Open Chao-NNU opened 12 months ago
SandraCastilloPriego
commented
12 months ago I've added some example files in the "data/annotations" section. The problem may be that different versions of EggNog produces different fields and CarveFungi is taking the wrong field. Could you check that your EggNog annotation file is similar to the one I've added: "data/annotations/functional/Saccharomyces_cerevisiae_s288c_sgd_nog.emapper.annotations" ?
Chao-NNU
commented
11 months ago Dear Sandra Castillo, I got a new problem when I tired the new download from github, I could not found these models from the link of http://doi.org/10.5281/zenodo.4436488. [image: image.png] Best wishes! Chao
Sandra Castillo @.***> 于2023年9月8日周五 15:24写道：
I've added some example files in the "data/annotations" section. The problem may be that different versions of EggNog produces different fields and CarveFungi is taking the wrong field. Could you check that your EggNog annotation file is similar to the one I've added: "data/annotations/functional/Saccharomyces_cerevisiae_s288c_sgd_nog.emapper.annotations" ?
— Reply to this email directly, view it on GitHub https://github.com/SandraCastilloPriego/CarveFungi/issues/1#issuecomment-1711202415, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABMLLMYRBYXGMHDTAK4ES73XZLB4VANCNFSM6AAAAAA4PVYAPE . You are receiving this because you authored the thread.Message ID: @.***>
-- 叶超 (Chao Ye) 江南大学国家重点实验室 (State Key Laboratory of Food Science and Technology, Jiangnan University)
SandraCastilloPriego
commented
11 months ago Dear Chao, that is weird. The same link you've written in the email for the modes works for me and it has been downloaded 13 times already. Could you please try again? The link is fine.
Best regards, Sandra
Chao-NNU
commented
11 months ago Dear Sandra That's weird for the link, when I opened the link, it just contains these information, and I had copied them into the folder "/bin/compartmentPredictions/deepModels". [image: image.png]
Sandra Castillo @.***> 于2023年9月18日周一 19:09写道：
Dear Chao, that is weird. The same link you've written in the email for the modes works for me and it has been downloaded 13 times already. Could you please try again? The link is fine.
Best regards, Sandra
— Reply to this email directly, view it on GitHub https://github.com/SandraCastilloPriego/CarveFungi/issues/1#issuecomment-1723193886, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABMLLM4Y7WLP2TUV7HLXTI3X3ATWFANCNFSM6AAAAAA4PVYAPE . You are receiving this because you authored the thread.Message ID: @.***>
-- 叶超 (Chao Ye) 江南大学国家重点实验室 (State Key Laboratory of Food Science and Technology, Jiangnan University)
When I tired to use CreateModelEggNogPool.carveme_pipeline("Scer", "Saccharomyces_cerevisiae_S288C_GCF_000146045.2","data/annotations/functional/example.fasta.emapper.annotations","data/annotations/fasta/example.fasta","data/annotations/localization/example.fasta.npy"), an error happend.
Traceback (most recent call last): File "", line 1, in
File "bin/CreateModelEggNogPool.py", line 382, in carveme_pipeline
fungi_id, eggnog_file)
File "bin/EggNogScoring.py", line 95, in get_gene_to_score_dict
ec_to_score_maximum[ec] = np.max(reaction_scores)
File "<__array_function__ internals>", line 6, in amax
File "/home/chao/anaconda3/envs/py37/lib/python3.7/site-packages/numpy/core/fromnumeric.py", line 2755, in amax
keepdims=keepdims, initial=initial, where=where)
File "/home/chao/anaconda3/envs/py37/lib/python3.7/site-packages/numpy/core/fromnumeric.py", line 86, in _wrapreduction
return ufunc.reduce(obj, axis, dtype, out, **passkwargs)
TypeError: cannot perform reduce with flexible type