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bebop / poly

A Go package for engineering organisms.
https://pkg.go.dev/github.com/bebop/poly
MIT License
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Genbank parser doesn't handle feature attributes with colliding names. #383

Open TimothyStiles opened 10 months ago

TimothyStiles commented 10 months ago

Describe the bug

The genbank parser cannot handle repeating attribute keys like with /db_xref below:

Screen Shot 2023-10-06 at 2 01 30 PM

Severity of the bug

This is blocking Ark's ability to cross reference other databases. (priority)

Steps to reproduce

You can debug this by debugging BenchmarkRead(b *testing.B){} in genbank_test.go within a couple of feature extraction loops you'll see that db_xref only keeps the last reference.

Expected behavior

We need to be able to track attributes with the same key name. List of tuples?

Screenshots

Screen Shot 2023-10-06 at 3 39 43 PM

Client information

TimothyStiles commented 10 months ago

adding @Koeng101 to the issue.

github-actions[bot] commented 8 months ago

This issue has had no activity in the past 2 months. Marking as stale.

carreter commented 8 months ago

Working on this now!

carreter commented 8 months ago

This should be an easy fix, but the entire genbank parser needs to be reworked, and it seems like it won't be trivial. I'll open a separate issue.

github-actions[bot] commented 6 months ago

This issue has had no activity in the past 2 months. Marking as stale.