def run(self):
"""
"""
if self.debug:
import pdb
pdb.set_trace()
db_250k = self.db_250k
#construct the bands to be highlighted in manhattan plot
highlightBandLs = []
rm = None
for peak_id in self.peak_id_ls:
result_peak = Stock_250kDB.ResultPeak.get(peak_id)
highlightBandLs.append(
[result_peak.chromosome, result_peak.start, result_peak.stop])
#take the 1st result_peak's result as the association result to get locus_type_id
if rm is None:
rm = result_peak.result
if not rm:
sys.stderr.write(
"Error: no results_method (association result) fetched from db.\n"
)
sys.exit(1)
if self.inputFname and os.path.isfile(self.inputFname):
locus_type_id = self.getLocusTypeIDFromInput(
self.inputFname, datasetName=self.datasetName)
pd = PassingData()
if rm.cnv_method_id and not db_250k._cnv_id2chr_pos:
db_250k.cnv_id2chr_pos = rm.cnv_method_id
pd.db_id2chr_pos = db_250k.cnv_id2chr_pos
elif rm.call_method_id:
db_250k.snp_id2chr_pos = (
False, locus_type_id
) #correspond to priorTAIRVersion, locus_type_id
pd.db_id2chr_pos = db_250k.snp_id2chr_pos
#need to setup a different db setting
db_genome = GenomeDB.GenomeDatabase(drivername=self.genome_drivername, username=self.genome_db_user,
password=self.genome_db_passwd, hostname=self.genome_hostname, database=self.genome_dbname, \
schema=self.genome_schema)
db_genome.setup(create_tables=False)
gwr_name = ''
gwr = SNP.GenomeWideResult(name=gwr_name, construct_chr_pos2index=False, \
construct_data_obj_id2index=False)
gwr.fillGenomeWideResultFromHDF5CorrelationFile(
self.inputFname, datasetName=self.datasetName, pdata=pd)
gwr.drawManhattanPlot(db_genome, outputFnamePrefix=self.outputFnamePrefix,\
min_value=None, need_svg=False, ylim_type=2,\
drawBonferroni=False, highlightBandLs=highlightBandLs)
else: #2012.3.28 input is invalid.
sys.stderr.write("inputFname %s is not valid (inexistent).\n" %
(self.inputFname))
sys.exit(0) #fake ok as I want pegasus workflow to keep running.
