Write fcs function

[mbuttner]

Pytometry should include a function to export an anndata file to fcs using the Gating ML 2.0 version and FCS standard 3.*

[quentinblampey]

In scyan, there is this write_fcs function that we could move to pytometry
But it uses fcswrite internally, and it seems this repository is not actively maintained, what do you think?

EDIT: we can also add this write_csv function, since FlowJO supports reading from CSV files

[grst]

A couple points from the discussion in scverse/governance#64:

• There was some agreement that it makes sense to keep IO separate from the rest in readfcs. I'm sure they would be happy to include functions for writing FCS filese
• Here it could make sense to either switch to @whitews's FlowIO package or use it as another backend in readfcs.

adata = readfcs.read("sample.fcs", backend="fcsparser")
adata = readfcs.read("sample.fcs", backend="flowio")
readfcs.write(adata, "sample.fcs", backend="flowio")

• Or maybe to add support for AnnData directly in FlowIO?

pip install flowio[anndata]

adata = flowio.FlowData('sample.fcs').to_anndata()

[Zethson]

Please let me know if someone wants write access to readfcs. I think that eventually renaming it to fcs-io would be even better then but one step after another.

[maltekuehl]

Pinging @harryhaller001 who recently created https://github.com/harryhaller001/anndata-fcs on this issue. I think having a single package that takes care of both input and output would make the most sense, so that it can then be used with pytometry and others. Now that both implementations already use flowio, perhaps there is some potential to bring efforts together?

[mbuttner]

I think that it would be great to bundle our efforts here. Is there any interest from @harryhaller001 to work together?

[mbuttner]

Please let me know if someone wants write access to readfcs. I think that eventually renaming it to fcs-io would be even better then but one step after another.

@Zethson what is the current status on the readfcs package? I quite liked the idea to provide two different backends (for the fcsparser and flowIO, but it also comes with greater overhead in maintenance.

[harryhaller001]

I think that it would be great to bundle our efforts here. Is there any interest from @harryhaller001 to work together?

Sure. I would be interested. Writing fcs data is currently implemented by the fcswrite and the FlowIO package, both without anndata support. I would prefer to start the write_fcs from anndata implementation here and move the code to an external dependency later (e.g. fcs-io).

[Zethson]

@Zethson what is the current status on the readfcs package?

I highly doubt it'll be further developed. Not a priority at all