alimanfoo
ImportError: No module named opt
Hi there,
My python verion is 2.7.11. I installed pysamstats from github master directly after installing pysam-0.15.1.
I got the following error. What do you think might be the problem and how should I fix it? Thank you for your time.
import pysam import pysamstats Traceback (most recent call last): File "
", line 1, in File "pysamstats/init.py", line 8, in from .pileup import * File "pysamstats/pileup.py", line 6, in import pysamstats.opt as opt ImportError: No module named 'pysamstats.opt'
Best, Yuan
Hi there, the error suggests that the Cython module did not compile or get installed for some reason. Could you say how you tried to install pysamstats?
On Tue, 13 Nov 2018, 08:35 lybird300 <[email protected] wrote:
Hi there,
My python verion is 2.7.11. I installed pysamstats from github master directly after installing pysam-0.15.1.
I got the following error. What do you think might be the problem and how should I fix it? Thank you for your time.
import pysam import pysamstats
Traceback (most recent call last): File "", line 1, in File "pysamstats/init.py", line 8, in from .pileup import * File "pysamstats/pileup.py", line 6, in import pysamstats.opt as opt
Best, Yuan
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Hi Alistair, thank you for your prompt reply. I followed the third installation option, i.e.,
$ git clone git://github.com/alimanfoo/pysamstats.git $ cd pysamstats $ python setup.py install
Not sure if that matters, but I did the above in a python virtual environment
Thanks! Yuan
I did get some warnings though (attached below)
[1/1] Cythonizing pysamstats/opt.pyx
/lustre1/gaog_pkuhpc/users/liny/rnaseq/pythonEnv/lib/python2.7/site-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /lustre1/gaog_pkuhpc/build/pysamstats/pysamstats/opt.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
running install
running bdist_egg
running egg_info
writing pysamstats.egg-info/PKG-INFO
writing top-level names to pysamstats.egg-info/top_level.txt
writing dependency_links to pysamstats.egg-info/dependency_links.txt
reading manifest file 'pysamstats.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching '*.pxd' under directory 'pysamstats'
writing manifest file 'pysamstats.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
running build_ext
building 'pysamstats.opt' extension
gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/lustre1/gaog_pkuhpc/users/liny/rnaseq/pythonEnv/lib/python2.7/site-packages/pysam -I/lustre1/gaog_pkuhpc/users/liny/rnaseq/pythonEnv/lib/python2.7/site-packages/pysam/include/htslib -I/lustre1/gaog_pkuhpc/users/liny/rnaseq/pythonEnv/lib/python2.7/site-packages/pysam/include/samtools -I/apps/bioinfo/python2.7.11/include/python2.7 -c pysamstats/opt.c -o build/temp.linux-x86_64-2.7/pysamstats/opt.o
In file included from /lustre1/gaog_pkuhpc/users/liny/rnaseq/pythonEnv/lib/python2.7/site-packages/pysam/include/htslib/htslib/hts.h:35:0,
from /lustre1/gaog_pkuhpc/users/liny/rnaseq/pythonEnv/lib/python2.7/site-packages/pysam/include/htslib/htslib/sam.h:31,
from /lustre1/gaog_pkuhpc/users/liny/rnaseq/pythonEnv/lib/python2.7/site-packages/pysam/htslib_util.h:4,
from pysamstats/opt.c:648:
/lustre1/gaog_pkuhpc/users/liny/rnaseq/pythonEnv/lib/python2.7/site-packages/pysam/include/htslib/htslib/hts_log.h:52:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
enum htsLogLevel hts_get_log_level();
^
In file included from /lustre1/gaog_pkuhpc/users/liny/rnaseq/pythonEnv/lib/python2.7/site-packages/pysam/pysam_stream.h:4:0,
from pysamstats/opt.c:658:
/lustre1/gaog_pkuhpc/users/liny/rnaseq/pythonEnv/lib/python2.7/site-packages/pysam/include/htslib/htslib/kseq.h:178:16: warning: ‘kseq_init’ defined but not used [-Wunused-function]
SCOPE kseq_t *kseq_init(type_t fd)
^
/lustre1/gaog_pkuhpc/users/liny/rnaseq/pythonEnv/lib/python2.7/site-packages/pysam/include/htslib/htslib/kseq.h:249:2: note: in expansion of macro ‘__KSEQ_BASIC’
__KSEQ_BASIC(SCOPE, type_t)
^
/lustre1/gaog_pkuhpc/users/liny/rnaseq/pythonEnv/lib/python2.7/site-packages/pysam/include/htslib/htslib/kseq.h:252:35: note: in expansion of macro ‘KSEQ_INIT2’
#define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
^
/lustre1/gaog_pkuhpc/users/liny/rnaseq/pythonEnv/lib/python2.7/site-packages/pysam/pysam_stream.h:9:1: note: in expansion of macro ‘KSEQ_INIT’
KSEQ_INIT(BGZF *, bgzf_read)
^
/lustre1/gaog_pkuhpc/users/liny/rnaseq/pythonEnv/lib/python2.7/site-packages/pysam/include/htslib/htslib/kseq.h:184:13: warning: ‘kseq_destroy’ defined but not used [-Wunused-function]
SCOPE void kseq_destroy(kseq_t *ks)
^
/lustre1/gaog_pkuhpc/users/liny/rnaseq/pythonEnv/lib/python2.7/site-packages/pysam/include/htslib/htslib/kseq.h:249:2: note: in expansion of macro ‘__KSEQ_BASIC’
__KSEQ_BASIC(SCOPE, type_t)
^
/lustre1/gaog_pkuhpc/users/liny/rnaseq/pythonEnv/lib/python2.7/site-packages/pysam/include/htslib/htslib/kseq.h:252:35: note: in expansion of macro ‘KSEQ_INIT2’
#define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
^
/lustre1/gaog_pkuhpc/users/liny/rnaseq/pythonEnv/lib/python2.7/site-packages/pysam/pysam_stream.h:9:1: note: in expansion of macro ‘KSEQ_INIT’
KSEQ_INIT(BGZF *, bgzf_read)
^
/lustre1/gaog_pkuhpc/users/liny/rnaseq/pythonEnv/lib/python2.7/site-packages/pysam/include/htslib/htslib/kseq.h:198:12: warning: ‘kseq_read’ defined but not used [-Wunused-function]
SCOPE int kseq_read(kseq_t *seq)
^
/lustre1/gaog_pkuhpc/users/liny/rnaseq/pythonEnv/lib/python2.7/site-packages/pysam/include/htslib/htslib/kseq.h:250:2: note: in expansion of macro ‘__KSEQ_READ’
__KSEQ_READ(SCOPE)
^
/lustre1/gaog_pkuhpc/users/liny/rnaseq/pythonEnv/lib/python2.7/site-packages/pysam/include/htslib/htslib/kseq.h:252:35: note: in expansion of macro ‘KSEQ_INIT2’
#define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
^
/lustre1/gaog_pkuhpc/users/liny/rnaseq/pythonEnv/lib/python2.7/site-packages/pysam/pysam_stream.h:9:1: note: in expansion of macro ‘KSEQ_INIT’
KSEQ_INIT(BGZF *, bgzf_read)
^
gcc -pthread -shared build/temp.linux-x86_64-2.7/pysamstats/opt.o -o build/lib.linux-x86_64-2.7/pysamstats/opt.so