trnascansehandler

class pdm_utils.classes.trnascansehandler.TRNAscanSEHandler(identifier, sequence)

Bases: object

parse_trnas()

Searches out_str for matches to a regular expression for tRNAscan-SE tRNAs. :return:

read_output()

Reads the Aragorn output file and joins the lines into a single string which it populates into out_str. :return:

run_trnascanse(x=10)

Set up tRNAscan-SE command, then run it. Explanation of arguments: :param x: score cutoff for tRNAscan-SE :type x: int :return:

write_fasta()

Writes the search sequence to input file in FASTA format. :return: