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Merge pull request #1 from nedialkova-lab/dev
Isodecoder level modification and stops analysis, new implementation of read counting and anticodon counting in tRNAtools.py
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,75 @@ | ||
| >URS000040774E_4896|Schizosaccharomyces_pombe|9606|Trp|TCA | ||
| AAGAGTATAGTTTAATTGGTAAAACTTCTGATTCCAAATTAGACATTGTTCGTTCAAGTC | ||
| GGACTGCTCTTG | ||
| >URS000052E18F_4896|Schizosaccharomyces_pombe|9606|Cys|GCA | ||
| GATAATGTTCAGTGGTCTGAAATTGAATTTGCAAAATTTGATATATGAGTTCAATTCTCA | ||
| TCATTATCT | ||
| >URS00002C4932_4896|Schizosaccharomyces_pombe|9606|Val|TAC | ||
| AGGAGAATAGCTTAATTGGTAGAGCACTTACCTTACAAGTAAGATTATAAGGGTTCAAAT | ||
| CCCTTTTCTCCTA | ||
| >URS00003B0065_4896|Schizosaccharomyces_pombe|9606|Leu|TAG | ||
| GCAGATGTGATGAAATTGGTAAACATGTTTACCTTAGGAGTAAAATCTTGAAGGTTCGAA | ||
| TCCTTCCATCTGTA | ||
| >URS00001AD663_4896|Schizosaccharomyces_pombe|9606|Leu|TAA | ||
| GCCTAAATGCTGGAATTTGGTAGACAGAACAAACTTAAGATTTGTCGCTTTCGAGCGTGT | ||
| TGGTTCGAGTCCAACTTTAGGTA | ||
| >URS00001DDDAC_4896|Schizosaccharomyces_pombe|9606|Ile|GAT | ||
| AGTTCTTTAACTTAAAAGGTCAGAGTGCAGACTTGATAAGTCTGTGGTATTGGTTCGATT | ||
| CCAATAAGAACTA | ||
| >URS00000E510A_4896|Schizosaccharomyces_pombe|9606|Ser|TGA | ||
| GGAAGGGTGTCCGAGTGGTTTAAGGAGCGATATTTGAGCTATTGTGATTTATTCATCGCA | ||
| GGTTCGAATCCTGCCCCTTTCG | ||
| >URS00000B84DA_4896|Schizosaccharomyces_pombe|9606|Arg|TCG | ||
| GCACTTTTAGCTTAATTGGTTAGAGTAACAATCTTCGAAATTGTTAGTATAGGTTCAAAT | ||
| CCTATAAAGTGTT | ||
| >URS00005E6A72_4896|Schizosaccharomyces_pombe|9606|Gly|TCC | ||
| GCAGATATAAGTCAATTGGCAGACCTTCTGATTTCCACTTAGATTATGTTCGTTCGAATC | ||
| GGACTATCTGCA | ||
| >URS00000E1077_4896|Schizosaccharomyces_pombe|9606|Asn|GTT | ||
| GTTGTTGTAGCTCAATGGTAGAGCAAGTCACTGTTAATGACCTGATAGTGGTTCGATTCC | ||
| ACTCAATAACG | ||
| >URS00000A90BD_4896|Schizosaccharomyces_pombe|9606|Lys|TTT | ||
| GGGGATGTAGCTCAATGGTTAGAGCTTTCGCCTTTTAAGCGATAGGATAAGGGTTCAAAT | ||
| CCCTTCAGACCCA | ||
| >URS0000226DF4_4896|Schizosaccharomyces_pombe|9606|Glu|TTC | ||
| GGCTCTATTGTCTAATGGTTAAGACCTTACATCTTCATTGTAAATATCTTGGTTCGATTC | ||
| CAAGTAGGGCTA | ||
| >URS000027C703_4896|Schizosaccharomyces_pombe|9606|Ser|GCT | ||
| GGAAAAATAGTTCTAATTGGTAAGAAGGATACTTGCTACGTATCTGGTGAATAACCTTGT | ||
| GAGTTCGAGTCTCACTTTTTCCG | ||
| >URS000012A615_4896|Schizosaccharomyces_pombe|9606|Thr|TGT | ||
| GCTAATTTAACTCAATTGGTAGAGTGCGTACCTTGTAAGTACGAAGTTAGAGGTTCAATT | ||
| CCTCTAATTAGCA | ||
| >URS0000519C3F_4896|Schizosaccharomyces_pombe|9606|Glu|TTC | ||
| TGGGTTGTTGACTAATAGGTAAGTCCCTGAAATTTGACTTCAGTCTATGTAAGTTCGAAT | ||
| CTTACCATCCCAT | ||
| >URS0000101C2D_4896|Schizosaccharomyces_pombe|9606|Met|CAT | ||
| TGCGATTTAATGTAATTGGTTAACATCTCTGACTCATGATCAGTGTATTAAGGTTCAAGT | ||
