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Add support to specify the start and end of a date range for sequence collection dates #6

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elray1 opened this issue May 7, 2024 · 3 comments
Open

Add support to specify the start and end of a date range for sequence collection dates #6

elray1 opened this issue May 7, 2024 · 3 comments
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needed for eval
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Variant Nowcast L...

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@elray1
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elray1 commented May 7, 2024

We will typically just need to get clade assignments (and summarize to counts of clade assignments) for samples that were collected within a particular date range. We should be able to specify those dates as part of a call to assign_clades. This is related to discussion in reichlab/variant-nowcast-hub#3 in that we'll need to be sure that when we pull the sequence data, we get everything that has a collection date within the specified range.

For more specificity, here's a suggestion that I'm not at all committed to: we could introduce command line arguments seq_start_date and seq_end_date and keep anything with seq_start_date <= collection_date <= seq_end_date.
@bsweger
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bsweger commented Jun 21, 2024

@elray1 quick clarification: how would these start and end dates interplay with the --released-after parameter we're already using when getting sequence data via the NCBI API?

Is the starting range of the sequence collection date the same date we'd use as --released-after on the API call, or a different parameter altogether?

@elray1
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elray1 commented Jun 21, 2024

I believe it should at least be closely related (maybe released-after = seq_start_date - 1??). But I'm not sure. Do you know of a place where these dates are documented?

@bsweger
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bsweger commented Jun 21, 2024

I couldn't find anything definitive on the relationship between the API's released-after parameter and the collection-date in the metadata.

collection-date definition from the metadata schema:

The collection date for the sample from which the viral nucleotide sequence was derived

reference to "released after" property of NCBI's virus dataset downloads:

genomes released after

Let's chat about how to get a definitive answer. In the meantime, I'll use your released-after = seq_start_date - 1 to get started.

@bsweger bsweger transferred this issue from reichlab/variant-nowcast-hub Aug 6, 2024
@bsweger bsweger added this to the Variant Nowcast Launch milestone Aug 6, 2024
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needed for eval
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Variant Nowcast Launch
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@bsweger @elray1