I ran into a bed file format term called : "WUSTL gateway compatible bed" I tried to search the term with Google, but got no obvious hits.
Does anyone know what that kind of bed file looks like? Thanks!
I came across with this term when I tried to read code of ROSE algorithm developed by Richard Young's group: https://bitbucket.org/young_computation/rose ( I tried to use the ROSE to analyze my own data, but had some issues: https://bitbucket.org/young_computation/rose/issues/26/unexpected-running-result-using-rose)
in the Python file ROSE_utils.py, they format bed file as follows:
''' formats a bed file from UCSC or MACS into a WUSTL gateway compatible bed ''' newBed =  if type(bed) == str: bed = parseTable(bed,'\t') indexTicker = 1 for line in bed: newLine = line[0:4] try: strand = line except IndexError: strand = '.' newLine+= [indexTicker,strand] indexTicker +=1 newBed.append(newLine) if len(output) > 0: unParseTable(newBed,output,'\t') else: return newBed
it seems to me that they added a fifth column column with " ." as value to the normal bed file generated from MACS to format the "WUSTL gateway compatible bed", is that correct? I wonder the fact that they used different format of bed file might be the cause of my issue.
Update: I could successfully apply ROSE to my other data "cooked" following exactly the same pipeline , so it seems the formatBed function has nothing to do with my previous issues. Also, after careful reading of the whole code, it seems to me actually the formatBed function were never called. so I will leave the question here for pure curiosity reasons.