NameError: name 'utils' is not defined

Question

[arsilan324]

I am trying to run convert_gff3_to_ncbi_tbl.py script but getting this error.

ubt80:EMBLmyGFF3 arslan$ python3 convert_gff3_to_ncbi_tbl.py -i juncus.fasta.transdecoder.refined.gff3 -o arslan.tbl -ln TEST -nap JE -gf juncus-rp.fasta
INFO: splitting mRNA off gene Transcript_138016|g.186294
Traceback (most recent call last):
  File "convert_gff3_to_ncbi_tbl.py", line 89, in <module>
    main()
  File "convert_gff3_to_ncbi_tbl.py", line 82, in main
    tbl.print_tbl_from_assemblies(assemblies=assemblies, ofh=ofh, go_obo=args.go_obo, lab_name=args.lab_name)
  File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/biocode/tbl.py", line 86, in print_tbl_from_assemblies
    print_biogene(gene=new_gene, fh=ofh, obo_dict=go_idx, lab_name=lab_name)
  File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/biocode/tbl.py", line 117, in print_biogene
    gene_coords = utils.interbase0_to_humancoords(gene_loc.fmin, gene_loc.fmax, gene_loc.strand)
NameError: name 'utils' is not defined

Can you please comment how can I fix it? Thanks

[h.mon]

Did you install biocode? The script is trying to import some biocode stuff (module / function / class? I don't know how python call them) and failing, hence the error. What happens if you start the python interpreter and try to import biocode?

[arsilan324]

Yes, I did install it using pip. What do you mean by?

• What happens if you start the python interpreter and try to import biocode

[h.mon]

Issue python3, the inteactive interpreter will open, then issue import biocode.

$ python3
Python 3.6.4 (default, Jan  5 2018, 02:13:53) 
[GCC 7.2.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import biocode
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
ModuleNotFoundError: No module named 'biocode'

You could try installing biocode with virtualenv + pip.

P.S.: did you use pip or pip3?

[jorvis]

The biocode libraries were all written with Python3, so installation is needed using pip3. (I'm the author) Here it looks like you might be trying to run it using a GitHub checkout instead. That's fine too, but you'd need to add the biocode/lib dir to your PYTHONPATH if you do it that way. This is all in the README.

https://github.com/jorvis/biocode/blob/master/README.rst

Answer 1

[tdmurphy]

Have you tried NCBI's converter, to go straight from GFF3 to ASN.1 submission files? See: https://www.ncbi.nlm.nih.gov/genbank/genomes_gff/

[arsilan324]

Thank you for mentioning this tool. I am trying to install it using chmod +x but it is not helping me. I am using mac. I am unable to find instructions as well. Can you suggest how to install. Thanks