Reactivity_comparisons

#Run RNA folding on different sequences with input of rho reactivity, with varied slope/intercept pairs; compare folded results #to crystal structures, score comparisons with sensitivity/PPV/F1-score #Run comparisons by calling find_SHAPE_parameters.py with inputs of reactivities files, crystal structures, intermediate #directory, output directory, heatmap directory, two_eight and boxplot values (true/false), and the path to #RNAstructureLinuxTextInterfaces #Ex. for reactivities: path to directory containing *.txt files for analysis, ending with .txt, such as "/home/ptarasul/#Downloads/#opts_fptest/.txt" #Ex. for crystal structures: path to directory containing crystal structure files for comparison, ending with .ct, such as "/#home/ptarasul/Downloads/opts_fpcrystal/.ct" #Ex. for intermediate directory: path to directory that will contain intermediate files like *.rho, *.seq, and *.theta, as well #as scorer and fold files while the comparison is running, such as "/home/ptarasul/Downloads/intermed_dir" #Ex.for output directory: path to directory that will contain *.txt files with output of slope/intercept pairs and their #associated sensitivity/PPV/F1-score, such as "/home/ptarasul/Downloads/output_dir" #Ex. for heatmaps directory: path to directory that will contain *.png files of heatmaps that have intercept and slope as the x #and y axes, and F1-score as the z-axis, such as "/home/ptarasul/Downloads/heatmaps_dir" #Ex. for two_eight and boxplot: "true" or "false" for each based on whether or not the reactivities should be normalized by #SU.two_eight_normalize or by SU.boxplot_normalize, or neither #Ex. for RNAstructure: path to RNAstructure files/code, such as "/home/ptarasul/Downloads/RNAstructureLinuxTextInterfaces64bit/RNAstructure"