Genbank parser doesn't handle feature attributes with colliding names.

Question

Genbank parser doesn't handle feature attributes with colliding names.

TimothyStiles opened this issue a year ago · 5 comments

TimothyStiles commented a year ago

Describe the bug

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

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

Client information

OS: Mac OSX 0.15.7
Golang version: 1.21
poly version v0.27.1

Answer 1 · 2023-10-06T23:22:41.000Z

adding @Koeng101 to the issue.

Answer 2 · 2023-12-06T18:30:27.000Z

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

Answer 3 · 2023-12-12T03:55:02.000Z

Working on this now!

Answer 4 · 2023-12-12T04:15:12.000Z

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.

Answer 5 · 2024-02-10T18:28:14.000Z

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