No ensembl.tsv in the utils folder

[JiawenChenn]

Hi Bryan,

I am trying to run the code. I download the stent folder and put it into /lib/python3.6/site-packages/ . And I also downloaded the whole folder and run the setup.py to set up the environment. I downloaded the data from https://data.mendeley.com/datasets/29ntw7sh4r/2 which is the breast cancer data. I put the stent.cfg file in my test folder and run python3 -m stnet prepare spatial from the test folder but it shows the following error:

FileNotFoundError: [Errno 2] No such file or directory: 'my environment path/lib/python3.6/site-packages/stnet/utils/ensembl.tsv'

My cfg file looks like this:
SPATIAL_RAW_ROOT = "test folder"/input
SPATIAL_PROCESSED_ROOT = "test folder"/input-patch

And the data in the input folder is BC23209_C1_stdata.tsv HE_BC23209_C1.jpg spots_BC23209_C1.csv.

I am new to python so maybe my question is silly. It would be super helpful if you can tell me where I am wrong. Thanks!

Jiawen

[jiangdydy]

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

[jiangdydy]

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?

[engrodawood]

@jiangdydy Have you resolve the concatenate error?

[mjt-zdz]

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

[chenyang1999]

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 374263410@qq.com

[chenyang1999]

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

[chenyang1999]

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

[JiawenChenn]

Thanks @jiangdydy .

[jiayiwus1x]

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?

[andrewbrown1022]

@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!

[chenyang1999]

@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

[andrewbrown1022]

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

[johnchen99]

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