Details
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Type:
Bug
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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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Sprint:Sprint 14, Sprint 15
Description
The default annotation labeling for the human genome is now set to "none".
The default annotation labeling SHOULD be "title" - the name of the gene.
Attachments
Activity
| Field | Original Value | New Value |
|---|---|---|
| Description |
The default annotation labeling for the human genome is now set to "none".
The default annotation labeling SHOULD be "id". |
The default annotation labeling for the human genome is now set to "none".
The default annotation labeling SHOULD be "title" - the name of the gene. |
| Assignee | David Norris [ dcnorris ] |
| Sprint | Sprint 14 [ 19 ] |
| Status | Open [ 1 ] | Needs Testing [ 10002 ] |
| Status | Needs Testing [ 10002 ] | In Progress [ 3 ] |
| Summary | Default labeling for Human genome annotations is "none" | Default labeling for several genome annotations does not match any property names |
./C_albicans_SC5314_Nov_2008/annots.xml:10: label_field="gene name"
./T_castaneum_Mar_2008/annots.xml:9: label_field="gene name"
./C_porcellus_Feb_2008/annots.xml:9: label_field="gene name"
./G_gallus_Nov_2011/annots.xml:9: label_field="gene name"
./C_elegans_Oct_2010/annots.xml:9: label_field="gene name"
./S_cerevisiae_Apr_2011/annots.xml:7: label_field="gene name"
./R_norvegicus_Mar_2012/annots.xml:9: label_field="gene name"
./B_taurus_Oct_2011/annots.xml:9: label_field="gene name"
./M_musculus_Jul_2007/annots.xml:9: label_field="gene name"
./E_caballus_Sep_2007/annots.xml:9: label_field="gene name"
./F_catus_Sep_2011/annots.xml:9: label_field="gene name"
./M_musculus_Dec_2011/annots.xml:9: label_field="gene name"
./D_melanogaster_Jul_2014/annots.xml:9: label_field="gene name"
./M_domestica_Oct_2006/annots.xml:9: label_field="gene name"
./D_rerio_Jul_2010/annots.xml:9: label_field="gene name"
./D_melanogaster_Apr_2006/annots.xml:9: label_field="gene name"
./P_troglodytes_Oct_2010/annots.xml:9: label_field="gene name"
./T_rubripes_Oct_2011/annots.xml:9: label_field="gene name"
./S_bicolor_Jan_2009/annots.xml:9: label_field="gene name"
./F_catus_Dec_2008/annots.xml:9: label_field="gene name"
./S_pombe_May_2012/annots.xml:9: label_field="gene name"
./O_aries_Feb_2010/annots.xml:9: label_field="gene name"
These will all be updated in addition to the human genome.
Changes have been applied to the above genomes
| Status | In Progress [ 3 ] | Needs Testing [ 10002 ] |
| Assignee | David Norris [ dcnorris ] | Mason Meyer [ mason ] |
It seems that some genomes from the list are still not being labeled by default (seems to relate to GFF files). See the list below for genomes that still need to be fixed.
./T_castaneum_Mar_2008/annots.xml:9: label_field="gene name"
./S_cerevisiae_Apr_2011/annots.xml:7: label_field="gene name"
./B_taurus_Oct_2011/annots.xml:9: label_field="gene name"
./S_bicolor_Jan_2009/annots.xml:9: label_field="gene name"
(I also noticed that S_bicolor_Jun_2013, which is the newest version, is being labeled by "ID" by default rather than "Title"...not sure if this is desired or not.)
| Assignee | Mason Meyer [ mason ] | David Norris [ dcnorris ] |
| Status | Needs Testing [ 10002 ] | Open [ 1 ] |
| Rank | Ranked higher |
| Rank | Ranked higher |
| Status | Open [ 1 ] | In Progress [ 3 ] |
updated these to id, and confirmed S_bicolor_Jun_2013 should be labled by id
| Status | In Progress [ 3 ] | Needs Testing [ 10002 ] |
| Assignee | David Norris [ dcnorris ] | Mason Meyer [ mason ] |
| Status | Needs Testing [ 10002 ] | Testing In Progress [ 10003 ] |
The four genomes listed above have now had their default labeling set to "ID". All of the genome versions listed in this story now have default labeling ("title" for bed files and "id" for GFF files).
Since this story is resolved it will now be closed.
| Resolution | Done [ 10000 ] | |
| Status | Testing In Progress [ 10003 ] | Closed [ 6 ] |
| Resolution | Done [ 10000 ] | |
| Status | Closed [ 6 ] | Open [ 1 ] |
| Sprint | Sprint 14 [ 19 ] | Sprint 14, Sprint 15 [ 19, 20 ] |
| Rank | Ranked higher |
| Rank | Ranked higher |
Reopening this story because I noticed that the genomes listed in this story are now not being labeled by default again. The GFF files are still being labeled by default it seems, which makes me think that this issue reopened due to refactoring of the bed parser (IGBF-443).
Reassigning to David to look into further.
| Assignee | Mason Meyer [ mason ] | David Norris [ dcnorris ] |
| Resolution | Done [ 10000 ] | |
| Status | Open [ 1 ] | Closed [ 6 ] |
| Workflow | Loraine Lab Workflow [ 15666 ] | Fall 2019 Workflow Update [ 19356 ] |
| Workflow | Fall 2019 Workflow Update [ 19356 ] | Revised Fall 2019 Workflow Update [ 21473 ] |
Fixed for all human genomes, but we should check other genomes to validate the previous default label field is still applicable.