Name error in running blockParse.py
Closed this issue · 11 comments
Hi,
I ran
python ../OligoMiner-master/blockParse.py -f 3.fa
and received this error:
File "blockParse.py", line 993, in main()
File "blockParse.py", line 983, in main runSequenceCrawler(inputFile, l, L, gcPercent, GCPercent, nn_table, tm, TM, NameError: name 'nn_table' is not defined
How can I fix this?
Thank you!
Hi Brian,
Thank you for your reply. Sorry I forgot to mention that I am just testing your scripts with your example files in Ubuntu on windows10. I am not passing my own variables to blockParse nor importing it as a module. Also I am using the Python 2.7 ver of Anaconda2.
Hello, Apologies, it is difficult for me to tell what is going on without more information. Can you please provide some more details about your environment and any other info that might be helpful? I can say if you are trying to pass your own variables to blockParse (eg if you are importing it as a module into another script), the ordering of the positional arguments in the runSequenceCrawler() command is important.
…
On Thu, Aug 8, 2019 at 10:13 AM xxsabrina @.***> wrote: Hi, I ran python ../OligoMiner-master/blockParse.py -f 3.fa and received this error: File "blockParse.py", line 993, in main() File "blockParse.py", line 983, in main runSequenceCrawler(inputFile, l, L, gcPercent, GCPercent, nn_table, tm, TM, NameError: name 'nn_table' is not defined How can I fix this? Thank you! — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#6?email_source=notifications&email_token=AHIXQ2U6SSNUBQ6XZHSULDTQDRH4TA5CNFSM4IKMXIDKYY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4HEGX5CQ>, or mute the thread https://github.com/notifications/unsubscribe-auth/AHIXQ2WULC5P7NFRVNMNXY3QDRH4TANCNFSM4IKMXIDA .
Hi,
My packages are:
Hello, Thank you for providing more information. I'm afraid I cannot replicate this error on my end. Can you please see which packages are in your conda environment using "conda list"? I am pasting a screenshot below of what should be a duplicate of what you are doing and the results of 'conda list' for my env: [image: image.png]
…
On Thu, Aug 8, 2019 at 1:12 PM xxsabrina @.> wrote: Hi Brian, Thank you for your reply. Sorry I forgot to mention that I am just testing your scripts with your example files in Ubuntu on windows10. I am not passing my own variables to blockParse nor importing it as a module. Also I am using the Python 2.7 ver of Anaconda2. Hello, Apologies, it is difficult for me to tell what is going on without more information. Can you please provide some more details about your environment and any other info that might be helpful? I can say if you are trying to pass your own variables to blockParse (eg if you are importing it as a module into another script), the ordering of the positional arguments in the runSequenceCrawler() command is important. … <#m_-3361906421857073660_> On Thu, Aug 8, 2019 at 10:13 AM xxsabrina @.> wrote: Hi, I ran python ../OligoMiner-master/blockParse.py -f 3.fa and received this error: File "blockParse.py", line 993, in main() File "blockParse.py", line 983, in main runSequenceCrawler(inputFile, l, L, gcPercent, GCPercent, nn_table, tm, TM, NameError: name 'nn_table' is not defined How can I fix this? Thank you! — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#6 <#6>?email_source=notifications&email_token=AHIXQ2U6SSNUBQ6XZHSULDTQDRH4TA5CNFSM4IKMXIDKYY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4HEGX5CQ>, or mute the thread https://github.com/notifications/unsubscribe-auth/AHIXQ2WULC5P7NFRVNMNXY3QDRH4TANCNFSM4IKMXIDA . — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#6?email_source=notifications&email_token=AHIXQ2SOSDNYJKFPYKEXIPDQDR43RA5CNFSM4IKMXIDKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD34YSXY#issuecomment-519670111>, or mute the thread https://github.com/notifications/unsubscribe-auth/AHIXQ2QOQUDIQK62ZBZIN3DQDR43RANCNFSM4IKMXIDA .
Hi,
I think I just did the regular conda create --name probemining. Then I installed the packages by pip using pip install.
