Mercurial > repos > bgruening > trna_prediction

annotate aragorn_out_to_gff3.py @ 3:b86f3e5626f4 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit 1b3f92275bb60e606cd4fdc394fb9df95232a5aa
author bgruening
date Tue, 28 Oct 2025 09:15:42 +0000
parents 358f58401cd6
children
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1 #!/usr/bin/env python
2
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2 import sys
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3
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4 full_gene_model = False
3
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5 if "--full" in sys.argv:
2
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6 full_gene_model = True
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7
2
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8 genome_id = None
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9 stdin_data = []
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10 KEY_ORDER = (
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11 "parent",
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12 "source",
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13 "type",
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14 "start",
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15 "end",
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16 "score",
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17 "strand",
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18 "8",
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19 "quals",
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20 )
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21
2
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22 # Table of amino acids
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23 aa_table = {
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24 "Ala": "A",
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25 "Arg": "R",
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26 "Asn": "N",
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27 "Asp": "D",
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28 "Cys": "C",
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29 "Gln": "Q",
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30 "Glu": "E",
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31 "Gly": "G",
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32 "His": "H",
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33 "Ile": "I",
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34 "Leu": "L",
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35 "Lys": "K",
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36 "Met": "M",
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37 "Phe": "F",
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38 "Pro": "P",
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39 "Ser": "S",
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40 "Thr": "T",
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41 "Trp": "W",
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42 "Tyr": "Y",
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43 "Val": "V",
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44 "Pyl": "O",
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45 "seC": "U",
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46 "???": "X",
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47 }
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49
2
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50 def output_line(gff3):
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51 print("\t".join(str(gff3[x]) for x in KEY_ORDER))
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52
3
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53
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54 print("##gff-version 3")
2
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55 for line in sys.stdin:
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56 if line.startswith(">"):
2
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57 genome_id = line[1:].strip()
3
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58 if " " in genome_id:
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59 genome_id = genome_id[0: genome_id.index(" ")]
2
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60 else:
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61 data = line.split()
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62 if len(data) == 5:
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63 # Parse data
3
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64 strand = "-" if data[2].startswith("c") else "+"
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65 start, end = data[2][data[2].index("[") + 1: -1].split(",")
2
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66
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67 gff3 = {
3
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68 "parent": genome_id,
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69 "source": "aragorn",
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70 "start": int(start),
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71 "end": int(end),
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72 "strand": strand,
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73 "score": ".",
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74 "8": ".",
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75 }
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76
2
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77 aa_long = data[1][5:]
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78 aa_short = aa_table[aa_long]
3
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79 anticodon = data[4][1: data[4].index(")")].upper().replace("T", "U")
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80 name = "trn{}-{}".format(aa_short, anticodon)
2
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81
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82 if not full_gene_model:
3
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83 gff3.update(
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84 {
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85 "type": "tRNA",
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86 "quals": "ID=tRNA{0}.{1};Name={name};product={2}".format(
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87 genome_id, *data, name=name
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88 ),
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89 }
b86f3e5626f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit 1b3f92275bb60e606cd4fdc394fb9df95232a5aa
bgruening
parents: 2
diff changeset
90 )
2
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44
bgruening
parents: 1
diff changeset
91 output_line(gff3)
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44
bgruening
parents: 1
diff changeset
92 else:
3
b86f3e5626f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit 1b3f92275bb60e606cd4fdc394fb9df95232a5aa
bgruening
parents: 2
diff changeset
93 gff3.update(
b86f3e5626f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit 1b3f92275bb60e606cd4fdc394fb9df95232a5aa
bgruening
parents: 2
diff changeset
94 {
b86f3e5626f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit 1b3f92275bb60e606cd4fdc394fb9df95232a5aa
bgruening
parents: 2
diff changeset
95 "type": "gene",
b86f3e5626f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit 1b3f92275bb60e606cd4fdc394fb9df95232a5aa
bgruening
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96 "quals": "ID=gene{0}.{1};Name={name};product={2}".format(
b86f3e5626f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit 1b3f92275bb60e606cd4fdc394fb9df95232a5aa
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diff changeset
97 genome_id, *data, name=name
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bgruening
parents: 2
diff changeset
98 ),
b86f3e5626f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit 1b3f92275bb60e606cd4fdc394fb9df95232a5aa
bgruening
parents: 2
diff changeset
99 }
b86f3e5626f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit 1b3f92275bb60e606cd4fdc394fb9df95232a5aa
bgruening
parents: 2
diff changeset
100 )
2
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44
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diff changeset
101 output_line(gff3)
3
b86f3e5626f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit 1b3f92275bb60e606cd4fdc394fb9df95232a5aa
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102 gff3.update(
b86f3e5626f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit 1b3f92275bb60e606cd4fdc394fb9df95232a5aa
bgruening
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103 {
b86f3e5626f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit 1b3f92275bb60e606cd4fdc394fb9df95232a5aa
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104 "type": "tRNA",
b86f3e5626f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit 1b3f92275bb60e606cd4fdc394fb9df95232a5aa
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105 "quals": "ID=tRNA{0}.{1};Parent=gene{0}.{1};Name={name};product={2}".format(
b86f3e5626f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit 1b3f92275bb60e606cd4fdc394fb9df95232a5aa
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diff changeset
106 genome_id, *data, name=name
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bgruening
