version bump

nedialkova-lab · Aug 9, 2023 · 899fad8 · 899fad8
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commit 899fad8
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Showing 16 changed files with 13 additions and 3,527 deletions.
diff --git a/build/lib/mimseq/data/gorGor4-eColitK/README.txt b/build/lib/mimseq/data/gorGor4-eColitK/README.txt
@@ -15,17 +15,6 @@ bedtools getfasta -fi /data/genome_misc/gorilla_gorGor4/Gorilla_gorilla.gorGor4.
 
 # Add E. coli Lys-TTT reference sequence to the top of gorGor4-tRNAs-all.fa
 
-### Manually removed sequences due to strange sequence, poor score and issues with infernal alignment with mimseq
-### See gorGor4-tRNAs-filtered.fa
-
->Gorilla_gorilla_tRX-Ala-GGC-9-1 (tRNAscan-SE ID: chr16.trna24) Ala (GGC) 77 bp Sc: 28.0 16:71652066-71652143(-)
->Gorilla_gorilla_tRX-Phe-GAA-5-1 (tRNAscan-SE ID: chr18.trna3) Phe (GAA) 69 bp Sc: 23.1 18:59921682-59921751(-)
->Gorilla_gorilla_tRX-Lys-CTT-13-1 (tRNAscan-SE ID: chr7.trna1) Lys (CTT) 84 bp Sc: 33.0 7:12541420-12541504(+)
->Gorilla_gorilla_tRX-Cys-GCA-8-1 (tRNAscan-SE ID: chr7.trna18) Cys (GCA) 84 bp Sc: 26.8 7:149223412-149223496(+)
->Gorilla_gorilla_tRX-Lys-TTT-17-1 (tRNAscan-SE ID: chr3.trna11) Lys (TTT) 81 bp Sc: 25.2 3:45318879-45318960(-)
->Gorilla_gorilla_tRX-Cys-GCA-6-1 (tRNAscan-SE ID: chr10.trna7) Cys (GCA) 96 bp Sc: 20.7 10:6238138-6238234(-)
->Gorilla_gorilla_tRNA-Asn-GTT-12-1 (tRNAscan-SE ID: chr1.trna19) Asn (GTT) 76 bp Sc: 52.9 1:125422054-125422130(+)
-
 ##### Manually rename problem reference names #######
 
 # >Gorilla_gorilla_tRNA-Gly-CCC-3-2 does not match sequence to Gly-CCC-3-1
@@ -44,8 +33,8 @@ bedtools getfasta -fi /data/genome_misc/gorilla_gorGor4/Gorilla_gorilla.gorGor4.
 #### Gene should end on CCA and gain an additional CCA after processing
 #### manually added this A
 
-#### NB! gorGor4-tRNAs-filtered2.fa is the one loaded by mimseq with --species Ggor ####
-####--------------------------------------------------------------------------------####
+#### NB! ####
+####-----####
 
