Details
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Type:
New Feature
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: None
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Labels:
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Story Points:4
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Epic Link:
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Sprint:Spring 2019 Sprint 1, Spring 2019 Sprint 2
Description
Write a python program that accepts data from Ensembl BioMart and from UCSC Table Browser EnsGene table and produces bed14 format file.
- Field 4 contains Ensembl transcript id (e.g., ENSCSAT00000001292.1)
- Field 13 contains Ensembl gene id for the transcript (e.g., ENSCSAG00000003267.1) from BioMart
- Field 14 contains descriptive information from BioMart
The key work of this script is to cross-reference gene ids and functional descriptions obtained from BioMart with transcript ids obtained from UCSC Genome Browser.
We developed this so that we could include vervet (African green monkey) gene annotations in IGB Quickload, a user request.
Attachments
Issue Links
- relates to
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IGBF-1401 Add Chlorocebus sabaeus ("green monkey") to IGB quickload
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- Closed
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Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-1395 [ 17470 ] |
| Status | Open [ 1 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Open [ 1 ] |
| Sprint | Spring 2019 Sprint 1 [ 59 ] | Spring 2019 Sprint 1, Spring 2019 Sprint 2 [ 59, 60 ] |
| Rank | Ranked higher |
| Status | Open [ 1 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Pull Request Submitted [ 10101 ] |
| Assignee | Jill Jenkins [ jill ] |
| Status | Pull Request Submitted [ 10101 ] | Needs Testing [ 10002 ] |
| Status | Needs Testing [ 10002 ] | Open [ 1 ] |
| Assignee | Jill Jenkins [ jill ] |
| Description |
Write a python program that accepts data from Ensembl BioMart and from UCSC Table Browser EnsGene table and produces bed14 format file.
* Field 4 contains Ensembl transcript id (e.g., ENSCSAT00000001292.1) * Field 13 contains Ensembl gene id for the transcript (e.g., ENSCSAG00000003267.1) from BioMart * Field 14 contains descriptive information from BioMart The key work of this script is to cross-reference gene ids and functional descriptions obtained from BioMart with transcript ids obtained from UCSC Genome Browser. We developed this so that we could include vervet (African green monkey) gene annotations in IGB Quickload, a user request. |
Write a python program that accepts data from Ensembl BioMart and from UCSC Table Browser EnsGene table and produces bed14 format file.
* Field 4 contains Ensembl transcript id (e.g., ENSCSAT00000001292.1) * Field 13 contains Ensembl gene id for the transcript (e.g., ENSCSAG00000003267.1) from BioMart * Field 14 contains descriptive information from BioMart The key work of this script is to cross-reference gene ids and functional descriptions obtained from BioMart with transcript ids obtained from UCSC Genome Browser. We developed this so that we could include vervet (African green monkey) gene annotations in IGB Quickload, a user request. |
Jill requests to upload a new version - moving back to "To-Do" so she can re-use this Jira issue to track progress.
New version added via branch IGBF-1522b. Pull request submitted.
| Status | Open [ 1 ] | Pull Request Submitted [ 10101 ] |
IGBF-1522b merged into master.
| Assignee | Jill Jenkins [ jill ] |
| Resolution | Done [ 10000 ] | |
| Status | Pull Request Submitted [ 10101 ] | Closed [ 6 ] |
Re-assigning to original developer.
| Assignee | Jill Jenkins [ jill ] |
Updated to use command line options for more flexible invocation.
| Workflow | Loraine Lab Workflow [ 18238 ] | Fall 2019 Workflow Update [ 20014 ] |
| Workflow | Fall 2019 Workflow Update [ 20014 ] | Revised Fall 2019 Workflow Update [ 22141 ] |
Notes for developer:
Details:
git checkout -b
IGBF-1522Along the way, move the issue through the kanban board. Before issuing pull request, move the issue to "Needs first level review" and add a link to your fork and branch as a comment.