def execute_coverageStats_fromTable(self,analysis_id_I):
'''Calculate coverage statistics'''
# get the analysis_info
analysis_rows = [];
# get the data
data_O = [];
for cnt,analysis in analysis_rows:
# get the sample_names
experiment_id = analysis['experiment_id'];
sn = analysis['sample_name'];
# get chromosomes
chromosomes = [];
for chromosome in chromosomes:
# get strands
strands = []
for strand in strands:
# get the indices/reads and other information
start,stop = None,None;
data_indices,data_reads = [],[];
# calculate the descriptive statistics
data_TTest = {};
data_TTest = self.r_calc.calculate_oneSampleTTest(data_reads, alternative_I = "two.sided", mu_I = 0, paired_I="FALSE", var_equal_I = "TRUE", ci_level_I = 0.95, padjusted_method_I = "bonferroni");
# calculate the interquartile range
min_O, max_O, median_O, iq_1_O, iq_3_O = None, None, None, None, None;
min_O, max_O, median_O, iq_1_O, iq_3_O=calculate_interface.calculate_interquartiles(data_reads);
# record data for
data_O.append({
'analysis_id':analysis_id,
'experiment_id':experiment_id,
'sample_name':sn,
'genome_chromosome':chromosome,
'genome_strand':strand,
'strand_start':start,
'strand_stop':stop,
'reads_min':min_O,
'reads_max':max_O,
'reads_lb':data_TTest['ci_lb'],
'reads_ub':data_TTest['ci_ub'],
'reads_iq1':iq_1_O,
'reads_iq3':iq_3_O,
'reads_median':median_O,
'reads_mean':data_TTest['mean'],
'reads_var':data_TTest['var'],
'reads_n':len(data_reads)
})
self.add_dataStage01ResequencingCoverageStats(data_O);
def execute_amplificationStats_fromTable(self,
#analysis_id_I,
experiment_id_I,
sample_names_I=[]):
'''Calculate coverage statistics'''
# get the data
data_O = [];
## get the analysis_info
#analysis_rows = [];
## query information from amplification table
#for cnt,analysis in analysis_rows:
# # get the sample_names
# experiment_id = analysis['experiment_id'];
# sn = analysis['sample_name'];
# get the sample_names
experiment_id = experiment_id_I;
if sample_names_I:
sample_names = sample_names_I;
else:
sample_names = [];
sample_names = self.get_sampleNames_experimentID_dataStage01ResequencingAmplifications(experiment_id_I);
for cnt,sn in enumerate(sample_names):
# get chromosomes
chromosomes = [];
chromosomes = self.get_chromosomes_experimentIDAndSampleName_dataStage01ResequencingAmplifications(experiment_id_I,sn);
for chromosome in chromosomes:
# get strands
strands = []
strands = self.get_strands_experimentIDAndSampleNameAndChromosome_dataStage01ResequencingAmplifications(experiment_id_I,sn,chromosome);
# remove visualization regions
strands = [s for s in strands if not 'mean' in s];
for strand in strands:
# get the start and stop of the indices
genomic_starts,genomic_stops = [],[]
genomic_starts,genomic_stops = self.get_startAndStops_experimentIDAndSampleNameAndChromosomeAndStrand_dataStage01ResequencingAmplifications(experiment_id_I,sn,chromosome,strand);
# get the start and stop regions
starts,stops = [],[]
starts,stops = self.get_amplificationRegions_experimentIDAndSampleNameAndChromosomeAndStrand_dataStage01ResequencingAmplifications(experiment_id_I,sn,chromosome,strand);
# get the indices/reads and other information
for start_cnt,start in enumerate(starts):
data_indices,data_reads = [],[];
data_indices,data_reads = self.get_genomeIndexAndReads_experimentIDAndSampleNameAndChromosomeAndStrandAndAmplificationRegions_dataStage01ResequencingAmplifications(experiment_id_I,sn,chromosome,strand,start,stops[start_cnt]);
# calculate using scipy
data_ave_O, data_var_O, data_lb_O, data_ub_O = calculate_interface.calculate_ave_var(data_reads,confidence_I = 0.95);
# calculate the interquartile range
min_O, max_O, median_O, iq_1_O, iq_3_O = None, None, None, None, None;
min_O, max_O, median_O, iq_1_O, iq_3_O=calculate_interface.calculate_interquartiles(data_reads);
# record data for
data_O.append({
#'analysis_id':analysis_id,
'experiment_id':experiment_id_I,
'sample_name':sn,
'genome_chromosome':chromosome,
'genome_strand':strand,
'strand_start':genomic_starts[0],
'strand_stop':genomic_stops[0],
'reads_min':min_O,
'reads_max':max_O,
#'reads_lb':data_TTest['ci_lb'],
#'reads_ub':data_TTest['ci_ub'],
'reads_lb':data_lb_O,
'reads_ub':data_ub_O,
'reads_iq1':iq_1_O,
'reads_iq3':iq_3_O,
'reads_median':median_O,
#'reads_mean':data_TTest['mean'],
#'reads_var':data_TTest['var'],
'reads_mean':data_ave_O,
'reads_var':data_var_O,
'reads_n':len(data_reads),
'amplification_start':start,
'amplification_stop':stops[start_cnt],
'used_':True,
'comment_':None
})
# add data to the DB
self.add_dataStage01ResequencingAmplificationStats(data_O);
