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karkman / gff_parser

Parser to add external gene calls and functional annotation from Prokka to Anvi'o.
GNU General Public License v3.0
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SyntaxError: invalid syntax #10

Closed eag-microbio closed 3 years ago

eag-microbio commented 3 years ago

Hello! I'm brand new to using anvio... I have been trying to use your importing prokka annotations into anvio script (https://merenlab.org/2017/05/18/working-with-prokka).

I run this script: python gff_parser.py PROKKA_JKS002657/PROKKA.gff --gene-calls JKS002657gene_calls.txt --annotation JKS002657gene_annot.txt

and get this error: File "gff_parser.py", line 124 print(f"Done. All {total_num_features} have been processed succesfully. There were {call_types['CDS']} coding " ^ SyntaxError: invalid syntax

It does not make the gene call or annotation files.

I've gone through and simplified my contigs names. I'm not sure what else I should be checking... I have anvio v7.

Thank you!

karkman commented 3 years ago

Hi, Which version of python you’re using? The script works only with python3.

If this is not the problem and this is a bug, unfortunately I won’t be able to fix this before early August.

Best regards Antti

eag-microbio commented 3 years ago

Hi Antti, Thank you for the fast reply! I realize we are using python 2 7.15.

Thank you! Emily

On Tue, Jul 20, 2021, 1:54 PM Antti Karkman @.***> wrote:

Hi, Which version of python you’re using? The script works only with python3.

If this is not the problem and this is a bug, unfortunately I won’t be able to fix this before early August.

Best regards Antti

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