Details
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Type:
Task
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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:None
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Story Points:0.5
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Epic Link:
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Sprint:Spring 8 : 11 May to 25 May, Spring 9 : 25 May to 8 Jun
Description
Dr. Beth Krizek (krizek@biol.sc.edu) has let us know about a problem with parsing the attached file.
It is GFF format, but when we view it in IGB, only a small part of the data are being shown.
When you click on one of the items, the "Id" field does not exactly match the "Id" fields in the GFF "extra feature" field, the section of semi-colon-separated characters in the final field.
Please investigate why this is happening. Is there a problem with our GFF parsing code, or is it an issue with the formatting of this file?
In addition, take a look at the unit testing code for this format. If the data in this file are OK, we should use some lines of data in the file to add new test cases to the testing code.
The file was generated using a program called "FIMO" which is a popular tool in bioinformatics. Therefore we should do our best to support visualizing the output in IGB.
Attachments
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-1765 [ 17855 ] |
| Rank | Ranked higher |
| Rank | Ranked higher |
| Assignee | Shamika Gajanan Kulkarni [ shamika ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Attachment | Screen Shot 2020-05-13 at 5.54.07 PM.png [ 14725 ] |
| Attachment | fimo file-version 1.JPG [ 14726 ] | |
| Attachment | fimo-version1-Windows.JPG [ 14727 ] |
| Attachment | Screen Shot 2020-05-13 at 6.49.45 PM.png [ 14728 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Assignee | Shamika Gajanan Kulkarni [ shamika ] | Philip Badzuh [ pbadzuh ] |
| Sprint | Spring 8 : 11 May to 25 May [ 94 ] | Spring 8 : 11 May to 25 May, Spring 9 : 25 May to 8 Jun [ 94, 95 ] |
| Rank | Ranked higher |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Assignee | Philip Badzuh [ pbadzuh ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Assignee | Nowlan Freese [ nfreese ] |
| Status | Post-merge Testing In Progress [ 10003 ] | Merged Needs Testing [ 10002 ] |
| Assignee | Nowlan Freese [ nfreese ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Assignee | Nowlan Freese [ nfreese ] |
| Status | Post-merge Testing In Progress [ 10003 ] | Merged Needs Testing [ 10002 ] |
| Attachment | 914_SmokeTestData.png [ 14743 ] | |
| Attachment | 916_withMerge_SmokeTestData.png [ 14744 ] | |
| Attachment | 916_withMerge_withFimo.png [ 14745 ] |
| Assignee | Nowlan Freese [ nfreese ] | Ann Loraine [ aloraine ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
| Assignee | Ann Loraine [ aloraine ] |
| Attachment | fimo_NO-ID.gff [ 14746 ] |
| Link | This issue relates to IGBF-2406 [ IGBF-2406 ] |