Which tRNAscan-SE parameters are needed to be used with this repo?

[lpryszcz]

Hi, I'm trying to assign tRNAscan-SE secondary structure (.ss) to canonical tRNA structure (sprinzl_positions). For that purpose, tRNA_position.py should be useful, right?

But there are two problems:

1. tRNAscan-SE v2.0.11 reports in .ss Str: lines, not #=GC SS_cons as refereed in parse-tRNAs.py (L244)
2. when I try to use .ss from above version with your code, I get an error

---> 59           while ss[regions[region_index + 2].upper - reverse_bp_index] == '.': reverse_bp_index += 1
     60           paired_base = regions[region_index + 2].upper - reverse_bp_index
     61           positions.append(Position(position='{}:{}'.format(position + 1, paired_base + 1), sprinzl=sprinzl_positions[sprinzl_index], index=len(positions), paired=True))

IndexError: list index out of range

That's example structure I'm trying to assign the posittions to:
>>>>>>>..>>>>.......<<<<.>>>>>.......<<<<<.....>>>>>.......<<<<<<<<<<<<.

My questions:

1. Which version (or which parameters) of tRNAscan-SE shall be used with this repo?
2. Could tRNA_position.py be tweaked to work with tRNAscan-SE v2.0.11?