genewise_bed_coverage.py - compute coverage of a .bed file over all genes
entrywise_bed_coverage.py - from the other direction, given a .bed file and 4 .bed files
		         containing promoters, exons, introns, and repeat regions, calculate
		         genomic partition of each entry in the .bed file (no UTRs)
			 

UPDATE THIS

bed_gene_feature_coverage.py is the main script here. It is used to compute various coverage statistics given
a .bed file and a reference genome, which can be in any format as long as you give a header file
with the format for it. This can be generated by downloading a table from the UCSC genome browser
and then putting the top line into the header file, like:
head -n 1 ref_file.txt > ref_header.txt

The script is run as follows:

python bed_gene_feature_coverage.py reffile ref_format bedfile output log

Where reffile and ref_format are the reference and header files described above, bedfile is the
.bed file you want to compute statistics on, output is the path to the output file, and log is
the path to a log file, which contains details of peak checking for debugging purposes.