def execute_findAmplificationsAndCalculateStats_fromGff(self,
#analysis_id_I,
experiment_id_I,
strand_start, strand_stop,
sample_names_I = [],
scale_factor=True, downsample_factor=2000,reads_min=1.5,reads_max=5.0, indices_min=200,consecutive_tol=10):
'''Calculate coverage statistics from gff file
NOTE: multiple chromosomes not yet supported in sequencing_utilities'''
# get the data
data_O = [];
stats_O = [];
#OPTION1
gffcoverage = gff_coverage();
## get the analysis_info
#analysis_rows = [];
# query information from coverage table
# 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_dataStage01ResequencingCoverage(experiment_id_I);
#for cnt,analysis in analysis_rows:
# # get the sample_names and experiment_ids
# experiment_id = analysis['experiment_id'];
# sn = analysis['sample_name'];
# filename = analysis['data_dir']
for cnt,sn in enumerate(sample_names):
# get the data_dir
filename = [];
filename = self.get_dataDirs_experimentIDAndSampleName_dataStage01ResequencingCoverage(experiment_id_I,sn);
#OPTION1
# find amplifications and calculate stats
gffcoverage.findAndCalculate_amplificationStats_fromGff(filename[0],strand_start, strand_stop, experiment_id_I=experiment_id, sample_name_I=sn, indices_min = indices_min, consecutive_tol = consecutive_tol, scale_factor=scale_factor, downsample_factor=downsample_factor)
data_O.extend(copy(gffcoverage.amplifications));
stats_O.extend(copy(gffcoverage.amplificationStats));
gffcoverage.clear_data();
##OPTION2
## find amplifications and calculate stats
#amplifications,amplificationStats=[],[];
#amplifications,amplificationStats = self.findAndCalculate_amplificationStats_fromGff(filename[0],strand_start, strand_stop, experiment_id_I=experiment_id, sample_name_I=sn, indices_min = indices_min, consecutive_tol = consecutive_tol, scale_factor=scale_factor, downsample_factor=downsample_factor)
#data_O.extend(amplifications);
#stats_O.extend(amplificationStats);
# add data to the DB
self.add_dataStage01ResequencingAmplifications(data_O);
self.add_dataStage01ResequencingAmplificationStats(stats_O);
def import_resequencingCoverageData_add(
self,
filename,
# analysis_id,
experiment_id,
sample_name,
strand_start,
strand_stop,
scale_factor=True,
downsample_factor=2000,
):
"""table adds
NOTE: multiple chromosomes not yet supported in sequencing_utilities"""
# OPTION1
gffcoverage = gff_coverage()
coverage_data = []
if ".bam" in filename:
# TODO convert .bam to .gff using makegff.py from sequencing_utilities
print("conversion of .bam to .gff not yet supported")
exit(2)
# filename_bam = filename;
# filename = filename.replace('.bam','.gff');
# extract_strandsFromGff(filename_bam,filename,separate_strand=False);
# convert strings to float and int
strand_start, strand_stop, scale_factor, downsample_factor = (
int(strand_start),
int(strand_stop),
bool(scale_factor),
float(downsample_factor),
)
# OPTION1
# parse the gff file
gffcoverage.extract_coverage_fromGff(
filename,
strand_start,
strand_stop,
scale_factor=scale_factor,
downsample_factor=downsample_factor,
experiment_id_I=experiment_id,
sample_name_I=sample_name,
)
coverage_data = gffcoverage.coverage
##OPTION2
## parse the gff file
# coverage_data = [];
# coverage_data = self.extract_coverage_fromGff(filename, strand_start, strand_stop, scale_factor=scale_factor, downsample_factor=downsample_factor,experiment_id_I = experiment_id,sample_name_I=sample_name);
# add data to the database:
self.add_dataStage01ResequencingCoverage(coverage_data)
def execute_findAmplifications_fromGff(self,
#analysis_id_I,
experiment_id_I,
strand_start, strand_stop,
sample_names_I = [],
scale_factor=True, downsample_factor=0,reads_min=1.5,reads_max=5.0, indices_min=200,consecutive_tol=10):
'''Calculate coverage statistics from gff file
NOTE: multiple chromosomes not yet supported in sequencing_utilities'''
#from sequencing_utilities.coverage import extract_strandsFromGff,find_highCoverageRegions
# get the data
data_O = [];
#OPTION1
gffcoverage = gff_coverage();
# 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_dataStage01ResequencingCoverage(experiment_id_I);
#for cnt,analysis in analysis_rows:
