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Tmrna features #165

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wants to merge 36 commits into from
Closed

Tmrna features #165

wants to merge 36 commits into from

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AntonPetrov
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  • tmRNA templates built by @nawrockie
  • lowercase nucleotides from user input are transferred to the final output
  • fix infernal mapping

AntonPetrov and others added 18 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
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Docker image tag(s) pushed:

rnacentral/r2dt:pr-165

Labels added to images:

org.opencontainers.image.created=2024-11-27T17:08:40.687Z
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=0eab75b51de31b896c5e7f0244a731b6c44e29af
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-165

@AntonPetrov AntonPetrov closed this Feb 2, 2025
@AntonPetrov AntonPetrov deleted the tmrna-features branch February 2, 2025 10:55
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2 participants
@AntonPetrov @nawrockie