Mercurial > repos > cpt > cpt_convert_trnascan_se
view cpt_trnascanse_to_gff/tRNAscan_to_gff_SE_format.py @ 2:09168094a98f draft default tip
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author | cpt |
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date | Fri, 20 May 2022 08:43:44 +0000 |
parents | b4134ad44443 |
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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))