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Data model - database #18

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skrakau opened this issue Dec 24, 2020 · 5 comments
Open

Data model - database #18

skrakau opened this issue Dec 24, 2020 · 5 comments
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@lkuchenb
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core functionality
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0.9.0

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@skrakau
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skrakau commented Dec 24, 2020

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@skrakau skrakau added the enhancement New feature or request label Dec 24, 2020
@skrakau skrakau changed the title Data structure Data model - database Dec 24, 2020
@skrakau skrakau added this to the 1.0.0 milestone Dec 24, 2020
@skrakau skrakau added core functionality and removed enhancement New feature or request labels Dec 24, 2020
@lkuchenb
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lkuchenb commented Dec 24, 2020 •
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Current draft proposal

metapep

@skrakau skrakau pinned this issue Dec 24, 2020
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skrakau commented Jan 6, 2021 •
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prediction_id is not needed ...

@skrakau
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skrakau commented Jan 8, 2021 •
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Regarding the size of the peptide tables and memory, for my current datasets:

# proteins:
1,855,616

# non-unique peptides (9mers) across proteins (multiple occurrences within one protein not counted!):
552,451,599

# unique peptides:
392,722,935

Peak memory for generate_peptides:
peak_vmem=176,900,708

@lkuchenb
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lkuchenb commented Jan 17, 2021 •
edited by skrakau
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New model containing entities as an additional link between microbiomes and proteins, modelling the linking entity aka taxa, MAGs/bins or assembly contigs

metapep

New color coding:

Orange -> provided or pre-computed entities
Gray -> associations
Purple -> Pipeline output

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skrakau commented Jan 18, 2021

protein_orig_id ist missing

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