Hello, Can you please provide me with the exact command you used to create your conda environment? It is possible a version difference of on the packages could be the issue. Thanks
…
On Thu, Aug 8, 2019 at 1:23 PM xxsabrina @.*> wrote: Hi, My packages are: Name Version Build Channel libgcc_mutex 0.1 main asn1crypto 0.24.0 pypi_0 pypi attrs 19.1.0 pypi_0 pypi automat 0.7.0 pypi_0 pypi bio 0.1.0 pypi_0 pypi biopython 1.74 pypi_0 pypi bowtie2 2.3.5 py37he860b03_0 bioconda bzip2 1.0.8 h516909a_0 conda-forge ca-certificates 2019.6.16 hecc5488_0 conda-forge certifi 2019.6.16 py37_1 conda-forge cffi 1.12.3 pypi_0 pypi constantly 15.1.0 pypi_0 pypi cryptography 2.7 pypi_0 pypi cssselect 1.0.3 pypi_0 pypi hyperlink 19.0.0 pypi_0 pypi idna 2.8 pypi_0 pypi incremental 17.5.0 pypi_0 pypi jellyfish 2.2.10 h6bb024c_1 bioconda jemalloc 4.5.0 0 bioconda joblib 0.13.2 pypi_0 pypi libblas 3.8.0 11_openblas conda-forge libcblas 3.8.0 11_openblas conda-forge libffi 3.2.1 he1b5a44_1006 conda-forge libgcc 7.2.0 h69d50b8_2 conda-forge libgcc-ng 9.1.0 hdf63c60_0 libgfortran-ng 7.3.0 hdf63c60_0 liblapack 3.8.0 11_openblas conda-forge libopenblas 0.3.6 h6e990d7_6 conda-forge libstdcxx-ng 9.1.0 hdf63c60_0 lxml 4.4.0 pypi_0 pypi ncurses 6.1 hf484d3e_1002 conda-forge numpy 1.17.0 py37h95a1406_0 conda-forge openssl 1.1.1c h516909a_0 conda-forge parsel 1.5.1 pypi_0 pypi perl 5.26.2 h516909a_1006 conda-forge pip 19.2.1 py37_0 conda-forge pyasn1 0.4.6 pypi_0 pypi pyasn1-modules 0.2.6 pypi_0 pypi pycparser 2.19 pypi_0 pypi pydispatcher 2.0.5 pypi_0 pypi pyhamcrest 1.9.0 pypi_0 pypi pyopenssl 19.0.0 pypi_0 pypi python 3.7.3 h33d41f4_1 conda-forge queuelib 1.5.0 pypi_0 pypi readline 8.0 hf8c457e_0 conda-forge regex 2019.6.8 pypi_0 pypi scikit-learn 0.21.3 py37hcdab131_0 conda-forge scipy 1.3.0 pypi_0 pypi scrapy 1.7.3 pypi_0 pypi service-identity 18.1.0 pypi_0 pypi setuptools 41.0.1 py37_0 conda-forge six 1.12.0 pypi_0 pypi sqlite 3.29.0 hcee41ef_0 conda-forge tbb 2019.7 hc9558a2_0 conda-forge tk 8.6.9 hed695b0_1002 conda-forge twisted 19.7.0 pypi_0 pypi w3lib 1.20.0 pypi_0 pypi wheel 0.33.4 py37_0 conda-forge xz 5.2.4 h14c3975_1001 conda-forge zlib 1.2.11 h516909a_1005 conda-forge zope-interface 4.6.0 pypi_0 pypi Hello, Thank you for providing more information. I'm afraid I cannot replicate this error on my end. Can you please see which packages are in your conda environment using "conda list"? I am pasting a screenshot below of what should be a duplicate of what you are doing and the results of 'conda list' for my env: [image: image.png] … <#m-3629228488473131120_> On Thu, Aug 8, 2019 at 1:12 PM xxsabrina @.> wrote: Hi Brian, Thank you for your reply. Sorry I forgot to mention that I am just testing your scripts with your example files in Ubuntu on windows10. I am not passing my own variables to blockParse nor importing it as a module. Also I am using the Python 2.7 ver of Anaconda2. Hello, Apologies, it is difficult for me to tell what is going on without more information. Can you please provide some more details about your environment and any other info that might be helpful? I can say if you are trying to pass your own variables to blockParse (eg if you are importing it as a module into another script), the ordering of the positional arguments in the runSequenceCrawler() command is important. … <#m_-3361906421857073660_> On Thu, Aug 8, 2019 at 10:13 AM xxsabrina @.