Stereoseq expected directory structure

[aadimator]

Hi Team,

Would it be possible to document the expected directory structure for the stereoseq reader? The results we got from the stereoseq team don't follow the directory structure being assumed by this implementation. So, if it's properly documented, like the folder names to expect and which files should be put in which folder, then we can manually restructure our directories to conform to this stereoseq reader implementation.

As an example, this is the results folder we receive from the Stereoseq team:

Thanks a bunch.

[LucaMarconato]

Thanks @aadimator for reporting this. @LLehner could you please have a look into this?

• Precisely, please I would add a line in the docstring of the stereoseq function specifying which stereoseq data version we expected and adding a link to the technical document from the STOmics website that specifies the file structure.

@aadimator which version of the data is the screenshot referring to?

[LucaMarconato]

This comment: #70 (comment) is from July 31st, 2023, therefore I believe that the reader is designed for the format 7.0.0: https://github.com/STOmics/SAW/tree/0808e44619f84b67d44c063b2fd24762f6633051/Documents/FileFormat and that the latest 7.1.1 (or even 7.1.0) is not supported.

[aadimator]

Thanks @aadimator for reporting this. @LLehner could you please have a look into this?

• Precisely, please I would add a line in the docstring of the stereoseq function specifying which stereoseq data version we expected and adding a link to the technical document from the STOmics website that specifies the file structure.

@aadimator which version of the data is the screenshot referring to?

We got this as is from the Stereoseq Team, and I think it's not following any particular format. I think I'll have to manually rename/place the files into their relative/expected directories. I'll try to follow the SAW 7.0.0. format for now.

[z-spider]

saw 8.0 has new output directory structure

from this manual:
https://en.stomics.tech/service/new-saw-operation-manual.html

[LucaMarconato]

Thank you for the comment. For the moment I will restrict the reader to operate only on 7.x. Unfortunately we don't have the bandwidth to support the latest version at the moment. But a community contribution is welcomed and we would be happy to review the code in such case.

Todo for us:

• restrict the stereoseq reader to 7.x.