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katholt / srst2

Short Read Sequence Typing for Bacterial Pathogens
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VFDB database problem #114

Closed aslangabriel closed 5 years ago

aslangabriel commented 5 years ago

I have followed all the instructions, however all the py scripts prompt error"line 9, in from Bio import SeqIO ImportError: No module named Bio" Could you help me to handle this problem

katholt commented 5 years ago

Bio is a module within BioPython - sounds like you just need to install BioPython correctly

aslangabriel commented 5 years ago

Thank you. I‘ll give it a go

Kat Holt notifications@github.com 于2019年1月21日周一 下午9:21写道：

Bio is a module within BioPython - sounds like you just need to install BioPython correctly

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/katholt/srst2/issues/114#issuecomment-456258062, or mute the thread https://github.com/notifications/unsubscribe-auth/AsvLUD9FiUUCn8gA05o2cC9sLVLkEpBPks5vFoOigaJpZM4aL25R .

-- Dr. Qi Feng College of Life Sciences Nanjing Normal University 1 Wenyuan Road 210046 Nanjing P.R. China

aslangabriel commented 5 years ago

I'm sorry to trouble you again. There's anther problem which is described as follows"(base) qifeng@ubuntu:~$ python mybin/VFDB_cdhit_to_csv.py --cluster_file Salmonella_cdhit90.clstr --infile Salmonella.fsa --outfile Salmonella_cdhit90.csv Traceback (most recent call last): File "mybin/VFDB_cdhit_to_csv.py", line 68, in sys.exit(main()) File "mybin/VFDB_cdhit_to_csv.py", line 29, in main outfile = file(args.outfile,"w") NameError: name 'file' is not defined "

Qi Feng luckystar204@gmail.com 于2019年1月21日周一 下午9:23写道：

Thank you. I‘ll give it a go

Kat Holt notifications@github.com 于2019年1月21日周一 下午9:21写道：

Bio is a module within BioPython - sounds like you just need to install BioPython correctly

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/katholt/srst2/issues/114#issuecomment-456258062, or mute the thread https://github.com/notifications/unsubscribe-auth/AsvLUD9FiUUCn8gA05o2cC9sLVLkEpBPks5vFoOigaJpZM4aL25R .

-- Dr. Qi Feng College of Life Sciences Nanjing Normal University 1 Wenyuan Road 210046 Nanjing P.R. China

-- Dr. Qi Feng College of Life Sciences Nanjing Normal University 1 Wenyuan Road 210046 Nanjing P.R. China