| CCTTAGGTCGCAC | ||
| >URS00003C6042_4896|Schizosaccharomyces_pombe|9606|Ile|GAT | ||
| AGGATTATAGCTTAACGGTTAAAGCAGAGAGCTCATAACTCTTGTATATTGGTTCGATTC | ||
| CAGTTTGTCCTA | ||
| >URS0000409C5E_4896|Schizosaccharomyces_pombe|9606|Phe|GAA | ||
| GCTCTGATAACTTAACGGTTAAAGTGCAGTATTGAAGCTGCTGAGATATTGGTTCGATTC | ||
| CATTTCAGAGCA | ||
| >URS00001B646E_4896|Schizosaccharomyces_pombe|9606|Met|CAT | ||
| GTTGGTATAGTTTAATTGGTTAAAATAATCTCCTCATGTGAGATTGATCTATAGGTTCGA | ||
| GCCCTTTTACCAACT | ||
| >URS00000FEDF7_4896|Schizosaccharomyces_pombe|9606|Ala|TGC | ||
| GGGGATTTAATTTAATTGGTTAGAATATTGTGTTTGCACCACAAAAATCTGGTTTCGAGT | ||
| ACCAGAATCTCCA | ||
| >URS000045D66C_4896|Schizosaccharomyces_pombe|9606|His|GTG | ||
| GGTGATTGTAATTCAATGGTAGAATGCTTATTTGTGGCATAAGAAGTTCTTGGTTCGATT | ||
| CCAAGTAATCACC | ||
| >URS000023E104_4896|Schizosaccharomyces_pombe|9606|Asp|GTC | ||
| GAATCTGTAGCTTAAAGTAAAGTATCGCCTTGTCACGGTGATGGATGCCCACTCGTACTG | ||
| GGTCAGATTCG | ||
| >URS000025B7E6_4896|Schizosaccharomyces_pombe|9606|Pro|TGG | ||
| CGGATAGAAACATGTATTGGTTCATGTACTTGCTTTGGGTGTGAGAATTTGTTAGTTCGA | ||
| ATCTAACCTATCCGA | ||
| >URS00004A6ED0_4896|Schizosaccharomyces_pombe|9606|Tyr|GTA | ||
| GGGGAGAATTCTTATGTTGGTTTTAAGAGGTGAGTTGTAGCCTCATTAGGTCAATCCTAT | ||
| CGCAGGTTCGATTCCTGCTCTCCTCA | ||
| >URS00003FFD19_4896|Schizosaccharomyces_pombe|9606|Arg|TCG | ||
| GTCTGTATAGCTCAATGGTAGAGCATCTCACTTCTAATGAGTCGATCTAAGTTCGATTCT | ||
| TAGTACAGATTCCACAC |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,75 @@ | ||
| >URS000040774E_4896|Schizosaccharomyces_pombe|9606|Trp|TCA | ||
| AAGAGTATAGTTTAATTGGTAAAACTTCTGATTCCAAATTAGACATTGTTCGTTCAAGTC | ||
| GGACTGCTCTTG | ||
| >URS000052E18F_4896|Schizosaccharomyces_pombe|9606|Cys|GCA | ||
| GATAATGTTCAGTGGTCTGAAATTGAATTTGCAAAATTTGATATATGAGTTCAATTCTCA | ||
| TCATTATCT | ||
| >URS00002C4932_4896|Schizosaccharomyces_pombe|9606|Val|TAC | ||
| AGGAGAATAGCTTAATTGGTAGAGCACTTACCTTACAAGTAAGATTATAAGGGTTCAAAT | ||
| CCCTTTTCTCCTA | ||
| >URS00003B0065_4896|Schizosaccharomyces_pombe|9606|Leu|TAG | ||
| GCAGATGTGATGAAATTGGTAAACATGTTTACCTTAGGAGTAAAATCTTGAAGGTTCGAA | ||
| TCCTTCCATCTGTA | ||
| >URS00001AD663_4896|Schizosaccharomyces_pombe|9606|Leu|TAA | ||
| GCCTAAATGCTGGAATTTGGTAGACAGAACAAACTTAAGATTTGTCGCTTTCGAGCGTGT | ||
| TGGTTCGAGTCCAACTTTAGGTA | ||
| >URS00001DDDAC_4896|Schizosaccharomyces_pombe|9606|Ile|GAT | ||
| AGTTCTTTAACTTAAAAGGTCAGAGTGCAGACTTGATAAGTCTGTGGTATTGGTTCGATT | ||
| CCAATAAGAACTA | ||
| >URS00000E510A_4896|Schizosaccharomyces_pombe|9606|Ser|TGA | ||
| GGAAGGGTGTCCGAGTGGTTTAAGGAGCGATATTTGAGCTATTGTGATTTATTCATCGCA | ||
| GGTTCGAATCCTGCCCCTTTCG | ||
| >URS00000B84DA_4896|Schizosaccharomyces_pombe|9606|Arg|TCG | ||
| GCACTTTTAGCTTAATTGGTTAGAGTAACAATCTTCGAAATTGTTAGTATAGGTTCAAAT | ||
