Details
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Type:
Bug
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Status: Closed (View Workflow)
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Priority:
Blocker
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Resolution: Fixed
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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:2
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Sprint:Sprint 1, Sprint 2
Description
I noticed this when working with files imported from Galaxy.
If I load a file from Galaxy and change the Load Mode to "Genome," then all the data are loaded into IGB, and if I click a new chromosome, I don't have to then click "Load Data" to see the data. And if I right-click a track label, I see an option to Save the track as a file. However, if I do that, only the data from the current loaded track are saved, even though I've loaded the entire genome.
It would be far, far better if all the data were saved to the file. Otherwise, I would have to click on each chromosome one by one and save the data as multiple files, one per chromosome. This is very tedious and painful and defeats the purpose of having such a nice feature.
Instead, what should happen is that everything the user has loaded into IGB for the selected track should be saved. If there are some file or track types where this is not feasible, then we can omit those, but for tracks loaded from BED, GFF, or GTF files, then we should save out ALL the data that the user has loaded.
By the way, this feature is extremely useful for converting GTF or GFF files to BED. To my knowledge, there is no really good, open source GFF or GTF to bed converter. And so I would LOVE it if we could provide this feature for users, especially now that we are making it very easy for users to run view output of CuffLinks via the Galaxy-to-IGB link.
Attachments
Activity
Field | Original Value | New Value |
---|---|---|
Rank | Ranked higher |
Summary | saving track only saves the current visible chromosome | save all the data, not just the current chromosomesaving track only saves the current visible chromosome |
Summary | save all the data, not just the current chromosomesaving track only saves the current visible chromosome | save all the data, not just the current chromosome |
Summary | save all the data, not just the current chromosome | Save all the data, not just the current chromosome |
Sprint | Sprint 1 [ 1 ] |
Rank | Ranked higher |
Story Points | 1 |
Story Points | 1 | 2 |
Assignee | David Norris [ dcnorris ] | Tarun Santosh [ tkanapar ] |
Sprint | Sprint 1 [ 1 ] | Sprint 2 [ 2 ] |
Sprint | Sprint 1 [ 2 ] | Sprint 1, Sprint 1 [ 2, 3 ] |
Workflow | classic default workflow [ 14544 ] | Loraine Lab Workflow [ 14643 ] |
Rank | Ranked higher |
Status | Open [ 1 ] | In Progress [ 3 ] |
Attachment | Galaxy36-[Cold_Treatment_assembled_transcripts].gtf.gz [ 12493 ] |
Sprint | Sprint 1, Sprint 1 [ 2, 3 ] | Sprint 1, Sprint 2 [ 2, 4 ] |
Rank | Ranked higher |
Status | In Progress [ 3 ] | Needs Testing [ 10002 ] |
Assignee | Tarun Santosh [ tkanapar ] |
Status | Needs Testing [ 10002 ] | Testing In Progress [ 10003 ] |
Status | Testing In Progress [ 10003 ] | Closed [ 6 ] |
Resolution | Fixed [ 1 ] |
Status | Closed [ 6 ] | Testing In Progress [ 10003 ] |
Assignee | Mason Meyer [ mason ] |
Status | Testing In Progress [ 10003 ] | Closed [ 6 ] |
Workflow | Loraine Lab Workflow [ 14643 ] | Fall 2019 Workflow Update [ 19159 ] |
Workflow | Fall 2019 Workflow Update [ 19159 ] | Revised Fall 2019 Workflow Update [ 21272 ] |