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Tmrna features#165

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AntonPetrov wants to merge 36 commits intodevelopr2dt-bio/R2DT:developfrom tmrna-featuresr2dt-bio/R2DT:tmrna-featuresCopy head branch name to clipboard

+68,326-50

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Commits on Nov 15, 2024

• Temporarily use local copy of infernal2mapping

  AntonPetrov

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  c58b379

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• Transfer pknots from local templates like in Rfam

  AntonPetrov

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  3161b21

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• Fix local_data template_sto location

  AntonPetrov

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  46f696a

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• Consolidate tempfile name creation

  AntonPetrov

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  cc934e7

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• Return locations of large insertions

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  AntonPetrov

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  570adbe

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• Use original sequence for 2D drawing

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  AntonPetrov

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  20c9862

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• Add a test for lowercase nucleotides

  AntonPetrov

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  bc3d41d

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Commits on Nov 25, 2024

• Adds tmrna config info

  nawrockie

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  997f294

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• Adds tmRNA support, by copying and modifying RNAase P lines

  nawrockie

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  fe4735a

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Commits on Nov 26, 2024

• tmRNA model file hierarchy support

  nawrockie

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  5d5375c

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• Fix: = to ==

  nawrockie

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  da48ece

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• Removes --1blast ribotyper flag for tmRNA

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  d2d1c87

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• Adds tmrna data

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  3e593b4

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Commits on Nov 27, 2024

• Renames tmrna files

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  15a2eca

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• Removes silly file

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  fda9927

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• Adds tmrna test

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  71ea59f

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• Fixes seq order

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  5eba3fe

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• Merge pull request #164 from r2dt-bio/tmrna-library

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  AntonPetrov

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  db1ac41

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Commits on Jan 13, 2025

• Adds cyano pseudoknot

  nawrockie

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  2c4ea8f

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Commits on Jan 17, 2025

• Updates to Rfam files (no params changed)

  nawrockie

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  6ef3ff3

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• Renames std_tmRNA to tmRNA

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  0f9f219

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• Fixes name

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  2090fcf

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• Fixes 10 seqs in intron seed, found by rfsearch.pl validation

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  0aa79f0

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• Renames intron model

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  d4cf0a2

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• Changes names

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  0e77afa

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• Changes names

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  b87e12d

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• Changes file names

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  c8a705d

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• Calibrates models

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  a0a0e49

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• Updates all* files

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  0da4c5a

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• Renames seq

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  b6536f1

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• Renames files

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  c8831eb

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• Fixes seq names

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  7eda21f

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• Renames files

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  3386f92

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• Renames files

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  ee5f459

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• Updates names'

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  2c8c9f3

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• Updates file names for tmrna tests

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  457d7c7

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