Use --detail option with tRNAscan-SE

[patriciaplchan]

Currently R2DT uses the predicted tRNA isotype from tRNAscan-SE to select the corresponding template for Traveler 2D image generation. However, mt-tRNA-Cys in armadillo and some reptides do not have the D-arm which has to use the specific "no-D-arm" template instead of the typical one. This problem can be resolved by adding the --detail option when running tRNAscan-SE to include the extra detailed information. In the last “Note” column of the standard output, a mt-tRNA-Cys that is missing the D-arm will say “No D-arm”. The secondary structure output that includes the alignment will also have an extra “Note” line for that tRNA, also saying “No D-arm”. Parsing this info will allow the selection of appropriate template.