Added MetatranscriptomicTypeV10

[charles-cowart]

@AmandaBirmingham @RodolfoSalido additional test is added. Thank you for your patience. Please feel free to continue reviewing!

[charles-cowart]

@RodolfoSalido should be okay. Since we decided on this one being v10, I took our legacy MetatranscriptomicSampleSheet class and renamed it MetatranscriptomicSampleSheetv0. I thought zero’th version was somewhat appropriate.

On Feb 8, 2024, at 4:22 PM, RodolfoSalido @.***> wrote:

@RodolfoSalido commented on this pull request.

In metapool/init.py https://urldefense.com/v3/__https://github.com/biocore/metagenomics_pooling_notebook/pull/178*discussion_r1483731908__;Iw!!Mih3wA!FyQu3zjbXIQObqCUOXoXXNiKszGoxUWjtfDlzvKxoB6Y97-fRMW9UySexqReBW31aFtnj7Tf1AFGJSdNMsGhSuKf$:

@@ -5,9 +5,9 @@ from .sample_sheet import (sample_sheet_to_dataframe, make_sample_sheet, AmpliconSampleSheet, MetagenomicSampleSheetv90, MetagenomicSampleSheetv100, AbsQuantSampleSheetv10,

• MetatranscriptomicSampleSheet, demux_sample_sheet,
• MetatranscriptomicSampleSheetv0, demux_sample_sheet, typo? Should be MetatranscriptomicSampleSheetv10

— Reply to this email directly, view it on GitHub https://urldefense.com/v3/__https://github.com/biocore/metagenomics_pooling_notebook/pull/178*pullrequestreview-1871476319__;Iw!!Mih3wA!FyQu3zjbXIQObqCUOXoXXNiKszGoxUWjtfDlzvKxoB6Y97-fRMW9UySexqReBW31aFtnj7Tf1AFGJSdNMoZl9Ru1$, or unsubscribe https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/AKFU7E5TFFRI7ZN4F3N2T4DYSVT4RAVCNFSM6AAAAABC6XUBW2VHI2DSMVQWIX3LMV43YUDVNRWFEZLROVSXG5CSMV3GSZLXHMYTQNZRGQ3TMMZRHE__;!!Mih3wA!FyQu3zjbXIQObqCUOXoXXNiKszGoxUWjtfDlzvKxoB6Y97-fRMW9UySexqReBW31aFtnj7Tf1AFGJSdNMhQsi86S$. You are receiving this because you authored the thread.

[antgonza]

Just as a reminder, there are lost of sample sheets (not sure about versions) that we need to recover from before the SPP so my guess is that the first version of the SPP is not the actual first version ...

[charles-cowart]

Left a comment on sample_sheet.py to make sure we are passing along the columns ['total_rna_concentration_ng_ul','vol_extracted_elution_ul'] to the samplesheet.

Okay I'm going to circle back on this after I issue the PR resolving these columns that aren't making it from sample-sheet to prep-info file, just to make sure we implement it right here as well.

[charles-cowart]

Hi @RodolfoSalido ! If you're okay with everything and approve this PR, I can merge it into master and we can test it against your use case. I don't expect any issues but if there is we can fix them.

[RodolfoSalido]

Sounds good to me.

On Feb 12, 2024, at 12:02 PM, Charles Cowart @.***> wrote:

Hi @RodolfoSalido https://github.com/RodolfoSalido ! If you're okay with everything and approve this PR, I can merge it into master and we can test it against your use case. I don't expect any issues but if there is we can fix them.

— Reply to this email directly, view it on GitHub https://github.com/biocore/metagenomics_pooling_notebook/pull/178#issuecomment-1939468739, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADEVFI5JFBBYAJKNRZQOK2LYTJYLRAVCNFSM6AAAAABC6XUBW2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSMZZGQ3DQNZTHE. You are receiving this because you were mentioned.

[charles-cowart]

I'll resolve the issue w/lint after the meeting.

[charles-cowart]

resolved

[charles-cowart]

Thanks @RodolfoSalido ! The new Metatranscriptomic type is merged in. If you want to pull down the latest version of master and give it a try, please feel free. Or if you want to meet or zoom and test through everything together I can do that as well.