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1 #!/usr/bin/env python
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2 import fileinput
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3
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4 print ("##gff-version-3")
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5 # process each trna in tsv file
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6 metaLines = 0
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7 for trna in fileinput.input():
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8 if metaLines < 3:
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9 metaLines += 1
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10 continue
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11 cols_tsv = trna.split("\t")
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12 if int(cols_tsv[2]) < int(cols_tsv[3]):
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13 cols_gff = [
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14 cols_tsv[0].strip(),
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15 "tRNAscan",
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16 "tRNA",
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17 cols_tsv[2].strip(),
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18 cols_tsv[3].strip(),
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19 cols_tsv[8],
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20 "+",
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21 ".",
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22 'ID=trna.%s;Anticodon=%s;Codon=tRNA-%s'
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23 % (cols_tsv[1], cols_tsv[5].lower(), cols_tsv[4]),
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24 ]
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25 else:
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26 cols_gff = [
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27 cols_tsv[0].strip(),
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28 "tRNAscan",
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29 "tRNA",
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30 cols_tsv[3].strip(),
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31 cols_tsv[2].strip(),
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32 cols_tsv[8],
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33 "-",
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34 ".",
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35 'ID=trna.%s;Anticodon=%s;Codon=tRNA-%s'
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36 % (cols_tsv[1], cols_tsv[5].lower(), cols_tsv[4]),
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37 ]
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38 print ("\t".join(cols_gff))
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