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Add all the standard views for the virulence factors #58

Merged
merged 40 commits into from
Feb 23, 2024
Merged

Add all the standard views for the virulence factors #58

merged 40 commits into from
Feb 23, 2024

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njohner
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@njohner njohner commented Feb 15, 2024 •
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With this pull request we add all the standard views for the virulence factors, i.e.

  • detail view
  • comparison index view
  • entry list
  • tabular comparison
  • Venn diagram
  • presence/absence table
  • heatmap
  • accumulation/rarefaction plot

Checklist

  • Changelog entry
  • Check that tests still pass
  • Add tests for new features and regression tests for bugfixes whenever possible.

njohner added 27 commits February 14, 2024 08:49
@njohner
Refactor entry list views to use type mixins.
25ad711
@njohner
Make getting column headers more flexible in mixins.
5342471
@njohner
Fix OrthogroupViewMixin.
5a15483
@njohner
Avoid symlinks in reference database.
2e46dc1 
Setting publishDir with the move option in nextflow processes
will actually move the symlinks and not the files themselves.
This is not the desired behavior for the reference database.
@njohner
Fix bug in annotation pipeline which can appear when resuming a run.
5326943
@njohner
Make imports homogeneous between nextflow runs and webapp.
e835e18
@njohner
Set number of threads for Swissprot and VFDB blasts.
f0d21ad
@njohner
Improve naming of columns in VF tables.
5146121
@njohner
Fix bug in VF annotation pipeline.
011fcd7 
Not all VF genes have an entry in the VF definition file, so we
now extract as much info as possible from the sequence description
and complement that info if there is an entry in the definition
file.
@njohner
Add VF queries.
38ec4fa
@njohner
Add VfViewMixin.
742d633
@njohner
Add Entry list view for virulence factors.
f3c3bcc
@njohner
Add header titles to VF mixin.
a4f6a42
@njohner
Fix imports in setup_base_db script.
a09199c
@njohner
Update zdb_base database to include new BLAST_vfdb configuration.
0549d50
@njohner
Add virulence factor links and version to home page.
de84eea
@njohner
Add virulence factor link to menu.
2564433
@njohner
Add comparison index view and link it in the menu and home page.
e3d6bac
@njohner
Fix AMR hit extraction view table headers.
76b8fbb
@njohner
Fix AMR hit extraction view.
700bd5e
@njohner
Add VF hit extraction view.
9a1b902
@njohner
Refactor hit extraction views to decrease code dupplication.
89d33ce
@njohner
Only use vf_id column as index for VF descriptions.
addfc7c
@njohner
Drop vf_id column and use vf_gene_id instead in VF tables.
a4394b7 
The vf_id column is not necessary as vf_gen_id is unique and can
be used as index. It also makes it easier to use the same column
as index and as identifier than having two distinct columns.
@njohner
Add VF Venn diagram view.
40e0869
@njohner
Remove unnecessary logging in setup_base_db script.
afbb6e1
@njohner
Add VF tabular comparison views.
737466b
@njohner njohner marked this pull request as ready for review February 20, 2024 08:59
@njohner njohner requested review from bkm and tpillone February 20, 2024 09:00
@njohner njohner changed the title Nj/vfdb views Add all the standard views for the virulence factors Feb 20, 2024
@njohner njohner merged commit 89524d1 into master Feb 23, 2024
@njohner njohner deleted the nj/vfdb_views branch February 23, 2024 07:31
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@bkm bkm Awaiting requested review from bkm

@tpillone tpillone Awaiting requested review from tpillone

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