> wrote: Hi, I ran python ../OligoMiner-master/blockParse.py -f 3.fa and received this error: File "blockParse.py", line 993, in main() File "blockParse.py", line 983, in main runSequenceCrawler(inputFile, l, L, gcPercent, GCPercent, nn_table, tm, TM, NameError: name 'nn_table' is not defined How can I fix this? Thank you! — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#6 <#6> <#6 <#6>>?email_source=notifications&email_token=AHIXQ2U6SSNUBQ6XZHSULDTQDRH4TA5CNFSM4IKMXIDKYY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4HEGX5CQ>, or mute the thread https://github.com/notifications/unsubscribe-auth/AHIXQ2WULC5P7NFRVNMNXY3QDRH4TANCNFSM4IKMXIDA . — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#6 <#6>?email_source=notifications&email_token=AHIXQ2SOSDNYJKFPYKEXIPDQDR43RA5CNFSM4IKMXIDKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD34YSXY#issuecomment-519670111>, or mute the thread https://github.com/notifications/unsubscribe-auth/AHIXQ2QOQUDIQK62ZBZIN3DQDR43RANCNFSM4IKMXIDA . — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#6?email_source=notifications&email_token=AHIXQ2U7UKFPXGS5P7HYWZDQDR6F3A5CNFSM4IKMXIDKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD34ZRGI#issuecomment-519674009>, or mute the thread https://github.com/notifications/unsubscribe-auth/AHIXQ2VZYMC6WS6UERBOZTLQDR6F3ANCNFSM4IKMXIDA .
Hi Brian,
I just had a check of my Python version and surprised to find it's actually 3.7. I thought it was 2.7. Maybe this is the problem?
Hello, Can you please provide me with the exact command you used to create your conda environment? It is possible a version difference of on the packages could be the issue. Thanks
…
On Thu, Aug 8, 2019 at 1:23 PM xxsabrina @.*> wrote: Hi, My packages are: Name Version Build Channel libgcc_mutex 0.1 main asn1crypto 0.24.0 pypi_0 pypi attrs 19.1.0 pypi_0 pypi automat 0.7.0 pypi_0 pypi bio 0.1.0 pypi_0 pypi biopython 1.74 pypi_0 pypi bowtie2 2.3.5 py37he860b03_0 bioconda bzip2 1.0.8 h516909a_0 conda-forge ca-certificates 2019.6.16 hecc5488_0 conda-forge certifi 2019.6.16 py37_1 conda-forge cffi 1.12.3 pypi_0 pypi constantly 15.1.0 pypi_0 pypi cryptography 2.7 pypi_0 pypi cssselect 1.0.3 pypi_0 pypi hyperlink 19.0.0 pypi_0 pypi idna 2.8 pypi_0 pypi incremental 17.5.0 pypi_0 pypi jellyfish 2.2.10 h6bb024c_1 bioconda jemalloc 4.5.0 0 bioconda joblib 0.13.2 pypi_0 pypi libblas 3.8.0 11_openblas conda-forge libcblas 3.8.0 11_openblas conda-forge libffi 3.2.1 he1b5a44_1006 conda-forge libgcc 7.2.0 h69d50b8_2 conda-forge libgcc-ng 9.1.0 hdf63c60_0 libgfortran-ng 7.3.0 hdf63c60_0 liblapack 3.8.0 11_openblas conda-forge libopenblas 0.3.6 h6e990d7_6 conda-forge libstdcxx-ng 9.1.0 hdf63c60_0 lxml 4.4.0 pypi_0 pypi ncurses 6.1 hf484d3e_1002 conda-forge numpy 1.17.0 py37h95a1406_0 conda-forge openssl 1.1.1c h516909a_0 conda-forge parsel 1.5.1 pypi_0 pypi perl 5.26.2 h516909a_1006 conda-forge pip 19.2.1 py37_0 conda-forge pyasn1 0.4.6 pypi_0 pypi pyasn1-modules 0.2.6 pypi_0 pypi pycparser 2.19 pypi_0 pypi pydispatcher 2.0.5 pypi_0 pypi pyhamcrest 1.9.0 pypi_0 pypi pyopenssl 19.0.0 pypi_0 pypi python 3.7.3 h33d41f4_1 conda-forge queuelib 1.5.0 pypi_0 pypi readline 8.0 hf8c457e_0 conda-forge regex 2019.6.8 pypi_0 pypi scikit-learn 0.21.3 py37hcdab131_0 conda-forge scipy 1.3.0 pypi_0 pypi scrapy 1.7.3 pypi_0 pypi service-identity 18.1.0 pypi_0 pypi setuptools 41.0.1 py37_0 conda-forge six 1.12.0 pypi_0 pypi sqlite 3.29.0 hcee41ef_0 conda-forge tbb 2019.7 hc9558a2_0 conda-forge tk 8.6.9 hed695b0_1002 conda-forge twisted 