From 5a1c8283db687315a2e0c092f0cc7832c7b153eb Mon Sep 17 00:00:00 2001 From: Eric Coissac Date: Thu, 5 Apr 2018 18:31:49 +0200 Subject: [PATCH] Freshly regerenrated CAU tRNA reference library with the new tool script Former-commit-id: b2808b9d4462c32d0d81fd4f8d134fb94ad9b51c Former-commit-id: a1db9d37bba3adf1100c4418b9211aa49aa00da7 --- data/trna/CAU_tRNA_DB.fasta | 62 ------------------------------------- data/trna/CAU_tRNA_DB.log | 21 +++++++++++++ 2 files changed, 21 insertions(+), 62 deletions(-) diff --git a/data/trna/CAU_tRNA_DB.fasta b/data/trna/CAU_tRNA_DB.fasta index fe251ab..acc6cc3 100644 --- a/data/trna/CAU_tRNA_DB.fasta +++ b/data/trna/CAU_tRNA_DB.fasta @@ -6,12 +6,6 @@ acctacttaactcagtggttagagtactgctttcatacggcgggagtcattggttcaaatccaatagtaggta gcatccatggctgaatggttaaagcgcccaactcataattggcgaattcgtaggttcaattcctactggatgcac >trnI_AC_000188 gbac=AC_000188; trna=trnI; taxid=4081; distance=1; gcatccatggctgaatggttaaagcgcccaactcataattggcgaattcgtaggttcaattcctactggatgcac ->trnM_NC_000925 gbac=NC_000925; trna=trnM; taxid=2787; distance=1; -tgcatctgtggccgaggggccgaaggcagcggactcataatccgccatttcgaaagagacgtcgctggttcgaatccagccagatgcat ->trnfM_NC_000925 gbac=NC_000925; trna=trnfM; taxid=2787; distance=2; -tcgcggggtagagcagtctggtagctcgtcgggctcataacccgaaggtcaatggttcaaatccattccccgctat ->trnI_NC_000925 gbac=NC_000925; trna=trnI; taxid=2787; distance=1; -tggctcagtagctcagtggttagagcaggggattcataagcccaaggtcgcaggttcaaatcccgcttgagccat >trnM_NC_000927 gbac=NC_000927; trna=trnM; taxid=31312; distance=1; gcctgcttagctcagttggttagagcgtccgtttcatacgcggattgtcactagttcaaatctagtagcaggcac >trnfM_NC_000927 gbac=NC_000927; trna=trnfM; taxid=31312; distance=0; @@ -36,12 +30,6 @@ tgcctacttaactcagtggttagagtattgctttcatacggcgggagtcattggttcaaatccaatagtaggtag gcatccatggctgaatggttaaagcgcccaactcataattggtaaatttgcgggttcaattcctgctggatgcac >trnI_NC_001666 gbac=NC_001666; trna=trnI; taxid=4577; distance=1; gcatccatggctgaatggttaaagcgcccaactcataattggtaaatttgcgggttcaattcctgctggatgcac ->trnfM_NC_001675 gbac=NC_001675; trna=trnfM; taxid=2762; distance=0; -cgcggagtagagcagtttggtagctcgtcgggctcataacccgaaggtcagtggttcaaatccactctccgcaa ->trnM_NC_001675 gbac=NC_001675; trna=trnM; taxid=2762; distance=2; -tgcatctgtggccgagcggttgaaggcagcgggctcataatccgtcatctgaaaagatatcactggttcgaatccagtcagatgcatc ->trnI_NC_001675 gbac=NC_001675; trna=trnI; taxid=2762; distance=1; -tggctcggtagctcagtggtagagcaggggactcataagcccttggtcgtgggttcaaatcccacttgagccat >trnI_NC_001865 gbac=NC_001865; trna=trnI; taxid=3077; distance=0; gcacctatggcagagtggtcgattgcaccgcactcataatgcggtttcgaaagaacatcgttggttcaaacccaactgggtgca >trnfM_NC_001865 gbac=NC_001865; trna=trnfM; taxid=3077; distance=0; @@ -70,12 +58,6 @@ acctacttaactcagcggttagagtattgctttcatacggcgggagtcattggttcaaatccaatagtaggta gcatccatggctgaatggttaaagcgcccaactcataattggcgaattcgtaggttcaattcctactggatgcac >trnI_NC_002202 