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tmRNA templates #175

Merged
merged 57 commits into from
Feb 2, 2025
Merged

tmRNA templates #175

merged 57 commits into from
Feb 2, 2025

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nawrockie
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This PR adds the tmRNA set of templates: tmRNA (standard, RF00023), tmRNA_intron, tmRNA_alpha (RF01849), tmRNA_beta (RF01850), tmRNA_cyano (RF01851) and tmRNA_mito (RF02544). Developed in collaboration with Kelly Williams and Anton Petrov as part of the update to Kelly's tmRNA database.

AntonPetrov and others added 30 commits November 15, 2024 11:04
@AntonPetrov
Temporarily use local copy of infernal2mapping
c58b379
@AntonPetrov
Transfer pknots from local templates like in Rfam
3161b21
@AntonPetrov
Fix local_data template_sto location
46f696a
@AntonPetrov
Consolidate tempfile name creation
cc934e7
@AntonPetrov
Return locations of large insertions
570adbe 
The coordinates are relative to the original sequence
@AntonPetrov
Use original sequence for 2D drawing
20c9862 
This preserves lowercase nucleotides, if any, in the output because intermediate steps convert all nts to uppercase.
@AntonPetrov
Add a test for lowercase nucleotides
bc3d41d
@nawrockie
Adds tmrna config info
997f294
@nawrockie
Adds tmRNA support, by copying and modifying RNAase P lines
fe4735a
@nawrockie
tmRNA model file hierarchy support
5d5375c
@nawrockie
Fix: = to ==
da48ece
@nawrockie
Removes --1blast ribotyper flag for tmRNA
d2d1c87
@nawrockie
Adds tmrna data
3e593b4
@nawrockie
Renames tmrna files
15a2eca
@nawrockie
Removes silly file
fda9927
@nawrockie
Adds tmrna test
71ea59f
@nawrockie
Fixes seq order
5eba3fe
@AntonPetrov
Merge pull request #164 from r2dt-bio/tmrna-library
db1ac41 
Adds support for tmRNA templates
@nawrockie
Adds cyano pseudoknot
2c4ea8f
@nawrockie
Updates to Rfam files (no params changed)
6ef3ff3
@nawrockie
Renames std_tmRNA to tmRNA
0f9f219
@nawrockie
Fixes name
2090fcf
@nawrockie
Fixes 10 seqs in intron seed, found by rfsearch.pl validation
0aa79f0
@nawrockie
Renames intron model
d4cf0a2
@nawrockie
Changes names
0e77afa
@nawrockie
Changes names
b87e12d
@nawrockie
Changes file names
c8a705d
@nawrockie
Calibrates models
a0a0e49
@nawrockie
Updates all* files
0da4c5a
@nawrockie
Renames seq
b6536f1
@nawrockie nawrockie requested a review from AntonPetrov January 21, 2025 22:55
@AntonPetrov AntonPetrov changed the base branch from main to develop January 28, 2025 22:37
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github-actions bot commented Jan 28, 2025 •
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Docker image tag(s) pushed:

rnacentral/r2dt:pr-175

Labels added to images:

org.opencontainers.image.created=2025-02-02T11:48:00.130Z
org.opencontainers.image.description=Visualise RNA secondary structure in consistent, reproducible and recognisable layouts
org.opencontainers.image.licenses=Apache-2.0
org.opencontainers.image.revision=86f7b98ba813e95b889c7506c07e8c49be312b61
org.opencontainers.image.source=https://github.com/r2dt-bio/R2DT
org.opencontainers.image.title=R2DT
org.opencontainers.image.url=https://github.com/r2dt-bio/R2DT
org.opencontainers.image.version=pr-175

AntonPetrov and others added 16 commits January 28, 2025 23:51
@AntonPetrov
Update Traveler and infernal2mapping.py
3d9f498
@nawrockie
Fixes tmRNA get_models call
a807c74
@nawrockie
Adds tmrna metadata
088210f
@nawrockie
Lowercases bacteria to avoid warning
8ecb57f
@AntonPetrov
Merge pull request #177 from r2dt-bio/tmrna-tweaks
2d864c4 
Tmrna tweaks
@AntonPetrov
Update number of tmRNA cms to fix a test
2622635
@AntonPetrov
Update tmRNA example hits.txt to match model names
0b07931
@AntonPetrov
Merge pull request #176 from r2dt-bio/update-traveler
cfef3da 
Update Traveler and infernal2mapping.py
@AntonPetrov
Merge branch 'tmrna-mito' of https://github.com/r2dt-bio/R2DT into tm…
55c8e52 
…rna-mito
@AntonPetrov
Remove local version of infernal2mapping.py
fad844f
@AntonPetrov
Update models.json using latest tmRNA names
149526d
@AntonPetrov
Blacklist Rfam tmRNA models
fa0ecdb 
Use specialised tmRNA library instead
@AntonPetrov
Add a tmRNA to SingleEntry tests
f0ea908
@AntonPetrov
Update example file
27c5d7a
@AntonPetrov
Delete sequential image builder
81c772b
@AntonPetrov
Allow to just run specific tags
eade147
@AntonPetrov AntonPetrov merged commit aeec288 into develop Feb 2, 2025
16 checks passed
@AntonPetrov AntonPetrov deleted the tmrna-mito branch February 2, 2025 11:51
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