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: