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biocore / metagenomics_pooling_notebook

Jupyter notebooks to assist with sample processing
MIT License
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remove manual creation of sample-sheet objects #194

Open charles-cowart opened 5 months ago

charles-cowart commented 5 months ago

SampleSheet() objects can be instantiated from csv files or using make_sample_sheet(). They can also be created manually by instantiating a blank object and adding in individual fields manually. This may occur in notebooks and does occur in unittests. It would be beneficial to replace these instantiations in the unittests and notebooks, as tests are often used as tutorials on proper use.

charles-cowart commented 5 months ago

Hello @mmbryant23 @RodolfoSalido @antgonza. I noticed that the legacy function _add_data_to_sheet() takes a list of lane numbers as a parameter. To my knowledge, we've always only used one lane value in a sample-sheet. Would you guys mind if I corrected this to accept just an integer value and remove the looping code that would duplicate a sample across multiple lanes? I've confirmed that the test code only uses lists of [1].

RodolfoSalido commented 5 months ago

Definitely a vestige of how we used to make samplesheets. The SPP handles lanes differently now and I’m confident you can can remove the looping code.

-Rodolfo

On May 2, 2024, at 8:31 PM, Charles Cowart @.***> wrote:

Hello @mmbryant23 https://github.com/mmbryant23 @RodolfoSalido https://github.com/RodolfoSalido @antgonza https://github.com/antgonza. I noticed that the legacy function _add_data_to_sheet() takes a list of lane numbers as a parameter. To my knowledge, we've always only used one lane value in a sample-sheet. Would you guys mind if I corrected this to accept just an integer value and remove the looping code that would duplicate a sample across multiple lanes? I've confirmed that the test code only uses lists of [1].

— Reply to this email directly, view it on GitHub https://github.com/biocore/metagenomics_pooling_notebook/issues/194#issuecomment-2092064155, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADEVFI43MG6TJLSITARS2TTZAMAKDAVCNFSM6AAAAABGHT6ZLWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAOJSGA3DIMJVGU. You are receiving this because you were mentioned.

charles-cowart commented 5 months ago

Definitely a vestige of how we used to make samplesheets. The SPP handles lanes differently now and I’m confident you can can remove the looping code.

thank you Rodolfo!