'],
+ }
+
+ def compare_headers(self, a, b):
+ '''compare two headers a and b.
+
+ Ignore M5 and UR field as they are set application specific.
+ '''
+ for ak, av in a.items():
+ self.assertTrue(ak in b, "key '%s' not in '%s' " % (ak, b))
+ self.assertEqual(
+ len(av), len(b[ak]),
+ "unequal number of entries for key {}: {} vs {}"
+ .format(ak, av, b[ak]))
+
+ for row_a, row_b in zip(av, b[ak]):
+ if isinstance(row_b, dict):
+ for x in ["M5", "UR"]:
+ try:
+ del row_b[x]
+ except KeyError:
+ pass
+ self.assertEqual(row_a, row_b)
+
+ def check_read_write(self, flag_write, header):
+
+ fn = get_temp_filename()
+ with pysam.AlignmentFile(
+ fn,
+ flag_write,
+ header=header,
+ reference_filename="pysam_data/ex1.fa") as outf:
+ a = pysam.AlignedSegment()
+ a.query_name = "abc"
+ outf.write(a)
+
+ with pysam.AlignmentFile(fn) as inf:
+ read_header = inf.header
+
+ os.unlink(fn)
+ self.compare_headers(header, read_header)
+
+ def test_SAM(self):
+ self.check_read_write("wh", self.header)
+
+ def test_BAM(self):
+ self.check_read_write("wb", self.header)
+
+ def test_CRAM(self):
+ header = copy.copy(self.header)
+ # for CRAM, \t needs to be quoted:
+ header['PG'][1]['CL'] = re.sub(r"\t", r"\\\\t", header['PG'][1]['CL'])
+ self.check_read_write("wc", header)
+
+
class TestUnmappedReads(unittest.TestCase):
# TODO
--
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