view tRNAscan_to_gff_SE_format.py @ 0:d5c3354c166d draft default tip

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#!/usr/bin/env python
import fileinput

print ("##gff-version-3")
# process each trna in tsv file
metaLines = 0
for trna in fileinput.input():
    if metaLines < 3:
      metaLines += 1
      continue
    cols_tsv = trna.split("\t")
    if int(cols_tsv[2]) < int(cols_tsv[3]):
      cols_gff = [
        cols_tsv[0].strip(),
        "tRNAscan",
        "tRNA",
        cols_tsv[2].strip(),
        cols_tsv[3].strip(),
        cols_tsv[8],
        "+",
        ".",
        'ID=trna.%s;Anticodon=%s;Codon=tRNA-%s'
        % (cols_tsv[1], cols_tsv[5].lower(), cols_tsv[4]),
      ]
    else:
      cols_gff = [
        cols_tsv[0].strip(),
        "tRNAscan",
        "tRNA",
        cols_tsv[3].strip(),
        cols_tsv[2].strip(),
        cols_tsv[8],
        "-",
        ".",
        'ID=trna.%s;Anticodon=%s;Codon=tRNA-%s'
        % (cols_tsv[1], cols_tsv[5].lower(), cols_tsv[4]),
      ] 
    print ("\t".join(cols_gff))