def run(self):
"""
2010-8-15
create a RBDict of gene-forms [chr, start, stop] with min_overlap_ratio=1.
value is a sub-RBDict of the gene structure (UTR, non-UTR-exon, intron)
given any CNV, use RBDict.findNodes() to find all gene-forms.
WATCH: use an alternative comparison function.
"""
if self.debug:
import pdb
pdb.set_trace()
genome_db = GenomeDB.GenomeDatabase(drivername=self.drivername, username=self.db_user,
password=self.db_passwd, hostname=self.hostname, database=self.genome_dbname, )
genome_db.setup(create_tables=False)
db_250k = Stock_250kDB.Stock_250kDB(drivername=self.drivername, username=self.db_user, password=self.db_passwd, \
hostname=self.hostname, database=self.dbname)
db_250k.setup(create_tables=False)
oneGenomeData = genome_db.getOneGenomeData(tax_id=self.tax_id, chr_gap=0)
cumuSpan2ChrRBDict = oneGenomeData.cumuSpan2ChrRBDict
genomeRBDict = genome_db.dealWithGenomeRBDict(self.genomeRBDictPickleFname, tax_id=self.tax_id, \
max_distance=self.max_distance, debug=self.debug)
#genomeRBDict = None
pd = PassingData(min_MAF=self.min_MAF,\
starting_rank=0, \
need_chr_pos_ls=0,\
need_candidate_association=False,\
min_big_overlap=self.min_big_overlap,\
no_of_permutations=self.no_of_permutations,\
no_of_min_breaks=self.no_of_min_breaks)
for result_id in self.result_id_ls:
candidate_gene_set = db_250k.dealWithCandidateGeneList(self.list_type_id, return_set=True) #internal cache
pd.candidate_gene_set = candidate_gene_set
#gwr = db_250k.getResultMethodContent(result_id, pdata=pd)
#top_loci = gwr.getTopLoci(no_of_top_loci=self.no_of_top_loci)
top_loci = self.getResultPeak(result_id, self.result_peak_type_id, pd)
top_loci_in_cumu_pos = self.translateChrPosDataObjectIntoCumuPos(top_loci, oneGenomeData.chr_id2cumu_start)
top_loci_in_chr_pos = self.translateCumuPosIntoChrPos(top_loci_in_cumu_pos, cumuSpan2ChrRBDict)
permData = self.prepareDataForPermutationRankTest(top_loci_in_chr_pos, genomeRBDict, pd, report=True)
#m = self.dealWithNoOfSNPsAssociatedWithCandidateGeneList(pd.list_type_id, rm, pd) #cache is internally going on
#n = permData.no_of_total_snps - m
candidate_sample_size = len(permData.captured_candidate_gene_set)
non_candidate_sample_size = len(permData.non_candidate_gene_snp_rank_ls)
return_data = self.get_enrichment_pvalue_by_gw_looping(candidate_sample_size, top_loci_in_cumu_pos, candidate_gene_set, \
genomeRBDict, cumuSpan2ChrRBDict=cumuSpan2ChrRBDict, \
no_of_permutations=pd.no_of_permutations, no_of_min_breaks=pd.no_of_min_breaks, param_data=pd)
pvalue = return_data.pvalue
no_of_tests = return_data.no_of_tests
no_of_tests_passed = return_data.no_of_tests_passed
sys.stderr.write("%s pvalue: %s.\n"%(result_id, pvalue))
if self.commit:
db_250k.session.flush()
def run(self):
"""
2010-8-15
create a RBDict of gene-forms [chr, start, stop] with min_overlap_ratio=1.
value is a sub-RBDict of the gene structure (UTR, non-UTR-exon, intron)
given any CNV, use RBDict.findNodes() to find all gene-forms.
WATCH: use an alternative comparison function.
