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: