Details
-
Type:
Bug
-
Status: Closed (View Workflow)
-
Priority:
Minor
-
Resolution: Fixed
-
Labels:None
Description
- open H sapiens
- Save, then drag in the IGIS Gene Models.GFF file (attached. Make sure to save the .tbi file to the same location as the main file.).
- zoom in until you have 1/2 of a gene showing on screen (make sure the other half is out of the field of view)
- hit load data. See that the IGIS models loaded.
- now zoom out, you will see the IGIS models end at the black and sometimes a single line extends into the grey, unloaded area. The exons on the ends are not showing.
- while zoomed out, hit Load Data again
this test passes if the rest of the exons load onto the 'parent' line. This fails if they are drawn as a new line
Attachments
Issue Links
- relates to
-
BUG-622 File format issues
-
- Closed
-
Activity
| Field | Original Value | New Value |
|---|---|---|
| Assignee | Hiral Vora [ hiralv ] | Alyssa Gulledge [ alyssa ] |
can you attach a file that shows the bug according to Hiral's specifications?
| Assignee | Alyssa Gulledge [ alyssa ] | Lance Frohman [ lfrohman ] |
| Attachment | IGIS Gene Models.gff.gz.tbi [ 11050 ] | |
| Attachment | IGIS Gene Models.gff.gz [ 11051 ] |
attached
| Assignee | Lance Frohman [ lfrohman ] | Hiral Vora [ hiralv ] |
Fixed in r11728.
| Assignee | Hiral Vora [ hiralv ] | Alyssa Gulledge [ alyssa ] |
| Attachment | image.png [ 11052 ] | |
| Attachment | image 2.png [ 11053 ] | |
| Description |
- H sapiens - Open the IGIS Gene Models.GFF file. - you need to zoom into a region so that there is a gene that extends beyond the visible zoom region on both sides on the refseq (the IGIS file is very similar to refseq) - hit load data - now zoom out, you will see the exons on the ends are not showing - if you hit Load Data again, some show and some do not. |
- H sapiens - Open the IGIS Gene Models.GFF file. - you need to zoom into a region so that there is a gene that extends beyond the visible zoom region on both sides on the refseq (the IGIS file is very similar to refseq) - hit load data - now zoom out, you will see the exons on the ends are not showing - if you hit Load Data again, some show and some do not. Steps 1) - select h sapiens - delete refseq - open file IGIS... - select view mode default - region "chr1 : 111,733,948 - 111,735,852" - load data (nothing shows) - region "chr1 : 111,728,298 - 111,744,083" - load data (see #1 below) 2) - select h sapiens - delete refseq - open file IGIS... - select view mode default - (leave full region for chr1) - load data - region "chr1 : 111,728,298 - 111,744,083" (this is how it should look, see #2 below) |
| Description |
- H sapiens - Open the IGIS Gene Models.GFF file. - you need to zoom into a region so that there is a gene that extends beyond the visible zoom region on both sides on the refseq (the IGIS file is very similar to refseq) - hit load data - now zoom out, you will see the exons on the ends are not showing - if you hit Load Data again, some show and some do not. Steps 1) - select h sapiens - delete refseq - open file IGIS... - select view mode default - region "chr1 : 111,733,948 - 111,735,852" - load data (nothing shows) - region "chr1 : 111,728,298 - 111,744,083" - load data (see #1 below) 2) - select h sapiens - delete refseq - open file IGIS... - select view mode default - (leave full region for chr1) - load data - region "chr1 : 111,728,298 - 111,744,083" (this is how it should look, see #2 below) |
- H sapiens - Open the IGIS Gene Models.GFF file. - you need to zoom into a region so that there is a gene that extends beyond the visible zoom region on both sides on the refseq (the IGIS file is very similar to refseq) - hit load data - now zoom out, you will see the exons on the ends are not showing - if you hit Load Data again, some show and some do not. Steps 1) - select h sapiens - delete refseq - open file IGIS... - select view mode default - region "chr1 : 111,733,948 - 111,735,852" - load data (nothing shows) - region "chr1 : 111,728,298 - 111,744,083" - load data (see image 2.png below) 2) - select h sapiens - delete refseq - open file IGIS... - select view mode default - (leave full region for chr1) - load data - region "chr1 : 111,728,298 - 111,744,083" (this is how it should look, see image.png below) |
I am still seeing that if you load data in the middle (or 1/2) of a gene model, the whole model does not load, even though much of it might be in the 'gray unloaded' area.
| Assignee | Alyssa Gulledge [ alyssa ] | Hiral Vora [ hiralv ] |
Yes, it won't load partial model.
It can only load whole gene model.
| Assignee | Hiral Vora [ hiralv ] | Alyssa Gulledge [ alyssa ] |
| Description |
- H sapiens - Open the IGIS Gene Models.GFF file. - you need to zoom into a region so that there is a gene that extends beyond the visible zoom region on both sides on the refseq (the IGIS file is very similar to refseq) - hit load data - now zoom out, you will see the exons on the ends are not showing - if you hit Load Data again, some show and some do not. Steps 1) - select h sapiens - delete refseq - open file IGIS... - select view mode default - region "chr1 : 111,733,948 - 111,735,852" - load data (nothing shows) - region "chr1 : 111,728,298 - 111,744,083" - load data (see image 2.png below) 2) - select h sapiens - delete refseq - open file IGIS... - select view mode default - (leave full region for chr1) - load data - region "chr1 : 111,728,298 - 111,744,083" (this is how it should look, see image.png below) |
- open H sapiens - Save, then drag in the IGIS Gene Models.GFF file (attached. Make sure to save the .tbi file to the same location as the main file.). - zoom in until you have 1/2 of a gene showing on screen (make sure the other half is out of the field of view) - hit load data. See that the IGIS models loaded. - now zoom out, you will see the IGIS models end at the black and sometimes a single line extends into the grey, unloaded area. The exons on the ends are not showing. - while zoomed out, hit Load Data again this test passes if the rest of the exons load onto the 'parent' line. This fails if they are drawn as a new line |
| Status | Open [ 1 ] | Resolved [ 5 ] |
| Assignee | Alyssa Gulledge [ alyssa ] | |
| Resolution | Fixed [ 1 ] |
| Status | Resolved [ 5 ] | Closed [ 6 ] |
| Resolution | Fixed [ 1 ] | |
| Status | Closed [ 6 ] | Reopened [ 4 ] |
| Summary | GFF file does not show correctly | Indexed GFF file does not partial load correctly |
| Reporter | Lance Frohman [ lfrohman ] | Alyssa Gulledge [ alyssa ] |
This issue still occurs. If the viewing region fractions a gene model and is loaded, then the remainder of the gene in the unloaded region will simply display a line symbolizing the overall length of the gene, void of exon blocks.
(see attached partial.model.png)
After moving the viewing region or zooming out to a larger view, then loading the data, the remaining exon blocks for the gene are displayed.
| Attachment | partial.model.png [ 11759 ] |
| Assignee | Alyssa Gulledge [ alyssa ] |
The partial loading of the models is correct. The bug is that when loading in the REST of the model, it should appaer asll appropriately as a single model on a sing 'line' as opposed to as a new model on a separate 'line'.
| Assignee | Alyssa Gulledge [ alyssa ] | Richard Linchangco [ richard ] |
Passed V.13624, Mac, Java 1.06.0_37
After loading more of the model, exons appear on the original, parent 'line' and not a separate line.
| Status | Reopened [ 4 ] | Resolved [ 5 ] |
| Assignee | Richard Linchangco [ richard ] | Alyssa Gulledge [ alyssa ] |
| Resolution | Fixed [ 1 ] |
| Resolution | Fixed [ 1 ] | |
| Status | Resolved [ 5 ] | Reopened [ 4 ] |
| Assignee | Alyssa Gulledge [ alyssa ] |
Passed V.13655, Mac, Java 1.06.0_37
Partially loaded gene model will create a 'parent line' which will hold exons when full gene model is in view and loaded.
See attached (PARTIAL and FULL)
| Attachment | PARTIAL.png [ 11765 ] | |
| Attachment | FULL.png [ 11766 ] |
| Status | Reopened [ 4 ] | Resolved [ 5 ] |
| Assignee | Alyssa Gulledge [ alyssa ] | |
| Resolution | Fixed [ 1 ] |
| Status | Resolved [ 5 ] | Closed [ 6 ] |
| Resolution | Fixed [ 1 ] | |
| Status | Closed [ 6 ] | Reopened [ 4 ] |
| Status | Reopened [ 4 ] | Closed [ 6 ] |
| Assignee | Alyssa Gulledge [ alyssa ] | |
| Resolution | Fixed [ 1 ] |
GFF does not support region in view if it does not have an index file. So bug is not valid in this case.
If it has index file, then it shows graph initially and annotation upon zooming in. Bug is valid in this case but cannot reproduce it.