def funcionprincipal(dato,variable,opciones):
from rpy import r
lista=dato.query(variable)
diccionario = {}
diccionario["KS"] = {}
if opciones[u"Distribución"]=="Uniforme":
resultado=r.ks_test(lista,"runif")
elif opciones[u"Distribución"]=="Normal":
resultado=r.ks_test(lista,"rnorm")
diccionario["KS"]["Variable"] = str(variable)
diccionario["KS"][u"Significación"]=resultado["p.value"]
return diccionario
def _calcKS_(scores,exp_scores=None):
ret = {}
ret["D"] = -1
try:
from rpy import r
if exp_scores:
res = r.ks_test(scores,exp_scores)
else:
res = r.ks_test(scores,"punif")
ret = res["statistic"]
ret["p.value"] = res["p.value"]
except Exception, message:
print "Calculating KS failed??",message
def run(self):
"""
01-06-06
01-14-06
add kolmogorov-smirnov test
--db_connect()
--get_gene_id2mt_no_set()
--get_ortholog_pairs()
--get_homo_genes_for_2_tax_ids()
--get_tfbs_similarity_ls()
--calculate_tfbs_similarity()
--draw_tfbs_similarity_ls_histogram()
"""
(conn, curs) = db_connect(self.hostname, self.dbname, self.schema)
if self.type==1:
gene_id2mt_no_set = self.get_gene_id2mt_no_set(curs)
elif self.type==2:
if self.input_fname_list==[]:
sys.stderr.write("Please specify -i, type=2 needs that.\n")
sys.exit(2)
prom_id2gene_id = self.get_prom_id2gene_id(curs)
mt_id2no = self.get_mt_id2no(curs)
gene_id2mt_no_set = self.get_gene_id2mt_no_set_from_file(self.input_fname_list, mt_id2no, prom_id2gene_id)
#get ortholog pairs
bad_ortholog_fname = '%s.bad_ortholog'%self.output_prefix
hs_gene_id_list, mm_gene_id_list = self.get_ortholog_pairs(curs, bad_ortholog_fname)
tfbs_similarity_ls = self.get_tfbs_similarity_ls(hs_gene_id_list, mm_gene_id_list, gene_id2mt_no_set)
ortholog_pair_hist_fname = '%s_ortholog_pair_hist.png'%self.output_prefix
self.draw_tfbs_similarity_ls_histogram(tfbs_similarity_ls, ortholog_pair_hist_fname)
#random
random.shuffle(mm_gene_id_list)
random_tfbs_similarity_ls = self.get_tfbs_similarity_ls(hs_gene_id_list, mm_gene_id_list, gene_id2mt_no_set)
random_pair_hist_fname = '%s_random_pair_hist.png'%self.output_prefix
self.draw_tfbs_similarity_ls_histogram(random_tfbs_similarity_ls, random_pair_hist_fname)
#do a kolmogorov-smirnov test
ks_result = r.ks_test(tfbs_similarity_ls,random_tfbs_similarity_ls)
print "kolmogorov-smirnov test p-value:", ks_result['p.value']