def __init__(self, switch) :
self.switch = switch.lower()
Annotator.__init__(self, "sift" )
self.input_file = "%s/input/%s.csv" % (self.root_dir,switch)
self.output_dir = "%s/output" % (self.root_dir)
self.indexOf = {"coordinates" : 0, \
"codons" : 1, \
"transcript id" : 2, \
"protein id" : 3, \
"substitutions" : 4, \
"region" : 5, \
"dbsnp id" : 6, \
"snp type" : 7, \
"prediction" : 8, \
"score" : 9, \
"median info" : 10, \
"# seqs at position" : 11, \
"gene id" : 12, \
"gene name" : 13, \
"gene desc" : 14, \
"omim disease" : 15, \
"average allele freqs" : 16, \
"ceu allele freqs" : 17, \
"user comment" : 18}
self.cols = ["region","snp type", "prediction","score","omim disease"]
self.db_cols = ["sift_region","sift_type","sift_prediction","sift_score","sift_omim"]
def __init__(self ) :
Annotator.__init__(self,"snpeff")
self.indexOf = indexOf