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diff changeset
107 ),
b86f3e5626f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit 1b3f92275bb60e606cd4fdc394fb9df95232a5aa
bgruening
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diff changeset
108 }
b86f3e5626f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit 1b3f92275bb60e606cd4fdc394fb9df95232a5aa
bgruening
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diff changeset
109 )
2
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44
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parents: 1
diff changeset
110 output_line(gff3)
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111
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44
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diff changeset
112 # If no introns
3
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diff changeset
113 if ")i(" not in data[4]:
b86f3e5626f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit 1b3f92275bb60e606cd4fdc394fb9df95232a5aa
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114 gff3["type"] = "exon"
b86f3e5626f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit 1b3f92275bb60e606cd4fdc394fb9df95232a5aa
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115 gff3["quals"] = "Parent=tRNA{0}.{1}".format(genome_id, *data)
2
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44
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diff changeset
116 output_line(gff3)
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bgruening
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117 else:
3
b86f3e5626f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit 1b3f92275bb60e606cd4fdc394fb9df95232a5aa
bgruening
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118 intron_location = data[4][data[4].rindex("(") + 1: -1].split(",")
2
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119 intron_start, intron_length = map(int, intron_location)
3
b86f3e5626f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit 1b3f92275bb60e606cd4fdc394fb9df95232a5aa
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120 if strand == "+":
b86f3e5626f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit 1b3f92275bb60e606cd4fdc394fb9df95232a5aa
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diff changeset
121 original_end = gff3["end"]
2
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44
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parents: 1
diff changeset
122 else:
3
b86f3e5626f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit 1b3f92275bb60e606cd4fdc394fb9df95232a5aa
bgruening
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diff changeset
123 original_end = gff3["start"]
1
d788d1abe238 Uploaded
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diff changeset
124
2
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44
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125 # EXON
3
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126 gff3.update(
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127 {
b86f3e5626f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit 1b3f92275bb60e606cd4fdc394fb9df95232a5aa
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128 "type": "exon",
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129 "quals": "Parent=tRNA{0}.{1}".format(genome_id, *data),
b86f3e5626f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit 1b3f92275bb60e606cd4fdc394fb9df95232a5aa
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130 }
b86f3e5626f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit 1b3f92275bb60e606cd4fdc394fb9df95232a5aa
bgruening
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diff changeset
131 )
b86f3e5626f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit 1b3f92275bb60e606cd4fdc394fb9df95232a5aa
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diff changeset
132 if strand == "+":
b86f3e5626f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit 1b3f92275bb60e606cd4fdc394fb9df95232a5aa
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diff changeset
133 gff3["end"] = gff3["start"] + intron_start - 2
2
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44
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parents: 1
diff changeset
134 else:
3
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diff changeset
135 gff3["start"] = gff3["end"] - intron_start + 2
2
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44
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diff changeset
136
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bgruening
parents: 1
diff changeset
137 output_line(gff3)
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diff changeset
138
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diff changeset
139 # INTRON
3
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diff changeset
140 gff3.update(
b86f3e5626f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit 1b3f92275bb60e606cd4fdc394fb9df95232a5aa
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diff changeset
141 {
b86f3e5626f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit 1b3f92275bb60e606cd4fdc394fb9df95232a5aa
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diff changeset
142 "type": "intron",
b86f3e5626f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit 1b3f92275bb60e606cd4fdc394fb9df95232a5aa
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diff changeset
143 "quals": "Parent=tRNA{0}.{1}".format(genome_id, *data),
b86f3e5626f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit 1b3f92275bb60e606cd4fdc394fb9df95232a5aa
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144 }
b86f3e5626f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit 1b3f92275bb60e606cd4fdc394fb9df95232a5aa
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diff changeset
145 )
b86f3e5626f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit 1b3f92275bb60e606cd4fdc394fb9df95232a5aa
bgruening
parents: 2
diff changeset
146 if strand == "+":
b86f3e5626f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit 1b3f92275bb60e606cd4fdc394fb9df95232a5aa
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diff changeset
147 gff3["start"] = gff3["end"] + 1
b86f3e5626f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit 1b3f92275bb60e606cd4fdc394fb9df95232a5aa
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diff changeset
148 gff3["end"] = gff3["start"] + intron_length + 2
2
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44
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parents: 1
diff changeset
149 else:
3
b86f3e5626f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit 1b3f92275bb60e606cd4fdc394fb9df95232a5aa
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diff changeset
150 gff3["end"] = gff3["start"] - 1
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diff changeset
151 gff3["start"] = gff3["end"] - intron_length + 1
2
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44
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parents: 1
diff changeset
152
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44
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diff changeset
153 output_line(gff3)
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diff changeset
154
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44
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diff changeset
155 # EXON
3
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diff changeset
156 gff3.update(
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diff changeset
157 {
b86f3e5626f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit 1b3f92275bb60e606cd4fdc394fb9df95232a5aa
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diff changeset
158 "type": "exon",
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diff changeset
159 "quals": "Parent=tRNA{0}.{1}".format(genome_id, *data),
b86f3e5626f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit 1b3f92275bb60e606cd4fdc394fb9df95232a5aa
bgruening
parents: 2
diff changeset
160 }
b86f3e5626f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit 1b3f92275bb60e606cd4fdc394fb9df95232a5aa
bgruening
parents: 2
diff changeset
161 )
b86f3e5626f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit 1b3f92275bb60e606cd4fdc394fb9df95232a5aa
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parents: 2
diff changeset
162 if strand == "+":
b86f3e5626f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit 1b3f92275bb60e606cd4fdc394fb9df95232a5aa
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parents: 2
diff changeset
163 gff3["start"] = gff3["end"] + 1
b86f3e5626f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit 1b3f92275bb60e606cd4fdc394fb9df95232a5aa
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diff changeset
164 gff3["end"] = original_end
2
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44
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parents: 1
diff changeset
165 else:
3
b86f3e5626f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit 1b3f92275bb60e606cd4fdc394fb9df95232a5aa
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diff changeset
166 gff3["end"] = gff3["start"] - 1
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diff changeset
167 gff3["start"] = original_end
2
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parents: 1
diff changeset
168
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44
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diff changeset
169 output_line(gff3)