| CCTATAAAGTGTT | ||
| >URS00005E6A72_4896|Schizosaccharomyces_pombe|9606|Gly|TCC | ||
| GCAGATATAAGTCAATTGGCAGACCTTCTGATTTCCACTTAGATTATGTTCGTTCGAATC | ||
| GGACTATCTGCA | ||
| >URS00000E1077_4896|Schizosaccharomyces_pombe|9606|Asn|GTT | ||
| GTTGTTGTAGCTCAATGGTAGAGCAAGTCACTGTTAATGACCTGATAGTGGTTCGATTCC | ||
| ACTCAATAACG | ||
| >URS00000A90BD_4896|Schizosaccharomyces_pombe|9606|Lys|TTT | ||
| GGGGATGTAGCTCAATGGTTAGAGCTTTCGCCTTTTAAGCGATAGGATAAGGGTTCAAAT | ||
| CCCTTCAGACCCA | ||
| >URS0000226DF4_4896|Schizosaccharomyces_pombe|9606|Glu|TTC | ||
| GGCTCTATTGTCTAATGGTTAAGACCTTACATCTTCATTGTAAATATCTTGGTTCGATTC | ||
| CAAGTAGGGCTA | ||
| >URS000027C703_4896|Schizosaccharomyces_pombe|9606|Ser|GCT | ||
| GGAAAAATAGTTCTAATTGGTAAGAAGGATACTTGCTACGTATCTGGTGAATAACCTTGT | ||
| GAGTTCGAGTCTCACTTTTTCCG | ||
| >URS000012A615_4896|Schizosaccharomyces_pombe|9606|Thr|TGT | ||
| GCTAATTTAACTCAATTGGTAGAGTGCGTACCTTGTAAGTACGAAGTTAGAGGTTCAATT | ||
| CCTCTAATTAGCA | ||
| >URS0000519C3F_4896|Schizosaccharomyces_pombe|9606|Glu|TTC | ||
| TGGGTTGTTGACTAATAGGTAAGTCCCTGAAATTTGACTTCAGTCTATGTAAGTTCGAAT | ||
| CTTACCATCCCAT | ||
| >URS0000101C2D_4896|Schizosaccharomyces_pombe|9606|Met|CAT | ||
| TGCGATTTAATGTAATTGGTTAACATCTCTGACTCATGATCAGTGTATTAAGGTTCAAGT | ||
| CCTTAGGTCGCAC | ||
| >URS00003C6042_4896|Schizosaccharomyces_pombe|9606|Ile|GAT | ||
| AGGATTATAGCTTAACGGTTAAAGCAGAGAGCTCATAACTCTTGTATATTGGTTCGATTC | ||
| CAGTTTGTCCTA | ||
| >URS0000409C5E_4896|Schizosaccharomyces_pombe|9606|Phe|GAA | ||
| GCTCTGATAACTTAACGGTTAAAGTGCAGTATTGAAGCTGCTGAGATATTGGTTCGATTC | ||
| CATTTCAGAGCA | ||
| >URS00001B646E_4896|Schizosaccharomyces_pombe|9606|Met|CAT | ||
| GTTGGTATAGTTTAATTGGTTAAAATAATCTCCTCATGTGAGATTGATCTATAGGTTCGA | ||
| GCCCTTTTACCAACT | ||
| >URS00000FEDF7_4896|Schizosaccharomyces_pombe|9606|Ala|TGC | ||
| GGGGATTTAATTTAATTGGTTAGAATATTGTGTTTGCACCACAAAAATCTGGTTTCGAGT | ||
| ACCAGAATCTCCA | ||
| >URS000045D66C_4896|Schizosaccharomyces_pombe|9606|His|GTG | ||
| GGTGATTGTAATTCAATGGTAGAATGCTTATTTGTGGCATAAGAAGTTCTTGGTTCGATT | ||
| CCAAGTAATCACC | ||
| >URS000023E104_4896|Schizosaccharomyces_pombe|9606|Asp|GTC | ||
| GAATCTGTAGCTTAAAGTAAAGTATCGCCTTGTCACGGTGATGGATGCCCACTCGTACTG | ||
| GGTCAGATTCG | ||
| >URS000025B7E6_4896|Schizosaccharomyces_pombe|9606|Pro|TGG | ||
| CGGATAGAAACATGTATTGGTTCATGTACTTGCTTTGGGTGTGAGAATTTGTTAGTTCGA | ||
| ATCTAACCTATCCGA | ||
| >URS00004A6ED0_4896|Schizosaccharomyces_pombe|9606|Tyr|GTA | ||
| GGGGAGAATTCTTATGTTGGTTTTAAGAGGTGAGTTGTAGCCTCATTAGGTCAATCCTAT | ||
| CGCAGGTTCGATTCCTGCTCTCCTCA | ||
| >URS00003FFD19_4896|Schizosaccharomyces_pombe|9606|Arg|TCG | ||
| GTCTGTATAGCTCAATGGTAGAGCATCTCACTTCTAATGAGTCGATCTAAGTTCGATTCT | ||
| TAGTACAGATTCCACAC |
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