Merge pull request #175 from r2dt-bio/tmrna-mito

tmRNA templates

base_image/Dockerfile

@@ -2,7 +2,7 @@ FROM gcc:13 AS build
 
 ENV tRNAscan_VER=2.0.11 \
     BioEasel_COMMIT=a52f0f7f7cae879bb95489bb794c04c1a0110aa7 \
-    traveler_COMMIT=8054f5bee8327bb158385893e0633d4242676f95 \
+    traveler_COMMIT=78c1cd63dcf40be83d97d07b8eb9eb6a9dc63f7f \
     jiffy_COMMIT=31d6c3b826d432a30620507830749cee58e15e68 \
     Rscape_VER=v2.0.4.c \
     Ribovore_COMMIT=5df943c6f2866d7979bb13c948ca9d8531076898 \

data/tmrna/cm/all.fa

@@ -0,0 +1,42 @@
+>tmRNA
+GGGGGUGAACUGGUUUCGACGGGAAUGUUGAUUCCAAAAGCUGCAUGCCGAGGUUGCCGG
+UGACCUCGUAAAACAACCGGCAAAAAAAUAAAUGCCAACAAUAAUUACUAUCGCUCUCGC
+UGCUUAAUAAGCAGCGAGCCGUCCCCCCAGCCCUUGCCUGUUGGGCUGGGAAGGGGCGUC
+AUAAAAGCGGGAUAGCCUUUAGGUUUGCCUGGGGCCUAAAGGCGAAAAUUAAAGAGGCUA
+GCCUUAAGGAAGCCUGUCUGUUGGCAUCCUUAAGGCGAAAAUAAAAAACAGACUAAGCAU
+GUAGAAGCUUUUGGAAUAACAUUUUCGGACGCGGGUUCGAUUCCCGCCACCUCCACCA
+>tmRNA_intron
+GGGGGUGAAUGGUUUCGACGGGGGGCCCUAGCGCCAAGGUUGCAUGCCGAGGAUGCCGGC
+GACCUCGUUAAAAAGCCGGCAAAAAUAUAAAUGCCAACAAUAAUAACUACGCUUUCGCUG
+CUUAAUGCAGCGAAGACGUCCUCCCCCUCCUCGCCUGAUGGAGGGGGAAAGGGCGUCAUU
+AAAGCGGGCUAGCCCACCCCAUUGCUUUGGGGGGGUGGGCGAAAAAUAAAAAGGCUGGCC
+UUAGCGCACCCUGUCUUUCGGGAGCGCUAAGGCGAAAAUAAAAAAGAGACUAAGCAUGUA
+GAAACCUUGGCGCUGGGCCCUCCGGACGCGGGUUCGAUUCAAAAAGAGUCGCCCUGGGGG
+GUAACCCCCAGGGGAAAACCCGGCUAAAUCAGGGAAACCCUAACCUGAAAGAAGGCUAGG
+GUAAUCCUGAGGGGUGCCCCGAAACGGGGAACCUGCAGAGACUCUGGCCCCCCUAAAAGG
+GGGGACCAGAUGGGAGGCAAAAUCGUUGAAUAAGUUUUAGAAUGCCUCCCAUAAAACGCC
+GGGCAUCCCGAAAGGGAUGAAGAGAUAGUCCACGCCCCUUGGAAAAUGGGGUAUACGUGU
+CCCGCCACCUCCACCA
+>tmRNA_alpha
+GCCCUUUAAAUUUUAAACAUAUUCUCCUAUAUUAGUAGUGCCGGUUUGCCGGCUAUGGCG
+AUAAACGCCCCGCGUAAUAAACGCAUCGGACCCGGGGGCGGUACCCGGCGCCUCCACCAA
+AAACCUUUCAUUUAUGUGUUUUUUUAUGGGGGCGAAAUAGGAUCGACGAGCGUGUAAAGG
+CGGGGCUUUCGCCCGGUAUGGUGCCACCGUUAUCGGCCCAAAAUUAUAAUUGCAAACGAC
+AACUAUGCUCCGGUUGCUCUUGCUGCGUAAGCAGUUUGAAAAAUUGAAAUUUAAGUCCUA
+AGGGUUAGCACCGUUAGGCGGGGUUCGGGGGCACCUGGCAACAGAAGCCCCCACU
+>tmRNA_beta
+ACACGCAAAUUGACUUGAAGCUGACGGCAACGCGCGUAUAAUCUAGAGCAUGGUUGUAUU
+CCGGCAACCUGGAGGCGUUCUGGACGGGGGUUCGAUUCCCCCCACCUCCACCCAAGGGCA
+UUCCACGGAGAGUGUUUAGAUGGGGGUGUACUGGUUUCGACAGGGCGGGCAAAGGUGAGC
+AGGCAACCCGUCAGGCGACGGACGUUAAUAAUGCAAAUCCAUAAAUGCCAACGAUGAGCA
+UUUCGCAAUGGCCGCCUAAAAACGGCUAGCCGGGGCUGCUGCUGCCUUGUUACCAAAGAG
+CAGCCGGCGGGGGCCUCGGGGCCCCCGCUCA
+>tmRNA_cyano
+CUGUCAGAAUAAAAAUGUCCGGCUUUAGCCGGACUAGGUGACCCACACCACUGUCCCGGA
+CAGCGGUUCGAUUCCGCUCAGCUCCAUUCCUCCUUCUUGGGGCUGCAAUGGUUUCGACGG
+GGCAGAAGGAGGGUGACUGAAGCCUGCUCGGUUAGAGCAAAAACAUAACUGCUAACAACA
+UCGUUAGUUUCUCCCGCCCAGCAGCCCCUGUGGCUGCCUGAGCCUUUAAAGGAGAUGGGG
+CGAGGUCAGCCUUAUCACCCAAAUGACCCAUGGGGCCCGGAAGGGCCC
+>tmRNA_mito
+UAAAUGGACCCAAAGGCAGUAUUUGGUAUUUCCAUAUAAAUUAAAUUAAAAGGGAAUAAU
+AAUAGAAUUGACAUUUA

data/tmrna/cm/all.fa.njs

@@ -0,0 +1,22 @@
+{
+  "version": "1.2",
+  "dbname": "all.fa",
+  "dbtype": "Nucleotide",
+  "db-version": 5,
+  "description": "all.fa",
+  "number-of-letters": 2025,
+  "number-of-sequences": 6,
+  "last-updated": "2025-01-21T14:21:00",
+  "number-of-volumes": 1,
+  "bytes-total": 38084,
+  "bytes-to-cache": 675,
+  "files": [
+    "all.fa.ndb",
+    "all.fa.nhr",
+    "all.fa.nin",
+    "all.fa.not",
+    "all.fa.nsq",
+    "all.fa.ntf",
+    "all.fa.nto"
+  ]
+}

data/tmrna/cm/modelinfo.txt

@@ -0,0 +1,7 @@
+*all* - - all.cm
+tmRNA tmRNA Bacteria tmRNA.cm
+tmRNA_intron tmRNA Bacteria tmRNA_intron.cm
+tmRNA_alpha tmRNA Alphaproteobacteria tmRNA_alpha.cm
+tmRNA_beta tmRNA Betaproteobacteria tmRNA_beta.cm
+tmRNA_cyano tmRNA Cyanobacteria tmRNA_cyano.cm
+tmRNA_mito tmRNA Eukarya tmRNA_mito.cm