# # get the sample_names and experiment_ids
# experiment_id = analysis['experiment_id'];
# sn = analysis['sample_name'];
# filename = analysis['data_dir']
for cnt,sn in enumerate(sample_names):
# get the data_dir
filename = [];
filename = self.get_dataDirs_experimentIDAndSampleName_dataStage01ResequencingCoverage(experiment_id_I,sn);
#OPTION1
gffcoverage.find_amplifications_fromGff(filename[0],strand_start, strand_stop, experiment_id, sn, scale=scale_factor, downsample=downsample_factor)
data_O.extend(copy(gffcoverage.amplifications))
gffcoverage.clear_data();
#OPTION2
#amplifications = [];
#amplifications = self.find_amplifications_fromGff(filename[0],strand_start, strand_stop, experiment_id, sn, scale=scale_factor, downsample=downsample_factor)
#data_O.extend(amplifications)
# add data to the DB
self.add_dataStage01ResequencingAmplifications(data_O);
def execute_coverageStats_fromGff(self,
#analysis_id_I,
experiment_id_I,
strand_start,strand_stop,scale_factor=True,downsample_factor=0,
sample_names_I=[]):
'''Calculate coverage statistics from gff file
NOTE: multiple chromosomes not yet supported in sequencing_utilities'''
#OPTION1
gffcoverage = gff_coverage();
## get the analysis_info
#analysis_rows = [];
#analysis_rows = self.get_rows_analysisID_dataStage01ResequencingAnalysis(analysis_id_I);
if sample_names_I:
sample_names = sample_names_I;
else:
sample_names = [];
sample_names = self.get_sampleNames_experimentID_dataStage01ResequencingCoverage(experiment_id_I);
# get the data
data_O = [];
for sn in sample_names:
# get the filename
filename = None;
filename = self.get_dataDirs_experimentIDAndSampleName_dataStage01ResequencingCoverage(experiment_id_I,sn);
#OPTION1
# calculate the coverage statistics
gffcoverage.calculate_coverageStats_fromGff(filename[0],
strand_start,strand_stop,scale_factor=scale_factor,downsample_factor=downsample_factor,
experiment_id_I=experiment_id_I, sample_name_I=sn);
data_O.extend(copy(gffcoverage.coverageStats));
gffcoverage.clear_data();
##OPTION2
## calculate the coverage statistics
#coverateStats = [];
#coverageStats = calculate_interface_coverageStats_fromGff(filename[0],
# strand_start,strand_stop,scale_factor=scale_factor,downsample_factor=downsample_factor,
# experiment_id_I=experiment_id_I, sample_name_I=sn);
#data_O.extend(coverageStats);
#add data to the database
self.add_dataStage01ResequencingCoverageStats(data_O);
# define search paths manually
import sys
# dependency dirs
sys.path.append('C:/Users/dmccloskey-sbrg/Documents/GitHub/sequencing_analysis')
sys.path.append('C:/Users/dmccloskey-sbrg/Documents/GitHub/io_utilities')
sys.path.append('C:/Users/dmccloskey-sbrg/Documents/GitHub/sequencing_utilities')
sys.path.append('C:/Users/dmccloskey-sbrg/Documents/GitHub/calculate_utilities')
from sequencing_analysis.genome_diff import genome_diff
from sequencing_analysis.mutations_lineage import mutations_lineage
from sequencing_analysis.mutations_endpoints import mutations_endpoints
from sequencing_analysis.mutations_heatmap import mutations_heatmap
from sequencing_analysis.gff_coverage import gff_coverage
#analyze the coverage for a particular strain
gffcoverage = gff_coverage();
gffcoverage.extract_coverage_fromGff(gff_file = '//proline/Users/dmccloskey/Resequencing_DNA/Evo04ptsHIcrrEvo04EP/Evo04ptsHIcrrEvo04EP/data/Evo04ptsHIcrrEvo04EP_reference.gff',
strand_start = 0,strand_stop = 4640000,
scale_factor = False,downsample_factor = 2000,
experiment_id_I = 'ALEsKOs01',
sample_name_I = 'Evo04ptsHIcrrEvo04EP');
# calculate the coverage statistics
gffcoverage.calculate_coverageStats_fromGff(gff_file = '//proline/Users/dmccloskey/Resequencing_DNA/Evo04ptsHIcrrEvo04EP/Evo04ptsHIcrrEvo04EP/data/Evo04ptsHIcrrEvo04EP_reference.gff',
strand_start = 0,strand_stop = 4640000,
scale_factor = False,downsample_factor = 0,
experiment_id_I = 'ALEsKOs01',
sample_name_I = 'Evo04ptsHIcrrEvo04EP')
gffcoverage.export_coverageStats('Evo04ptsHIcrrEvo04EP_coverage.csv');
gffcoverage.export_coverage_js();
# find amplifications
gffcoverage.findAndCalculate_amplificationStats_fromGff(gff_file = '//proline/Users/dmccloskey/Resequencing_DNA/Evo04ptsHIcrrEvo04EP/Evo04ptsHIcrrEvo04EP/data/Evo04ptsHIcrrEvo04EP_reference.gff',