19.7.0 pypi_0 pypi w3lib 1.20.0 pypi_0 pypi wheel 0.33.4 py37_0 conda-forge xz 5.2.4 h14c3975_1001 conda-forge zlib 1.2.11 h516909a_1005 conda-forge zope-interface 4.6.0 pypi_0 pypi Hello, Thank you for providing more information. I'm afraid I cannot replicate this error on my end. Can you please see which packages are in your conda environment using "conda list"? I am pasting a screenshot below of what should be a duplicate of what you are doing and the results of 'conda list' for my env: [image: image.png] … <#m-3629228488473131120_> On Thu, Aug 8, 2019 at 1:12 PM xxsabrina @.> wrote: Hi Brian, Thank you for your reply. Sorry I forgot to mention that I am just testing your scripts with your example files in Ubuntu on windows10. I am not passing my own variables to blockParse nor importing it as a module. Also I am using the Python 2.7 ver of Anaconda2. Hello, Apologies, it is difficult for me to tell what is going on without more information. Can you please provide some more details about your environment and any other info that might be helpful? I can say if you are trying to pass your own variables to blockParse (eg if you are importing it as a module into another script), the ordering of the positional arguments in the runSequenceCrawler() command is important. … <#m_-3361906421857073660_> On Thu, Aug 8, 2019 at 10:13 AM xxsabrina @.> wrote: Hi, I ran python ../OligoMiner-master/blockParse.py -f 3.fa and received this error: File "blockParse.py", line 993, in main() File "blockParse.py", line 983, in main runSequenceCrawler(inputFile, l, L, gcPercent, GCPercent, nn_table, tm, TM, NameError: name 'nn_table' is not defined How can I fix this? Thank you! — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#6 <#6> <#6 <#6>>?email_source=notifications&email_token=AHIXQ2U6SSNUBQ6XZHSULDTQDRH4TA5CNFSM4IKMXIDKYY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4HEGX5CQ>, or mute the thread https://github.com/notifications/unsubscribe-auth/AHIXQ2WULC5P7NFRVNMNXY3QDRH4TANCNFSM4IKMXIDA . — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#6 <#6>?email_source=notifications&email_token=AHIXQ2SOSDNYJKFPYKEXIPDQDR43RA5CNFSM4IKMXIDKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD34YSXY#issuecomment-519670111>, or mute the thread https://github.com/notifications/unsubscribe-auth/AHIXQ2QOQUDIQK62ZBZIN3DQDR43RANCNFSM4IKMXIDA . — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#6?email_source=notifications&email_token=AHIXQ2U7UKFPXGS5P7HYWZDQDR6F3A5CNFSM4IKMXIDKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD34ZRGI#issuecomment-519674009>, or mute the thread https://github.com/notifications/unsubscribe-auth/AHIXQ2VZYMC6WS6UERBOZTLQDR6F3ANCNFSM4IKMXIDA .
Hi,
I did exactly what you said. And got the following error:
(pm_test) user@**********:~/OligoMiner-master$ python blockParse.py -f 3.fa Traceback (most recent call last): File "blockParse.py", line 47, in from Bio.SeqUtils import MeltingTemp as mt ImportError: No module named Bio.SeqUtils
Hello, Yes, that would be a problem, although I would expect the error the script would throw would be different (invalid syntax on a 'print' statement') Can you please try making a new conda environment with this command: conda create --name pm_test numpy scipy biopython scikit-learn python=2.7.12 I just made a brand-new env with that command and can still run blockParse without issue. You can of course give the env a different name if you'd prefer.