gbac=NC_002202; trna=trnI; taxid=3562; distance=1; gcatccatggctgaatggttaaagcgcccaactcataattggcgaattcgtaggttcaattcctactggatgcac ->trnI_NC_002652 gbac=NC_002652; trna=trnI; taxid=3037; distance=1; -tgcatttatggcagagaggacgatagcacgggactcataatctcgttccgaaaggacatcgctggttcaaatccagctgaatgcat ->trnfM_NC_002652 gbac=NC_002652; trna=trnfM; taxid=3037; distance=0; -ggcgaagtagagtaaaaggttagctcgtgggcctcatgaccccaaggttaaaggttcgaatcctttcttcgcca ->trnM_NC_002652 gbac=NC_002652; trna=trnM; taxid=3037; distance=0; -ggttcaatagctcaaaggtagagcataggattcataagcctcaggtcacaagttcaaatcttgtttgaacca >trnfM_NC_002762 gbac=NC_002762; trna=trnfM; taxid=4565; distance=2; gagcggagtagagcagtttggtagctcacgaggctcataaccttgaggtcacgggttcgattcccgtctccgcact >trnM_NC_002762 gbac=NC_002762; trna=trnM; taxid=4565; distance=1; @@ -116,12 +98,6 @@ cgcggggtggagcagcttggtagctcgcgaggctcataacctcgaggtcacgggttcaaatcccgtctccgcaa gcctacttaactcagcggtgagagtatcgctttcatacggcgagagtcattggttcgaatccaatagtaggta >trnI_NC_004766 gbac=NC_004766; trna=trnI; taxid=13818; distance=0; gcatccatggctgaacggtcaaagcacccaactcataattggcgaattcacaggttcaactcctgttggatgca ->trnM_NC_004799 gbac=NC_004799; trna=trnM; taxid=280699; distance=1; -tgcatctatggccgagcggcttaaggcagcggactcataatccgtggacaagaatttgtcatcgctggttcgaatccagctggatgcat ->trnfM_NC_004799 gbac=NC_004799; trna=trnfM; taxid=280699; distance=0; -cgcggagtagagcagtctggtagctcgtcgggctcataacccgaaggccaatggttcaaatccattctccgcta ->trnI_NC_004799 gbac=NC_004799; trna=trnI; taxid=280699; distance=0; -ggctcagtagctcagaggttagagcgggggactcataagcctcaggtcgtaggttcaaatcttacctgagcca >trnfM_NC_005086 gbac=NC_005086; trna=trnfM; taxid=13333; distance=0; cgcggggtagagcagtttggtagctcgcaaggctcataaccttgaggtcacgggttcaaatcctgtctccgcaa >trnM_NC_005086 gbac=NC_005086; trna=trnM; taxid=13333; distance=1; @@ -320,18 +296,6 @@ acctacttaactcagtggttagagtattgctttcatacggcgagagtcattggttcaaatccaatagtaggta gcatccatggctgaatggttaaagcgcccaactcataattggcgaattcgtaggttcaattcctactggatgcac >trnI_NC_008535 gbac=NC_008535; trna=trnI; taxid=13443; distance=1; gcatccatggctgaatggttaaagcgcccaactcataattggcgaattcgtaggttcaattcctactggatgcac ->trnI_NC_008588 gbac=NC_008588; trna=trnI; taxid=2850; distance=0; -ggctctgtagctcagtggttagagcaggggactcataagcccaaggtcgtaggttcaaatcccaccagagcca ->trnfM_NC_008588 gbac=NC_008588; trna=trnfM; taxid=2850; distance=1; -tcgcggagtagagcagcctggtagctcgttgggctcataacccgaaggtcaatggttcaaatccattctccgctag ->trnM_NC_008588 gbac=NC_008588; trna=trnM; taxid=2850; distance=1; -tgcattcgtggccgagtggttgaaggcaccggactcataatccgttttcctctggaacgtcactggttcgaacccagtcgaatgcag ->trnM_NC_008589 gbac=NC_008589; trna=trnM; taxid=35128; distance=0; -gcattcgtggccgagtggttgaaggcaccggactcataatccgttttcctctggaacgtcactggttcgaacccagtcggatgca ->trnI_NC_008589 gbac=NC_008589; trna=trnI; taxid=35128; distance=0; -ggctctgtagctcagtggttagagcaggggactcataagcccaaggtcgtaggttcaaatcccaccagagcca ->trnfM_NC_008589 gbac=NC_008589; trna=trnfM; taxid=35128; distance=1; -tcgcggagtagagcagtctggtagctcgttgggctcataacccgaaggtcaatggttcaaatccattctccgctag >trnfM_NC_008590 gbac=NC_008590; trna=trnfM; taxid=112509; distance=1; gagcggagtagagcagtttggtagctcacgaggctcataaccttgaggtcacgggttcgattcccgtctccgcact >trnM_NC_008590 gbac=NC_008590; trna=trnM; taxid=112509; distance=1; @@ -732,12 +696,6 @@ acctacttaactcagtggttagagtattgctttcatacggcaggagtcattggttcaaatccaatagtaggta cgcggagtagagcaacttggtagctcgcaaggctcataaccttgaggtcacgggttcaaatcccgtctccgcaac >trnI_NC_011163 gbac=NC_011163; trna=trnI; taxid=3827; distance=1; gcatccatggctgaatggttaaagcacccaactcataattggcgaagtcgtaggttcaattcctactggatgcac ->trnI_NC_011600 gbac=NC_011600; trna=trnI; taxid=109269; distance=1; -tggctttgtagctcagtggttagagcaggggactcataagcccaaggtcgcaggttcaaatcccgccaaagccaa ->trnM_NC_011600 gbac=NC_011600; trna=trnM; taxid=109269; distance=1; -tgcatccgtggccgagcggttgatggcaacgggctcataatccgttttcctttggaacaccactggttcaaatccagtcggatgcaa ->trnfM_NC_011600 gbac=NC_011600; trna=trnfM; taxid=109269; distance=0; -agcggagtagagcagcatggtagctcgttgggctcataacccgaaggtcagaggttcaaatccactctccgcta >trnI_NC_011828 gbac=NC_011828; trna=trnI; taxid=3900; distance=1; gcatccatggctgaatggttaaagcacccaactcataattggcgaagtcgtaggttcaattcctactggatgcac >trnfM_NC_011828 gbac=NC_011828; trna=trnfM; taxid=3900; distance=1; @@ -828,20 +786,6 @@ acctacttaactcagtggttagagtattgctttcatacggcaggagtcattggttcaaatccaatagtaggta ggcggagtggagcaacttggtagctcgcaaggctcataaccttgaggttacgggttcaaatcctgtctccgcacc >trnI_NC_014063 gbac=NC_014063; trna=trnI; taxid=3860; distance=0; gcatccatggctgagtggttaaagcacccaactcataattggcgaagtcgtgggttcaattcctactggatgca ->trnfM_NC_014340 gbac=NC_014340; trna=trnfM; taxid=505693; distance=0; -aatgaaatagagcagtatggccagctcgccgggctcatgccccggaggtcacaggttcaactcctgttttcatta ->trnI_NC_014340 gbac=NC_014340; trna=trnI; taxid=505693; distance=0; -gactctgtagcttagttggttagagcatgggattcataagcccaaggtcgtaggttcaaatccaaccagagtca ->trnM_NC_014340 gbac=NC_014340; trna=trnM; taxid=505693; distance=0; -atacctatggctgagaggtcgaaagcactagactcataatctagctccaaatggaatcgatggttcaaatccatctaggtata ->trnI_NC_014345 gbac=NC_014345; trna=trnI; taxid=348535; distance=0; -ggctctgtagctcagtaggtcagagcgcgggactcataagcccaaggccgcaggttcaaatcctgccagagtcac ->trnM_NC_014345 gbac=NC_014345; trna=trnM; taxid=348535; distance=0; -gtacccgtggctgagcggtcgaaagcgatggactcataatccattctcttataagcatcagtggttcgaacccactcgggtaca ->trnfM_NC_014345 gbac=NC_014345; trna=trnfM; taxid=348535; distance=0; -ggcggggtagagcagcgcggtacagctcatcgggctcatgacccggaggtcagtggttcgaccccactccccgctc ->trnfM_NC_014345 gbac=NC_014345; trna=trnfM; taxid=348535; distance=0; -ggcggggtagagcagcgcggtacagctcatcgggctcatgacccggaggtcagtggttcgaccccactccccgctc >trnfM_NC_014348 