 Gorilla_gorilla_tRNA-Pro-AGG-6-1 has been removed as NNN repeat causes problems with clustering
 This is a high-confidence tRNA so removing it might not be the best fix, but the AGG anticodon family has very very few reads aligned anyway
diff --git a/build/lib/mimseq/data/gorGor4-eColitK/gorGor4-tRNAs-all.fa b/build/lib/mimseq/data/gorGor4-eColitK/gorGor4-tRNAs-all.fa
@@ -14,7 +14,7 @@ TCCCTGGTGGTCTAGTGGCTAGGATTTGGCGCTTTCACCGCTGCAGCCCCAGTCGATTCCTGGTCAGGGAA
 TCCCTGGTGGTCTAGTGGCTAGGATTCGGCGCTTTCACCGCCGCGGCCCCGGTTTGATTCCCGGTCTGGGAA
 >Gorilla_gorilla_tRNA-Gly-CCC-3-1 (tRNAscan-SE ID: chr1.trna97) Gly (CCC) 71 bp Sc: 69.6 1:16519564-16519635(-)
 GCATTGGTGTTTCAGTGGTAGAATTCTCGCCTCCCACGCGGGAGACCCGGGTTCAATTCCCGGCCAATGCA
->Gorilla_gorilla_tRNA-Gly-CCC-3-2 (tRNAscan-SE ID: chr1.trna1) Gly (CCC) 71 bp Sc: 65.2 1:16605563-16605634(+)
+>Gorilla_gorilla_tRNA-Gly-CCC-6-1 (tRNAscan-SE ID: chr1.trna1) Gly (CCC) 71 bp Sc: 65.2 1:16605563-16605634(+)
 GCATTGGTGTTTCAGTGGTAGAATTCTCGCCTCCCACGTGGGAGACCCGGGTTCAATTCCCGGCCAATGCA
 >Gorilla_gorilla_tRX-Glu-TTC-4-1 (tRNAscan-SE ID: chr1.trna2) Glu (TTC) 72 bp Sc: 42.9 1:16617069-16617141(+)
 TCCCTGGTGGTCTAGTGGCTAGGATTCGGCGCTTTCACCACCACAACCCGGGTTGGATTCCCGGTCAGGGAA
@@ -68,7 +68,7 @@ GCCCGGCTAGCTCAGTCGGTAGAGCATGAGACTCTTAATCTCAGGGTCGTGGGTTCGAGCCCCACGTTGGGCG
 GCCGTGATCGTATAGTGGTTAGTACTCTGCGTTGTGGCCGCAGCAACCTCGGTTCGAATCCGAGTCACGGCA
 >Gorilla_gorilla_tRNA-Gly-TCC-1-1 (tRNAscan-SE ID: chr1.trna89) Gly (TCC) 72 bp Sc: 73.8 1:125434314-125434386(-)
 GCGTTGGTGGTATAGTGGTGAGCATAGCTGCCTTCCAAGCAGTTGACCCGGGTTCGATTCCCGGCCAACGCA
->Gorilla_gorilla_tRNA-Glu-CTC-1-1 (tRNAscan-SE ID: chr1.trna88) Glu (CTC) 72 bp Sc: 66.3 1:125435682-125435754(-)
+>Gorilla_gorilla_tRNA-Glu-CTC-2-1 (tRNAscan-SE ID: chr1.trna88) Glu (CTC) 72 bp Sc: 66.3 1:125435682-125435754(-)
 TCCCTGGTGGTCTGGTGGTTAGGATTCGGCGCTCTCACCGCCGCGGCCCGGGTTCGATTCCCGGTCAGGGAA
 >Gorilla_gorilla_tRNA-Gln-CTG-3-1 (tRNAscan-SE ID: chr1.trna20) Gln (CTG) 72 bp Sc: 71.9 1:125966917-125966989(+)
 GGTTCCATGGTGTAATGGTGAGCACTCTGGACTCTGAATCCAGCGATCCGAGTTCGAGTCTCGGTGGAACCT
@@ -242,8 +242,6 @@ GCCCGGATAGCTCAGTCGGTAGAGCATCAGACTTTTAATCTGAGGGTCCAGGGTTCAAGTCCCTGTTCGGGCG
 GCCGAAATAGCTCAGTTGGGAGAGCGTTAGACTGAAGATCTAAAGGTCCCTGGTTCAATCCCGGGTTTCGGCA
 >Gorilla_gorilla_tRNA-Ser-GCT-1-1 (tRNAscan-SE ID: chr11.trna6) Ser (GCT) 82 bp Sc: 89.1 11:65551292-65551374(+)
