aragornhandler

class pdm_utils.classes.aragornhandler.AragornHandler(identifier, sequence)

Bases: object

parse_determinate_trnas()

Searches out_str for matches to a regular expression for Aragorn tRNAs of determinate isotype. :return:

parse_indeterminate_trnas()

Searches out_str for matches to a regular expression for Aragorn tRNAs of indeterminate isotype. :return:

parse_tmrnas()

Searches out_str for matches to a regular expression for Aragorn tmRNAs. :return:

parse_trnas()

Calls two helper methods to parse determinate and indeterminate 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_aragorn(c=False, d=True, m=False, t=True)

Set up Aragorn command, then run it. Default arguments will assume linear sequence to be scanned on both strands for tRNAs only (no tmRNAs). :param c: treat sequence as circular :type c: bool :param d: search both strands of DNA :type d: bool :param m: search for tmRNAs :type m: bool :param t: search for tRNAs :type t: bool :return:

write_fasta()

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