VFDB Parse the cluster output and tabulate the results using the specific Virulence gene DB compatible script:

katholt / srst2

Short Read Sequence Typing for Bacterial Pathogens

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VFDB Parse the cluster output and tabulate the results using the specific Virulence gene DB compatible script: #115

Open aslangabriel opened 5 years ago

aslangabriel commented 5 years ago

When I run this step: the error indicated that "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 '

HumbiFred commented 4 years ago

Hi,

I am facing the same problem. Is there maybe a solution out yet?

Thank you for your help in advance :)

Kind regards

katholt commented 4 years ago

This looks like a python3 issue - note srst2 is written for python2.

HumbiFred commented 4 years ago

Thank you! That's it. Now its workinge perfectly.

Could have figured that out myself, so sorry for bothering.