No ensembl.tsv in the utils folder about st-net HOT 13 OPEN

Sorry,I met the same question.I don't know if you've solved the problem. @JiawenChenn
Or could you tell us how to slove this problem? @bryanhe

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it seems that the file can be download from https://www.genenames.org/download/custom/ if you have a look at ensembl.py @JiawenChenn But i have got another problem.
When i run python3 -m stnet prepare spatial.I get ValueError: need at least one array to concatenate .Do you have the same problem?

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@jiangdydy Have you resolve the concatenate error?

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@jiangdydy Have you resolve the concatenate error? I have the same problem.

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I have the same problem

FileNotFoundError: [Errno 2] No such file or directory: '/home/chenyang/ST-Net/stnet/utils/ensembl.tsv'
could anyone help me?
my email is [email protected]

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Thanks @jiangdydy a lot,
I download the emseml.tsv from https://www.genenames.org/cgi-bin/download/custom?col=gd_hgnc_id&col=gd_app_sym&col=gd_app_name&col=md_ensembl_id&status=Approved&status=Entry%20Withdrawn&hgnc_dbtag=on&order_by=gd_app_sym_sort&format=text&submit=submit
you can download it

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兄弟们,要不要加个微信,讨论怎么复现代码?
我的微信是: cyang23333

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Thanks @jiangdydy .

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it seems that the file can be download from https://www.genenames.org/download/custom/ if you have a look at ensembl.py @JiawenChenn But i have got another problem.
When i run python3 -m stnet prepare spatial.I get ValueError: need at least one array to concatenate .Do you have the same problem?

Probably because the data is empty?

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@jiayiwus1x it is because in the load_raw function located in stnet > cmd > prepare > spatial.py, where the variable "images" is initialized, it is trying to match a file structure that they didn't give us. I assume in the version they were using, the data was structured into folders by patient. @chenyang1999 seems to have a fix here: #4, however, I just modified the spatial.py script to change the location it tries to match instead of the file structure. However, even after that fix, I and others are having the issue where there is a file called "_Coords.tsv" missing. Good luck!

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@jiayiwus1x it is because in the load_raw function located in stnet > cmd > prepare > spatial.py, where the variable "images" is initialized, it is trying to match a file structure that they didn't give us. I assume in the version they were using, the data was structured into folders by patient. @chenyang1999 seems to have a fix here: #4, however, I just modified the spatial.py script to change the location it tries to match instead of the file structure. However, even after that fix, I and others are having the issue where there is a file called "_Coords.tsv" missing. Good luck!

我不是很关心癌症具体的位置,我只是想预测空间转录组基因表达,所以去掉这tumor部分的预测就行了

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@chenyang1999 Where do you remove the tumor prediction part? It seems to be fairly embedded in several parts within the processing script.

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ValueError: need at least one array to concatenate

Have the same ValueError: need at least one array to concatenate error as above. May I know is there any solution for it? @jiangdydy @engrodawood @mjt-zdz @JiawenChenn @jiayiwus1x @andrewbrown1022

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