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
https://bitbucket.org/lorainelab/integrated-genome-browser/pull-request/102/igbf-103/diff
The current pull request addresses the issue but for in the case of graphs.
IGBF-144 issue is created to address graphs.
Story: IGBF-103 (Save all the data, not just the current chromosome)
Date: August 4, 2014
Intro: Previously in IGB, when a user saved a track IGB would just save data loaded in the current track, not from all the chromosomes. Changes have been made so that when a user saves a track IGB will save all the data that has been loaded, not just the current chromosome. This issue is now ready for testing.
Story IGBF-103 was tested on:
*IGB Version: 8.2.0
-(My Mac) Mac OS X Version 10.9.3 using JRE version 1.8.0_11-b12 Java HotSpot(TM) 64-Bit Server
The story was tested using this workflow:
1) I loaded a BED file, changed it to whole genome load mode, and then saved it. In then reloaded it into the viewer and made sure it looked the same.
-Observed: The saved file contains the same data as the orginal file. = PASS
2) I loaded a BED detail file and then saved it and I made sure that fields 13 and 14 were saved correctly.
-Observed: The saved BED Detail file contained fields 13 and 14 appropriately. Nothing was truncated. = PASS
3) I loaded a GTF file and saved it as a BED file. Then I checked to see if the BED file was saved properly.
-Observed: The BED file was saved properly. = PASS
4) I opened a GTF file and loaded it on 2 chromosomes (out of 7 possible chromosomes). Then I checked to see if the BED file contained data just for those 2 chromosomes that were loaded.
-Observed: The BED file only contained data for the 2 chromosomes that had been loaded. = PASS
5) I made a new track from another track using track operations and then I saved the output. Then I made sure that all places where data were added to the new track got saved.
-Observed: All of the places where data were added to the new track were saved properly. = PASS
Summary:
Story IGBF-103 was tested on my Mac. My observations were in accordance with the IGB Team's expectations.
Ideas for testing:
1) Load a BED file, change it to whole genome load mode, and the save it. Next, load it back into the viewer and make sure it looks the same.
2) Load a BED detail file and make sure it saves fields 13 and 14 correctly. Check that nothing gets truncated.
3) Load a GTF file and try to save it as BED format. You can GTF files from Galaxy. Look at output of CuffLinks.
4) Load a GTF file, load part of it on several different chromosomes, save it as BED, and then make sure that the load data got saved.
5) Make a new track from another track using track operations and then save the output. Make sure that all places where data were added to the new track get saved. Open the saved file and check that it looks right.