SyntaxWarning: "is" with a literal. Did you mean "=="?

xgrau / possvm-orthology

Possvm: find clusters of orthologs in phylogenies using species overlap & MCL

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SyntaxWarning: "is" with a literal. Did you mean "=="? #21

Open Z1997B opened 1 month ago

Z1997B commented 1 month ago

hi xgrau, When I run this script to identify the ortholog of my gene tree, I got two issues: First, I got one warning: possvm1/lib/python3.10/site-packages/ete3-3.1.2-py3.7.egg/ete3/evol/parser/codemlparser.py:221: SyntaxWarning: "is" with a literal. Did you mean "=="?

Second, All genes are classified into the same orthologous group OG1.

My run script is as follows. python ~/2_software/possvm-orthology-master/possvm.py -i all.trimal.contree -p ortho -skiproot -refsps root -method mclw -o ./

Could you please give me some suggestions to solve the above problem? I would be very grateful.

xgrau commented 1 month ago

Dear Z,

Thanks, I'm aware of this warning about the use of ==. Since it depends on an external library (ete3) I can't fix it myself though. Maybe they'll do it in a future release.

Regarding your issue in particular, I'm not sure what's wrong — difficult to tell without a toy example input. I'd suggest you double check the species info is correctly encoded in the gene names (by default, a prefix separated from the gene name by an underscore character _).

Cheers