[FEATURE REQUEST] Add ID-style structure comments to GenBank
Open
Nobody has claimed this yet.
enhancement
- Dominant language
- Python
- Stars
- 2
- Forks
- 0
- Avg merge
- 20m
- Merged PRs (30d)
- 5
Description
In addition to adding the metadata to Biosample as expected, ID needs to continue adding fields into GenBank's structure comments. example: https://www.ncbi.nlm.nih.gov/nuccore/PP309127.1
##FluData-START##
EPI_ISOLATE_ID :: EPI_ISL_18527521
NAME :: A/Washington/39/2023
TYPE :: H1
Segment_name :: M
HOST_AGE :: 7
HOST_SEX :: M
PASSAGE :: Original
LOCATION :: United States / Washington
COLLECT_DATE :: 21-Sep-2023
Lineage :: A(H1N1)pdm09
RESIST_TO_OSELTAMIVIR :: Sensitive
RESIST_TO_ZANAMVIR :: Sensitive
SPECIMEN_ID :: WA0956978 ORIGINAL
SENDER_LAB :: Washington State Public Health Laboratory
SEQLAB_SAMPLE_ID :: 3030759156
EPI_SEQUENCE_ID :: EPI2798254
##FluData-END##
Contributor guide
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First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by locating the Python entry points that generate Biosample metadata and GenBank output, then compare the requested structure-comment block with the linked GenBank example. Done means the generated GenBank record includes the FluData fields in the requested format while the existing Biosample metadata continues to be produced.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- data
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100