def _parse_impact_header(hdr_dict):
    """Parse fields for impact, taken from vcf2db
    """
    desc = hdr_dict["Description"]
    if hdr_dict["ID"] == "ANN":
        parts = [x.strip("\"'") for x in re.split("\s*\|\s*", desc.split(":", 1)[1].strip('" '))]
    elif hdr_dict["ID"] == "EFF":
        parts = [x.strip(" [])'(\"") for x in re.split("\||\(", desc.split(":", 1)[1].strip())]
    elif hdr_dict["ID"] == "CSQ":
        parts = [x.strip(" [])'(\"") for x in re.split("\||\(", desc.split(":", 1)[1].strip())]
    elif hdr_dict["ID"] == "BCSQ":
        parts = desc.split(']', 1)[1].split(']')[0].replace('[','').split("|")
    else:
        raise Exception("don't know how to use %s as annotation" % hdr_dict["ID"])
    return parts
def _parse_impact_header ( hdr_dict ) : desc = hdr_dict [ "Description" ] if hdr_dict [ "ID" ] == "ANN" : parts = [ x . strip ( "\"'" ) for x in re . split ( "\s*\|\s*" , desc . split ( ":" , 1 ) [ 1 ] . strip ( '" ' ) ) ] elif hdr_dict [ "ID" ] == "EFF" : parts = [ x . strip ( " [])'(\"" ) for x in re . split ( "\||\(" , desc . split ( ":" , 1 ) [ 1 ] . strip ( ) ) ] elif hdr_dict [ "ID" ] == "CSQ" : parts = [ x . strip ( " [])'(\"" ) for x in re . split ( "\||\(" , desc . split ( ":" , 1 ) [ 1 ] . strip ( ) ) ] elif hdr_dict [ "ID" ] == "BCSQ" : parts = desc . split ( ']' , 1 ) [ 1 ] . split ( ']' ) [ 0 ] . replace ( '[' , '' ) . split ( "|" ) else : raise Exception ( "don't know how to use %s as annotation" % hdr_dict [ "ID" ] ) return parts
Parse fields for impact, taken from vcf2db