help converting .biom file to .spf file in qiime2-2023.7 in conda

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(qiime2-2023.7) sam@Samss-MacBook-Air mohammad % biom convert -i /Users/sam/mohammad/deblur_output_exported/feature-table_w_tax.biom -o feature-table_w_tax.spf --to-json --table-type="OTU table" --process-obs-metadata taxonomy

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Hi @Sam_Ola,
We would be more able to help you if you could include some additional information!
Did you get an error when you ran this command?
Can you give us a little overview of what you are trying to do?
It looks like you are trying to convert a biom to a .spf and you want the OTU taxonomy labels to a list?

Also, I am not familar with a .SPF file. Can you explain what that is? Additionally, I don't see documentation that indicates that this is a valid file format for biom convert. But I could be wrong about that I'm not a biom convert expert!

For future reference, the more context you can provide, the faster and more effective our answer will be! :qiime2:

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I have a BIOM table (with taxonomy added as metadata)- "feature-table_w_tax.biom" file created in qiime2-2023.7 in conda. However I am trying to get significant abundant visual analysis done in the STAMP software. The file input in STAMP are1) feature table in ".spf" format and 2) metadata. I tried converting my "feature-table_w_tax.biom" file to .spf file using the command below

pip install biom-format

(qiime2-2023.7) sam@Samss-MacBook-Air mohammad % biom convert -i /Users/sam/mohammad/deblur_output_exported/feature-table_w_tax.biom -o feature-table_w_tax.spf --to-json --table-type="OTU table" --process-obs-metadata taxonomy

The output was a "feature-table_w_tax.spf" file which I ran in STAMP and got the error 'Unknown parsing error'

Is there a better way of creating this STAMP accessible file from the .BIOM file I have ?

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Hi @Sam_Ola,
Looking through the STAMP docs: I don't think the input for STAMP is a .spf file, I think it is a .tsv. I again could be wrong, I am not very familiar with STAMP. Could you try using BIOM convert to convert your file to a .tsv and then try running STAMP again?

Also, I do not know if STAMP is being actively maintained. Their github was last updated in 2020 and the last official release of the software was in 2015.

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