Exporting a tsv table and metadata file separately from a BIOM format file.

[matomoniwano]

In order to exchange contingency tables and the corresponding metadata among other researchers, I was packaging a tsv table with sample and observation metadata into BIOM file with biom add-metadata command.

However, I was not able to find a way to export a tsv table and its metadata SEPARATELY from the BIOM file, meaning I would like to have two output files, a tsv table and a text file that includes all the metadata that I added earlier (sample name, taxonomy, environmental data, and so on.).

There has been a relevant issue in the past, (/issues/632), but it's been 4 years ever since this issue was closed.

I was wondering if there is any way that I can export a table and metadata separately or the developers are working on the reverse function of biom add-metadata .

Thanks

NOTE: I do not wish to use the convert option --header-key 'taxonomy' --tsv-metadata-formatter since the metadata is merged in the table.

[raissameyer]

Hi BIOM dev team,

Running into the same problem. I'd really like to work with BIOM files but if one can't handle the components of the biom file separately I think it would impede exchangeability.

I tried pretty much the same thing that @matomoniwano described above.

Any advice would be greatly appreciated!

[wasade]

Hi Raissa, thank you for reaching out. We currently do not have a way to do this from the command line but it can be done through the Python API without too many steps. See [here]( http://biom-format.org/documentation/generated/biom.table.Table.metadata_to_dataframe.html#biom.table.Table.metadata_to_dataframe) for an example of obtaining metadata on an axis in a pandas DataFrame. We would certainly welcome a pull request to expose this functionality! But we haven't been able to get to this particular task yet.

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On Fri, Nov 15, 2019, 7:49 AM Raissa Meyer ***@***.***> wrote: Hi BIOM dev team, Running into the same problem. I'd really like to work with BIOM files but if one can't handle the components of the biom file separately I think it would impede exchangeability. I tried pretty much the same thing that @matomoniwano <https://github.com/matomoniwano> described above. Any advice would be greatly appreciated! — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#820?email_source=notifications&email_token=AADTZMXPTALHH57PGRJJRR3QT3AIPA5CNFSM4IIFN7M2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEEF22TY#issuecomment-554413391>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AADTZMWVU7KBCWZP2BOA2YTQT3AIPANCNFSM4IIFN7MQ> .

[raissameyer]

Hi @wasade
thanks for the quick response, I'll check it out.

@pieterprovoost this is the issue we discussed in the call. Linking you to it in case you're interested in checking it out 😃

[wasade]

Great!! If there is interest in a PR, I would aim to rapidly review and additionally to cut a micro release quickly after merge.

[pieterprovoost]

@wasade Is it acceptable if I just wrap metadata_to_dataframe() in the CLI? I have a proof-of-concept here: pieterprovoost@c6a7d0f

[wasade]

@pieterprovoost, yes! That's wonderful! Would you like to issue that as a PR?

[pieterprovoost]

Created PR #826

[wasade]

Fixed in #826. Thanks again @pieterprovoost -- I'll see if we can issue a release this week.