search

WGLab / RepeatHMM

a hidden Markov model to infer simple repeats from genome sequences
Other
34 stars 14 forks source link

ImportError: cannot import name _UnsymmetricPairAlignment #55

Open aishsk87 opened 1 year ago

aishsk87 commented 1 year ago

I have following versions of Python 2 and 3 respectively, Python 2.7.18 :: Anaconda, Inc. Python 3.8.10 and I ran the steps as per the installation instructions, however I still the following error

python RepeatHMM/bin/repeatHMM.py FASTQinput --repeatName atxn3 --GapCorrection 1 --FlankLength 30 --UserDefinedUniqID sca3_pcr25_raw_test --fastq SRR5363632.fastq --outFolder logfq --Patternfile RepeatHMM/bin/reference_sts/hg38/hg38.predefined.pa --hgfile hg38/hg38.fa --hg hg38 Traceback (most recent call last): File "RepeatHMM/bin/repeatHMM.py", line 18, in from RepeatHMM_scripts import myBAMhandler File "/tools/RepeatHMM/bin/RepeatHMM_scripts/myBAMhandler.py", line 24, in from . import getAlignment File "/tools/RepeatHMM/bin/RepeatHMM_scripts/getAlignment.py", line 7, in from UnsymmetricPairAlignment import UnsymmetricPairAlignment File "/tools/RepeatHMM/bin/RepeatHMM_scripts/UnsymmetricPairAlignment/UnsymmetricPairAlignment.py", line 13, in from . import _UnsymmetricPairAlignment ImportError: cannot import name _UnsymmetricPairAlignment

Any help will be extremely appreciated

liuqianhn commented 1 year ago

@aishsk87 could you please check #32 to see whether that solution works for you.

aishsk87 commented 1 year ago

I did follow all the issues and followed the steps:

git clone https://github.com/WGLab/RepeatHMM.gitCloning into 'RepeatHMM'... remote: Enumerating objects: 911, done. remote: Counting objects: 100% (8/8), done. remote: Compressing objects: 100% (7/7), done. remote: Total 911 (delta 1), reused 3 (delta 1), pack-reused 903 Receiving objects: 100% (911/911), 901.78 KiB | 9.11 MiB/s, done. Resolving deltas: 100% (503/503), done.

source activate repeathmmenv

cd RepeatHMM/bin/RepeatHMM_scripts/UnsymmetricPairAlignment

make swig -python UnsymmetricPairAlignment.i python setup.py build_ext --inplace running build_ext building '_UnsymmetricPairAlignment' extension creating build creating build/temp.linux-x86_64-3.8 x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.8 -c UnsymmetricPairAlignment_wrap.c -o build/temp.linux-x86_64-3.8/UnsymmetricPairAlignment_wrap.o x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.8 -c UnsymmetricPairAlignment.c -o build/temp.linux-x86_64-3.8/UnsymmetricPairAlignment.o x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.8/UnsymmetricPairAlignment_wrap.o build/temp.linux-x86_64-3.8/UnsymmetricPairAlignment.o -o /tools/RepeatHMM/bin/RepeatHMM_scripts/UnsymmetricPairAlignment/_UnsymmetricPairAlignment.cpython-38-x86_64-linux-gnu.so

This is the content in UnsymmetricPairAlignment directory RepeatHMM/bin/RepeatHMM_scripts/UnsymmetricPairAlignment build _UnsymmetricPairAlignment.cpython-38-x86_64-linux-gnu.so init.py UnsymmetricPairAlignment.i Makefile UnsymmetricPairAlignment.py setup.py UnsymmetricPairAlignment_wrap.c UnsymmetricPairAlignment.c

/RepeatHMM/bin/RepeatHMM_scripts/UnsymmetricPairAlignment/build/temp.linux-x86_64-3.8 UnsymmetricPairAlignment.o UnsymmetricPairAlignment_wrap.o

I then ran the script as follows and this is what I get:

python RepeatHMM/bin/repeatHMM.py FASTQinput --repeatName atxn3 --GapCorrection 1 --FlankLength 30 --UserDefinedUniqID sca3_pcr25_raw_test --fastq SRR5363632.fastq --outFolder logfq --Patternfile RepeatHMM/bin/reference_sts/hg38/hg38.predefined.pa --hgfile hg38/hg38.fa --hg hg38 Traceback (most recent call last): File "RepeatHMM/bin/repeatHMM.py", line 18, in from RepeatHMM_scripts import myBAMhandler File "/tools/RepeatHMM/bin/RepeatHMM_scripts/myBAMhandler.py", line 24, in from . import getAlignment File "/tools/RepeatHMM/bin/RepeatHMM_scripts/getAlignment.py", line 7, in from UnsymmetricPairAlignment import UnsymmetricPairAlignment ModuleNotFoundError: No module named 'UnsymmetricPairAlignment'