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Display posterior probabilities #95

Merged
merged 98 commits into from
Aug 15, 2023
Merged

Display posterior probabilities #95

merged 98 commits into from
Aug 15, 2023

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AntonPetrov
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@AntonPetrov AntonPetrov commented Nov 12, 2022 •
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Fix #54

  • Visualise data layers
  • Support Apple silicon
  • Update dependencies
  • Update Rfam templates to release 14.9
  • Display pseudo knots
  • Generate HTML reports when tests fail
  • Template-free visualisation

@AntonPetrov
Generate posterior probability tsv file
34f235b
@AntonPetrov
Refactor and add comments
86b16ac
@AntonPetrov
Remove CRW-specific visualisation function
d5d9e6b
@AntonPetrov
Fix a broken f-string
18aef32
@AntonPetrov
Remove Rfam-specific visualisation function
f64142a
@AntonPetrov
Do not use deleted visualisation function
c583322
@AntonPetrov
Simplify generate_2d function
121ecb0
@AntonPetrov
Use model_id instead of rfam_acc
b98e893
@AntonPetrov
Update Traveler
ee3261c
@AntonPetrov
Install develop branch of easel
63622c5
@AntonPetrov
Update Rfam templates for release 14.9
1e4b24d
@AntonPetrov
Update jiffy-infernal-hmmer-scripts
0e80fb8
@AntonPetrov
Rename TestRfam to TestRfamAccession
0851a66
@AntonPetrov
Add a new test for Rfam pseudoknots
bb59d62
@AntonPetrov
Ignore Rfam seed files used for pseudoknot mapping
ce4633a
@AntonPetrov
Update Rfam examples to include pseudoknots
41b7bc6
@AntonPetrov
Fix an f-string bug
a7c4707
@AntonPetrov
Add pseudoknots styling to test examples
ea1791b
@AntonPetrov
Add pseudoknot to the single entry Rfam example
b7c2fa4
@AntonPetrov
Update example test files
149f2d2
@AntonPetrov
Update more example test files
7123cfd
@AntonPetrov
Pylint fixes for tests.py
4e6798c
@AntonPetrov
Display pseudoknots for eligible Rfam templates
adb042c
@AntonPetrov
Pylint fixes in shared.py
c5a7526
@AntonPetrov
Merge tRNA-specific visualisation function
b7e630e
@AntonPetrov
Pylint fixes
3a873e8
@AntonPetrov
Hide esl-alidepair output
7d460df
@AntonPetrov
Fix a bug with large insertion detection
e3887c6
@AntonPetrov
Generate HTML reports with SVGs when tests fail
91cb01d
@AntonPetrov
Add a command to update example files for a given test
bf3a996
@AntonPetrov
Document template free visualisation
2685400
@AntonPetrov
Document creating templates JSON schema
5b5587e
@AntonPetrov
Add a test for template generation
3b52fef
@AntonPetrov
Add example file for template generation
349df49
@AntonPetrov
Enable generating template from JSON
7f08bb6
@AntonPetrov
Refactor organise_results
cfe976d
@AntonPetrov
Update isort hook
e52df6c
@AntonPetrov
Update dockerignore
1499a10
@AntonPetrov
Remove the unneeded ssi file
762e90d
@AntonPetrov
Update base image to gcc:11 for Traveler
2c70995
@AntonPetrov
Update to latest Traveler
c861be8
@AntonPetrov
Update R-scape installation
965b8c9
@AntonPetrov
Install autoconf required by Infernal
7dc7e60
@AntonPetrov
Install ribovore and infernal together
da9a095
@AntonPetrov
Update environment variables
5978e2e
@AntonPetrov
Put statements in correct order
219a3ae
@AntonPetrov
Update ribotyper command
9c39fa3
@AntonPetrov
Update sphinx, myst-parser and rtd theme
fba8923
@AntonPetrov
Update installation docs
55bfe01
@AntonPetrov
Add .git to dockerignore
437d52d
@AntonPetrov
Delete folder after install is complete
aecfc09
@AntonPetrov
Fix typo
2e80ab8
@AntonPetrov
Update version header
086793e
@AntonPetrov
Typo fix
067885d
@AntonPetrov
Update CRW SVG examples
93ca621
@AntonPetrov
Handle possible crash of enrich_json.py
f2fc18c
@AntonPetrov
Infernal mapping fixes
69da0e0
@AntonPetrov AntonPetrov marked this pull request as ready for review August 15, 2023 12:21
@AntonPetrov AntonPetrov merged commit f6b39ef into develop Aug 15, 2023
6 checks passed
@AntonPetrov AntonPetrov deleted the display-posterior-probabilities branch August 15, 2023 12:51
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@AntonPetrov