…
On Thu, Aug 8, 2019 at 1:56 PM xxsabrina @.> wrote: Hi Brian, I just had a check of my Python version and surprised to find it's actually 3.7. I thought it was 2.7. Maybe this is the problem? Hello, Can you please provide me with the exact command you used to create your conda environment? It is possible a version difference of on the packages could be the issue. Thanks … <#m_9081611609966635100_> On Thu, Aug 8, 2019 at 1:23 PM xxsabrina @.> wrote: Hi, My packages are: Name Version Build Channel libgcc_mutex 0.1 main asn1crypto 0.24.0 pypi_0 pypi attrs 19.1.0 pypi_0 pypi automat 0.7.0 pypi_0 pypi bio 0.1.0 pypi_0 pypi biopython 1.74 pypi_0 pypi bowtie2 2.3.5 py37he860b03_0 bioconda bzip2 1.0.8 h516909a_0 conda-forge ca-certificates 2019.6.16 hecc5488_0 conda-forge certifi 2019.6.16 py37_1 conda-forge cffi 1.12.3 pypi_0 pypi constantly 15.1.0 pypi_0 pypi cryptography 2.7 pypi_0 pypi cssselect 1.0.3 pypi_0 pypi hyperlink 19.0.0 pypi_0 pypi idna 2.8 pypi_0 pypi incremental 17.5.0 pypi_0 pypi jellyfish 2.2.10 h6bb024c_1 bioconda jemalloc 4.5.0 0 bioconda joblib 0.13.2 pypi_0 pypi libblas 3.8.0 11_openblas conda-forge libcblas 3.8.0 11_openblas conda-forge libffi 3.2.1 he1b5a44_1006 conda-forge libgcc 7.2.0 h69d50b8_2 conda-forge libgcc-ng 9.1.0 hdf63c60_0 libgfortran-ng 7.3.0 hdf63c60_0 liblapack 3.8.0 11_openblas conda-forge libopenblas 0.3.6 h6e990d7_6 conda-forge libstdcxx-ng 9.1.0 hdf63c60_0 lxml 4.4.0 pypi_0 pypi ncurses 6.1 hf484d3e_1002 conda-forge numpy 1.17.0 py37h95a1406_0 conda-forge openssl 1.1.1c h516909a_0 conda-forge parsel 1.5.1 pypi_0 pypi perl 5.26.2 h516909a_1006 conda-forge pip 19.2.1 py37_0 conda-forge pyasn1 0.4.6 pypi_0 pypi pyasn1-modules 0.2.6 pypi_0 pypi pycparser 2.19 pypi_0 pypi pydispatcher 2.0.5 pypi_0 pypi pyhamcrest 1.9.0 pypi_0 pypi pyopenssl 19.0.0 pypi_0 pypi python 3.7.3 h33d41f4_1 conda-forge queuelib 1.5.0 pypi_0 pypi readline 8.0 hf8c457e_0 conda-forge regex 2019.6.8 pypi_0 pypi scikit-learn 0.21.3 py37hcdab131_0 conda-forge scipy 1.3.0 pypi_0 pypi scrapy 1.7.3 pypi_0 pypi service-identity 18.1.0 pypi_0 pypi setuptools 41.0.1 py37_0 conda-forge six 1.12.0 pypi_0 pypi sqlite 3.29.0 hcee41ef_0 conda-forge tbb 2019.7 hc9558a2_0 conda-forge tk 8.6.9 hed695b0_1002 conda-forge twisted 19.7.0 pypi_0 pypi w3lib 1.20.0 pypi_0 pypi wheel 0.33.4 py37_0 conda-forge xz 5.2.4 h14c3975_1001 conda-forge zlib 1.2.11 h516909a_1005 conda-forge zope-interface 4.6.0 pypi_0 pypi Hello, Thank you for providing more information. I'm afraid I cannot replicate this error on my end. Can you please see which packages are in your conda environment using "conda list"? I am pasting a screenshot below of what should be a duplicate of what you are doing and the results of 'conda list' for my env: [image: image.png] … <#m-3629228488473131120_> On Thu, Aug 8, 2019 at 1:12 PM xxsabrina @.> wrote: Hi Brian, Thank you for your reply. Sorry I forgot to mention that I am just testing your scripts with your example files in Ubuntu on windows10. I am not passing my own variables to blockParse nor importing it as a module. Also I am using the Python 2.7 ver of Anaconda2. Hello, Apologies, it is difficult for me to tell what is going on without more information. Can you please provide some more details about your environment and any other info that might be helpful? I can say if you are trying to pass your own variables to blockParse (eg if you are importing it as a module into another script), the ordering of the positional arguments in the runSequenceCrawler() command is important. … <#m_-3361906421857073660_> On Thu, Aug 8, 2019 at 10:13 AM xxsabrina @.