"""
if self.debug:
import pdb
pdb.set_trace()
genome_db = GenomeDB.GenomeDatabase(
drivername=self.drivername,
username=self.db_user,
password=self.db_passwd,
hostname=self.hostname,
database=self.genome_dbname,
)
genome_db.setup(create_tables=False)
db_250k = Stock_250kDB.Stock_250kDB(drivername=self.drivername, username=self.db_user, password=self.db_passwd, \
hostname=self.hostname, database=self.dbname)
db_250k.setup(create_tables=False)
oneGenomeData = genome_db.getOneGenomeData(tax_id=self.tax_id,
chr_gap=0)
genomeRBDict = genome_db.dealWithGenomeRBDict(self.genomeRBDictPickleFname, tax_id=self.tax_id, \
max_distance=self.max_distance, debug=self.debug)
#genomeRBDict = None
pd = PassingData(min_MAF=self.min_MAF,\
min_score=self.min_score, \
results_directory=self.results_directory, \
no_of_top_loci=self.no_of_top_loci, \
starting_rank=0, \
need_chr_pos_ls=0,\
need_candidate_association=False,\
min_big_overlap=self.min_big_overlap,\
no_of_permutations=self.no_of_permutations,\
no_of_min_breaks=self.no_of_min_breaks)
compareIns = CNVCompareByOverlapLen(
min_overlap_len=100) #any overlap is an overlap
translationData = None
for result_id in self.result_id_ls:
#establish the map from cnv.id from chr_pos
rm = Stock_250kDB.ResultsMethod.get(result_id)
if not rm.cnv_method_id:
sys.stderr.write(
"ResultsMethod %s doesn't have cnv_method_id. Skip.\n" %
(result_id))
continue
if not db_250k._cnv_id2chr_pos:
db_250k.cnv_id2chr_pos = rm.cnv_method_id
translationData = self.getTranslationDataStructureForBackgroundLoci(
db_250k,
cnv_method_id=rm.cnv_method_id,
min_MAF=self.min_MAF)
if not translationData.chrSpan2cumuStartRBDict:
sys.stderr.write(
"Error: translationData.chrSpan2cumuStartRBDict is empty for cnv method %s. exit.\n"
% (rm.cnv_method_id))
sys.exit(3)
pd.db_id2chr_pos = db_250k.cnv_id2chr_pos
candidate_gene_set = db_250k.dealWithCandidateGeneList(
self.list_type_id, return_set=True) #internal cache
pd.candidate_gene_set = candidate_gene_set
gwr = db_250k.getResultMethodContent(
result_id, pdata=pd, min_value_cutoff=self.min_score)
top_loci = gwr.getTopLoci(no_of_top_loci=self.no_of_top_loci,
min_score=self.min_score)
top_loci_in_cumu_pos = self.translateChrPosDataObjectIntoCumuPos(
top_loci, translationData.chrSpan2cumuStartRBDict)
top_loci_in_chr_pos = self.translateCumuPosIntoChrPos(top_loci_in_cumu_pos, translationData.cumuSpan2ChrSpanRBDict, \
compareIns=compareIns)
permData = self.prepareDataForPermutationRankTest(
top_loci_in_chr_pos, genomeRBDict, pd, report=True)
#m = self.dealWithNoOfSNPsAssociatedWithCandidateGeneList(pd.list_type_id, rm, pd) #cache is internally going on
#n = permData.no_of_total_snps - m
candidate_sample_size = len(permData.captured_candidate_gene_set)
non_candidate_sample_size = len(
permData.non_candidate_gene_snp_rank_ls)
return_data = self.get_enrichment_pvalue_by_gw_looping(candidate_sample_size, top_loci_in_cumu_pos, candidate_gene_set, \
genomeRBDict, cumuSpan2ChrSpanRBDict=translationData.cumuSpan2ChrSpanRBDict, \
no_of_permutations=pd.no_of_permutations, no_of_min_breaks=pd.no_of_min_breaks, param_data=pd,\
compareIns=compareIns)
pvalue = return_data.pvalue
no_of_tests = return_data.no_of_tests
no_of_tests_passed = return_data.no_of_tests_passed
sys.stderr.write("%s pvalue: %s.\n" % (result_id, pvalue))
if self.commit:
db_250k.session.flush()