Doesn't work for the the sequences in variable lengths.

[ruizhideng]

Hi @AvantiShri,

Thanks for the amazing work!

In the following notebook, you mentioned the pipeline also works for the sequences in different lengths. However, when I was testing the notebook with input data with shape of [100, length, 4], the length ranges from 500-1000 bp, it raised the ValueError: setting an array element with a sequence. The requested array has an inhomogeneous shape after 1 dimensions. The detected shape was (100,) + inhomogeneous part.
Then if I crop the sequences and contribution scores to the same length, it works again. I am wondering is there any version available for the sequences with different length?
https://github.com/kundajelab/tfmodisco/blob/master/examples/simulated_TAL_GATA_deeplearning/TF_MoDISco_TAL_GATA.ipynb

Thank you again!

Best wishes,
Ruizhi

[AvantiShri]

Hi Ruizhi, Sorry for the slow response, and thanks for using tfmodisco! My first thought is whether the outermost iterable is a python list? That is, rather than input data of shape [100, length, 4], you want to provide a python list of length 100 with entries that are arrays, where each array has dimensions (length, 4). As an aside, you may want to use tfmodisco-lite (mentioned in the readme) as that is being actively maintained.

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On Fri, 31 Mar, 2023, 15:56 ruizhideng, ***@***.***> wrote: Hi @AvantiShri <https://github.com/AvantiShri>, Thanks for the amazing work! In the following notebook, you mentioned the pipeline also works for the sequences in different lengths. However, when I was testing the notebook with input data with shape of [100, length, 4], the length ranges from 500-1000 bp, it raised the *ValueError: setting an array element with a sequence. The requested array has an inhomogeneous shape after 1 dimensions. The detected shape was (100,) + inhomogeneous part.* Then if I crop the sequences and contribution scores to the same length, it works again. I am wondering is there any version available for the sequences with different length? https://github.com/kundajelab/tfmodisco/blob/master/examples/simulated_TAL_GATA_deeplearning/TF_MoDISco_TAL_GATA.ipynb Thank you again! Best wishes, Ruizhi — Reply to this email directly, view it on GitHub <#107>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AARSFBR2CQFY6FZOICCTNATW62EZZANCNFSM6AAAAAAWOJTBBI> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[ruizhideng]

Thanks for the reply.

Yes, the outermost iterable is a python list. I am wondering whether you still have the pipeline for that version.

I also tried lite version, it only works for arraries in the same length.

But it's fine. If it's too tricky, I will just pad the input data.