> wrote: Hi, I ran python ../OligoMiner-master/blockParse.py -f 3.fa and received this error: File "blockParse.py", line 993, in main() File "blockParse.py", line 983, in main runSequenceCrawler(inputFile, l, L, gcPercent, GCPercent, nn_table, tm, TM, NameError: name 'nn_table' is not defined How can I fix this? Thank you! — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#6 <#6> <#6 <#6>> <#6 <#6> <#6 <#6>>>?email_source=notifications&email_token=AHIXQ2U6SSNUBQ6XZHSULDTQDRH4TA5CNFSM4IKMXIDKYY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4HEGX5CQ>, or mute the thread https://github.com/notifications/unsubscribe-auth/AHIXQ2WULC5P7NFRVNMNXY3QDRH4TANCNFSM4IKMXIDA . — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#6 <#6> <#6 <#6>>?email_source=notifications&email_token=AHIXQ2SOSDNYJKFPYKEXIPDQDR43RA5CNFSM4IKMXIDKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD34YSXY#issuecomment-519670111>, or mute the thread https://github.com/notifications/unsubscribe-auth/AHIXQ2QOQUDIQK62ZBZIN3DQDR43RANCNFSM4IKMXIDA . — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#6 <#6>?email_source=notifications&email_token=AHIXQ2U7UKFPXGS5P7HYWZDQDR6F3A5CNFSM4IKMXIDKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD34ZRGI#issuecomment-519674009>, or mute the thread https://github.com/notifications/unsubscribe-auth/AHIXQ2VZYMC6WS6UERBOZTLQDR6F3ANCNFSM4IKMXIDA . — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#6?email_source=notifications&email_token=AHIXQ2SU5OHFB3HYMQK5CYTQDSCBHA5CNFSM4IKMXIDKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD344DGQ#issuecomment-519684506>, or mute the thread https://github.com/notifications/unsubscribe-auth/AHIXQ2WS47N3T22E6L7OXFTQDSCBHANCNFSM4IKMXIDA .
Hi,
I tried to uninstall and re-install anaconda. Now everything is working! Thank you so much!
It seems like your interpreter is not able to find your Biopython install. I am not sure why. I would recommend uninstalling and re-installing Anaconda, then trying the environment creation command from my last message again.
…
On Thu, Aug 8, 2019 at 2:14 PM xxsabrina @.> wrote: Hi, I did exactly what you said. And got the following error: (pm_test) user@*****:~/OligoMiner-master$ python blockParse.py -f 3.fa Traceback (most recent call last): File "blockParse.py", line 47, in from Bio.SeqUtils import MeltingTemp as mt ImportError: No module named Bio.SeqUtils Hello, Yes, that would be a problem, although I would expect the error the script would throw would be different (invalid syntax on a 'print' statement') Can you please try making a new conda environment with this command: conda create --name pm_test numpy scipy biopython scikit-learn python=2.7.12 I just made a brand-new env with that command and can still run blockParse without issue. You can of course give the env a different name if you'd prefer. … <#m_8542974403958476619_> On Thu, Aug 8, 2019 at 1:56 PM xxsabrina @.> wrote: Hi Brian, I just had a check of my Python version and surprised to find it's actually 3.7. I thought it was 2.7. Maybe this is the problem? Hello, Can you please provide me with the exact command you used to create your conda environment? It is possible a version difference of on the packages could be the issue. Thanks … <#m_9081611609966635100_> On Thu, Aug 8, 2019 at 1:23 PM xxsabrina @.