def Run(self):
self.transit_message("Starting TnseqStats")
start_time = time.time()
datasets = self.wigs
if self.combined_wig == None:
(data, sites) = tnseq_tools.get_data(self.wigs)
else:
(sites, data,
datasets) = tnseq_tools.read_combined_wig(self.combined_wig)
# write table of stats (saturation,NZmean)
file = sys.stdout
if self.outfile != None: file = open(self.outfile, "w")
PTI = True
if PTI == True:
file.write(
"dataset\tdensity\tmean_ct\tNZmean\tNZmedian\tmax_ct\ttotal_cts\tskewness\tkurtosis\tpickands_tail_index\n"
)
else:
file.write(
"dataset\tdensity\tmean_ct\tNZmean\tNZmedian\tmax_ct\ttotal_cts\tskewness\tkurtosis\n"
)
for i in range(data.shape[0]):
density, meanrd, nzmeanrd, nzmedianrd, maxrd, totalrd, skew, kurtosis = tnseq_tools.get_data_stats(
data[i, :])
nzmedianrd = int(nzmedianrd) if numpy.isnan(
nzmedianrd) == False else 0
pti = self.pickands_tail_index(data[i, :])
vals = [
datasets[i],
"%0.3f" % density,
"%0.1f" % meanrd,
"%0.1f" % nzmeanrd,
"%d" % nzmedianrd, maxrd,
int(totalrd),
"%0.1f" % skew,
"%0.1f" % kurtosis
]
if PTI == True: vals.append("%0.3f" % pti)
file.write('\t'.join([str(x) for x in vals]) + '\n')
if self.outfile != None: file.close()
self.finish()
self.transit_message("Finished TnseqStats")
def updateFiles(self):
self.index_stats = 0
try:
for j,row in enumerate(self.normdata):
name = transit_tools.basename(self.wigList[j])
(density, meanrd, nzmeanrd, nzmedianrd, maxrd, totalrd, skew, kurtosis) = tnseq_tools.get_data_stats(row)
self.statsListCtrl.InsertStringItem(self.index_stats, name)
self.statsListCtrl.SetStringItem(self.index_stats, 1, "%1.1f" % (density*100.0))
self.statsListCtrl.SetStringItem(self.index_stats, 2, "%1.1f" % (meanrd))
self.statsListCtrl.SetStringItem(self.index_stats, 3, "%1.1f" % (nzmeanrd))
self.statsListCtrl.SetStringItem(self.index_stats, 4, "%1.1f" % (nzmedianrd))
self.statsListCtrl.SetStringItem(self.index_stats, 5, "%d" % (maxrd))
self.statsListCtrl.SetStringItem(self.index_stats, 6, "%d" % (totalrd))
self.statsListCtrl.SetStringItem(self.index_stats, 7, "%1.1f" % (skew))
self.statsListCtrl.SetStringItem(self.index_stats, 8, "%1.1f" % (kurtosis))
print(self.qc_prefix, "Adding dataset (%d): %s" % (self.index_stats, name))
self.index_stats+=1
except Exception as e:
print(self.qc_prefix, "Error:", e)
exc_type, exc_obj, exc_tb = sys.exc_info()
fname = os.path.split(exc_tb.tb_frame.f_code.co_filename)[1]
print(exc_type, fname, exc_tb.tb_lineno)
def updateFiles(self):
self.index_stats = 0
try:
for j,row in enumerate(self.normdata):
name = transit_tools.basename(self.wigList[j])
(density, meanrd, nzmeanrd, nzmedianrd, maxrd, totalrd, skew, kurtosis) = tnseq_tools.get_data_stats(row)
self.statsListCtrl.InsertStringItem(self.index_stats, name)
self.statsListCtrl.SetStringItem(self.index_stats, 1, "%1.1f" % (density*100.0))
self.statsListCtrl.SetStringItem(self.index_stats, 2, "%1.1f" % (meanrd))
self.statsListCtrl.SetStringItem(self.index_stats, 3, "%1.1f" % (nzmeanrd))
self.statsListCtrl.SetStringItem(self.index_stats, 4, "%1.1f" % (nzmedianrd))
self.statsListCtrl.SetStringItem(self.index_stats, 5, "%d" % (maxrd))
self.statsListCtrl.SetStringItem(self.index_stats, 6, "%d" % (totalrd))
self.statsListCtrl.SetStringItem(self.index_stats, 7, "%1.1f" % (skew))
self.statsListCtrl.SetStringItem(self.index_stats, 8, "%1.1f" % (kurtosis))
print self.qc_prefix, "Adding dataset (%d): %s" % (self.index_stats, name)
self.index_stats+=1
except Exception as e:
print self.qc_prefix, "Error:", e
exc_type, exc_obj, exc_tb = sys.exc_info()
fname = os.path.split(exc_tb.tb_frame.f_code.co_filename)[1]
print(exc_type, fname, exc_tb.tb_lineno)