takes input and output paths as arguments
keeping the gene results in the same folder as the predictions now
after running the hmm, fetches the # of hits in promoter/gb regions for each gene..
hardcoded the parameters in accordance with the paper
say when the hmm is running...
include strand information in the gs_gb list (for HMM)
deleted a space
tidier
includes quality control now
spacing
delete the header line...
added a logfile
differentiates suffices
restrict to consistent regions
now includes dREG hit locations
including all the columns in the first filter
intermediate...
takes infile and outfile for more transparent pipeline
takes input and output file paths
big changes - now we have a high confidence and low confidence set... do identical analysis on each, except for threshold and additioanl QC on the high-confidence