ImportError: No module named opt

[lybird300]

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

[alimanfoo]

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 ***@***.*** 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 — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#95>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAq8Qt0fIXe3620-dvm-VkPrq8-_3cL1ks5uuoQ3gaJpZM4YbJpG> .

[lybird300]

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

[lybird300]

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