> wrote: Hi, My packages are: Name Version Build Channel libgcc_mutex 0.1 main asn1crypto 0.24.0 pypi_0 pypi attrs 19.1.0 pypi_0 pypi automat 0.7.0 pypi_0 pypi bio 0.1.0 pypi_0 pypi biopython 1.74 pypi_0 pypi bowtie2 2.3.5 py37he860b03_0 bioconda bzip2 1.0.8 h516909a_0 conda-forge ca-certificates 2019.6.16 hecc5488_0 conda-forge certifi 2019.6.16 py37_1 conda-forge cffi 1.12.3 pypi_0 pypi constantly 15.1.0 pypi_0 pypi cryptography 2.7 pypi_0 pypi cssselect 1.0.3 pypi_0 pypi hyperlink 19.0.0 pypi_0 pypi idna 2.8 pypi_0 pypi incremental 17.5.0 pypi_0 pypi jellyfish 2.2.10 h6bb024c_1 bioconda jemalloc 4.5.0 0 bioconda joblib 0.13.2 pypi_0 pypi libblas 3.8.0 11_openblas conda-forge libcblas 3.8.0 11_openblas conda-forge libffi 3.2.1 he1b5a44_1006 conda-forge libgcc 7.2.0 h69d50b8_2 conda-forge libgcc-ng 9.1.0 hdf63c60_0 libgfortran-ng 7.3.0 hdf63c60_0 liblapack 3.8.0 11_openblas conda-forge libopenblas 0.3.6 h6e990d7_6 conda-forge libstdcxx-ng 9.1.0 hdf63c60_0 lxml 4.4.0 pypi_0 pypi ncurses 6.1 hf484d3e_1002 conda-forge numpy 1.17.0 py37h95a1406_0 conda-forge openssl 1.1.1c h516909a_0 conda-forge parsel 1.5.1 pypi_0 pypi perl 5.26.2 h516909a_1006 conda-forge pip 19.2.1 py37_0 conda-forge pyasn1 0.4.6 pypi_0 pypi pyasn1-modules 0.2.6 pypi_0 pypi pycparser 2.19 pypi_0 pypi pydispatcher 2.0.5 pypi_0 pypi pyhamcrest 1.9.0 pypi_0 pypi pyopenssl 19.0.0 pypi_0 pypi python 3.7.3 h33d41f4_1 conda-forge queuelib 1.5.0 pypi_0 pypi readline 8.0 hf8c457e_0 conda-forge regex 2019.6.8 pypi_0 pypi scikit-learn 0.21.3 py37hcdab131_0 conda-forge scipy 1.3.0 pypi_0 pypi scrapy 1.7.3 pypi_0 pypi service-identity 18.1.0 pypi_0 pypi setuptools 41.0.1 py37_0 conda-forge six 1.12.0 pypi_0 pypi sqlite 3.29.0 hcee41ef_0 conda-forge tbb 2019.7 hc9558a2_0 conda-forge tk 8.6.9 hed695b0_1002 conda-forge twisted 19.7.0 pypi_0 pypi w3lib 1.20.0 pypi_0 pypi wheel 0.33.4 py37_0 conda-forge xz 5.2.4 h14c3975_1001 conda-forge zlib 1.2.11 h516909a_1005 conda-forge zope-interface 4.6.0 pypi_0 pypi Hello, Thank you for providing more information. I'm afraid I cannot replicate this error on my end. Can you please see which packages are in your conda environment using "conda list"? I am pasting a screenshot below of what should be a duplicate of what you are doing and the results of 'conda list' for my env: [image: image.png] … <#m-3629228488473131120_> On Thu, Aug 8, 2019 at 1:12 PM xxsabrina @.> wrote: Hi Brian, Thank you for your reply. Sorry I forgot to mention that I am just testing your scripts with your example files in Ubuntu on windows10. I am not passing my own variables to blockParse nor importing it as a module. Also I am using the Python 2.7 ver of Anaconda2. Hello, Apologies, it is difficult for me to tell what is going on without more information. Can you please provide some more details about your environment and any other info that might be helpful? I can say if you are trying to pass your own variables to blockParse (eg if you are importing it as a module into another script), the ordering of the positional arguments in the runSequenceCrawler() command is important. … <#m_-3361906421857073660_> On Thu, Aug 8, 2019 at 10:13 AM xxsabrina @.> wrote: Hi, I ran python ../OligoMiner-master/blockParse.py -f 3.fa and received this error: File "blockParse.py", line 993, in main() File "blockParse.py", line 983, in main runSequenceCrawler(inputFile, l, L, gcPercent, GCPercent, nn_table, tm, TM, NameError: name 'nn_table' is not defined How can I fix this? Thank you! — You are receiving this because you are subscribed to this thread. 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