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Trouble with db.region(..., completely_within=True) #234

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Lservi opened this issue Jun 19, 2024 · 1 comment
Open

Trouble with db.region(..., completely_within=True) #234

Lservi opened this issue Jun 19, 2024 · 1 comment

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@Lservi
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Lservi commented Jun 19, 2024

I'm using your amazing library to work with some DNA modifications, which generally are 1 or 2 nucleotide "spots". while using the "completely_within=True" param I'm not getting anything back as I show in this example:

list(db.region(region=("scaffold_1", 6326, 6350), completely_within=True))
> []
list(db.region(region=("scaffold_1", 6326, 6350)))
> [<Feature region (scaffold_1:1-4111717[+]) at 0x7adce9063790>,
 <Feature tRNA (scaffold_1:6316-6404[+]) at 0x7adce94ca5d0>]

Am I using this parameter properly or is it just a bug?

Thanks in advance.

@aliciaaevans
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I would not expect the features that were returned without that param to be included with it since they overlap the region but are not completely within the bounds of that region.

Can you provide some sample input showing some entries you are expecting to be returned? For example, some of those spots that are located within the range 6326 to 6350.

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