CDCgov / CDCgov/seqsender

[FEATURE REQUEST] Add Biosample for Genebank Submission

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enhancement
Dominant language
Python
Stars
2
Forks
0
Avg merge
20m
Merged PRs (30d)
5

Description

Is this feature for general SeqSender usage or for submitting to a specific database, if so what database?
Genbank

Is your feature request related to a problem? If so please describe.
The metadata table includes the BioProject ID as a column, which is incorporated into the generated .sqn file. In contrast, the BioSample ID is not included as an input column in the metadata table.

Describe the solution you'd like
Include the biosample as one column of the input metadata table. So that the .sqn file could include both bioproject and biosample ID, like:

user {
      type str "DBLink",
      data {
        {
          label str "BioProject",
          num 1,
          data strs {
            "PRJEBXXXXX"
          }
        },
        {
          label str "BioSample",
          num 1,
          data strs {
            "SAMNXXXXXXXX"
          }
        }
      }
    },

Additional context
If the feature has been implemented, please let me know how to use it.

Contributor guide

No contributing guide indexed for this repository

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by tracing how the input metadata table is read and how BioProject IDs are incorporated into the generated .sqn file. Add the BioSample metadata path alongside it, then verify that GenBank submissions include both BioProject and BioSample IDs and document how to use the new column.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
database
Issue type
Feature
Difficulty
3/5
Estimated time
1-2 days
Activity status
Quiet
Clarity
Mostly clear
Newbie friendliness
64/100

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