gbac=NC_014348; trna=trnfM; taxid=104588; distance=0; cgcggggtagagcagcttggtagctcgcaaggctcataaccttgaggtcacgggttcaaatcctgtctccgcaa >trnM_NC_014348 gbac=NC_014348; trna=trnM; taxid=104588; distance=0; @@ -2190,12 +2134,6 @@ gcctacttaactcagtggttagagtattgctttcatacggcagtagtcattggttcaaatccaatagtaggta cgcggagtagagtagtttggtatctcgcaaggctcataaccttgagatcgcaggttcaaatcctgtctccgcaa >trnI_NC_023132 gbac=NC_023132; trna=trnI; taxid=223125; distance=1; gcatccatggctgaatggttaaagcgcccaactcataattggcgattttgtaggttcaattcctactggatgcac ->trnM_NC_023133 gbac=NC_023133; trna=trnM; taxid=35688; distance=0; -ggctcagtagctcagtggttagagcaggggactcataagcccaaggtcgcaggttcaaatcccgcctgagcca ->trnI_NC_023133 gbac=NC_023133; trna=trnI; taxid=35688; distance=0; -gcatctgtggccgagtggccgaaggcaacggactcataatccgtttctcgtaagagacgtcgctggttcgaacccagccggatgca ->trnfM_NC_023133 gbac=NC_023133; trna=trnfM; taxid=35688; distance=0; -cgcggggtagagcagtctggtagctcgtcgggctcataacccgaaagtcaatggttcaaatccattccccgcta >trnfM_NC_023213 gbac=NC_023213; trna=trnfM; taxid=47600; distance=1; cgcgggatagagcagtttggtagctcgcaaggctcataaccttgaggtcatgggttcaaatcccgttcccgcaac >trnM_NC_023213 gbac=NC_023213; trna=trnM; taxid=47600; distance=0; diff --git a/data/trna/CAU_tRNA_DB.log b/data/trna/CAU_tRNA_DB.log index 71e21ca..09f3216 100644 --- a/data/trna/CAU_tRNA_DB.log +++ b/data/trna/CAU_tRNA_DB.log @@ -16,3 +16,24 @@ 2015-10-10 19:03:11 [OA INFO ] 63859 -- Done 2015-10-10 19:03:11 [OA INFO ] 63859 -- Installing the CAU tRNA database... 2015-10-10 19:03:11 [OA INFO ] 63859 -- Done +2018-04-05 18:17:45 [OA INFO ] 1072 -- Selecting Viridiplantae genebank entries... +2018-04-05 18:17:45 [OA INFO ] 1072 -- --> 0 entries selected +2018-04-05 18:17:45 [OA INFO ] 1072 -- Done +2018-04-05 18:17:45 [OA INFO ] 1072 -- Extracting the CAU tRNA from the plants entries... +2018-04-05 18:17:45 [OA INFO ] 1072 -- Done +2018-04-05 18:17:45 [OA INFO ] 1072 -- Installing the CAU tRNA database... +2018-04-05 18:17:45 [OA INFO ] 1072 -- Done +2018-04-05 18:18:34 [OA INFO ] 1170 -- Selecting Viridiplantae genebank entries... +2018-04-05 18:18:36 [OA INFO ] 1170 -- --> 0 entries selected +2018-04-05 18:18:36 [OA INFO ] 1170 -- Done +2018-04-05 18:18:36 [OA INFO ] 1170 -- Extracting the CAU tRNA from the plants entries... +2018-04-05 18:18:36 [OA INFO ] 1170 -- Done +2018-04-05 18:18:36 [OA INFO ] 1170 -- Installing the CAU tRNA database... +2018-04-05 18:18:36 [OA INFO ] 1170 -- Done +2018-04-05 18:19:01 [OA INFO ] 1778 -- Selecting Viridiplantae genebank entries... +2018-04-05 18:19:09 [OA INFO ] 1778 -- --> 461 entries selected +2018-04-05 18:19:09 [OA INFO ] 1778 -- Done +2018-04-05 18:19:09 [OA INFO ] 1778 -- Extracting the CAU tRNA from the plants entries... +2018-04-05 18:26:03 [OA INFO ] 1778 -- Done +2018-04-05 18:26:03 [OA INFO ] 1778 -- Installing the CAU tRNA database... +2018-04-05 18:26:03 [OA INFO ] 1778 -- Done