 GACGAGGTGGCCGAGTGGTTAAGGCGATGGACTGCTAATCCATTGTGCTTTGCACGCGTGGGTTCGAATCCCATCCTCGTCG
->Gorilla_gorilla_tRNA-Pro-AGG-6-1 (tRNAscan-SE ID: chr11.trna7) Pro (AGG) 98 bp Sc: 52.5 11:75308145-75308243(+)
-GGCTCGTTGGTCTAGGGGTATGNNNNNNNNNNNNNNNNNNNNGGTATGATTCTCGCTTAGGGTGCGAGAGGTCCCGGGTTCAAATCCCGGACGAGCCC
 >Gorilla_gorilla_tRNA-Pro-TGG-5-1 (tRNAscan-SE ID: chr11.trna12) Pro (TGG) 72 bp Sc: 70.5 11:75308484-75308556(-)
 GGCTCGTTGGTCTAGGGGTATGATTCTCGGTTTGGGTCCGAGAGGTCCCGGGTTCAAATCCCGGACGAGCCC
 >Gorilla_gorilla_tRX-Ser-AGA-1-1 (tRNAscan-SE ID: chr11.trna9) Ser (AGA) 83 bp Sc: 34.5 11:109093745-109093828(+)
@@ -810,7 +808,7 @@ GTAGTCGTGGCCGAGTGGTTAAGGCGATGGACTTGAAATCCATTGGGGTTTCCCCGCGCAGGTTCGAATCCTGCCGGCTA
 GGTTCCATGGTGTAATGGTTAGCACTCTGGACTCTGAATCCAGCGATCCGAGTTCAAATCTCGGTGGAACCT
 >Gorilla_gorilla_tRNA-Ser-AGA-1-1 (tRNAscan-SE ID: chr6.trna48) Ser (AGA) 82 bp Sc: 90.3 6:28116743-28116825(+)
 GTAGTCGTGGCCGAGTGGTTAAGGCGATGGACTAGAAATCCATTGGGGTTTCCCCGCGCAGGTTCGAATCCTGCCGACTACG
->Gorilla_gorilla_tRNA-Ser-AGA-1-2 (tRNAscan-SE ID: chr6.trna142) Ser (AGA) 82 bp Sc: 83.9 6:28126158-28126240(-)
+>Gorilla_gorilla_tRNA-Ser-AGA-4-1 (tRNAscan-SE ID: chr6.trna142) Ser (AGA) 82 bp Sc: 83.9 6:28126158-28126240(-)
 GTAGTCGTGGCCGAGTGGTTAAGGCGATGGACTAGAAATCCATTGGGGTTTCTCCGCGCAGGTTCGAATCCTGCCGACTACG
 >Gorilla_gorilla_tRNA-Ser-TGA-4-1 (tRNAscan-SE ID: chr6.trna49) Ser (TGA) 82 bp Sc: 85.8 6:28130066-28130148(+)
 GTAGTCGTGGCCGAGTGGTTAAGGCGATGGACTTGAAATCCATTGGGGTGTCCCCGCGCAGGTTCGAATCCTGCCGACTACG
@@ -970,7 +968,7 @@ GCCCGGATAGCTCAGTCGGTAGAGCATCAGACTTTTAATCTGAGGGTCCAGGGTTCAAGTCCCTGTTCGGGCG
 GCCTCCTTAGCGCAGTAGGCAGCGCGTCAGTCTCATAATCTGAAGGTCCTGAGTTCGAACCTCAGAGGGGGCA
 >Gorilla_gorilla_tRNA-Phe-GAA-1-1 (tRNAscan-SE ID: chr6.trna89) Phe (GAA) 73 bp Sc: 88.9 6:29614476-29614549(-)
 GCCGAAATAGCTCAGTTGGGAGAGCGTTAGACTGAAGATCTAAAGGTCCCTGGTTCGATCCCGGGTTTCGGCA
->Gorilla_gorilla_tRNA-Glu-CTC-2-1 (tRNAscan-SE ID: chr6.trna75) Glu (CTC) 72 bp Sc: 73.2 6:29615000-29615072(+)
+>Gorilla_gorilla_tRNA-Glu-CTC-1-6 (tRNAscan-SE ID: chr6.trna75) Glu (CTC) 72 bp Sc: 73.2 6:29615000-29615072(+)
 TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCTCTCACCGCCGCGGCCCGGGTTCGATTCCCGGTCAGGGAA
 >Gorilla_gorilla_tRNA-Leu-AAG-2-5 (tRNAscan-SE ID: chr6.trna76) Leu (AAG) 82 bp Sc: 74.8 6:29621762-29621844(+)
 GGTAGCGTGGCCGAGCGGTCTAAGGCGCTGGATTAAGGCTCCAGTCTCTTCGGGGGCGTGGGTTCGAATCCCACCGCTGCCA