def analyze_coverage(self, bam): self.coverage.run(bam, self, method='accurate') for split in self.splits: split.coverage = Coverage() split.coverage.c = self.coverage.c[split.start:split.end] split.coverage.process_c(split.coverage.c)
def analyze_coverage(self, bam, progress): contig_coverage = [] for split in self.splits: progress.update('Coverage (split: %d of %d)' % (split.order, len(self.splits))) split.coverage = Coverage() split.coverage.run(bam, split) contig_coverage.extend(split.coverage.c) self.coverage.process_c(contig_coverage)
def __init__(self, name): self.name = name self.parent = None self.splits = [] self.length = 0 self.abundance = 0.0 self.coverage = Coverage() self.min_coverage_for_variability = 10 self.report_variability_full = False
def analyze_coverage(self, bam): contig_coverage = [] counter = 1 for split in self.splits: split.coverage = Coverage() split.coverage.run(bam, split) contig_coverage.extend(split.coverage.c) counter += 1 self.coverage.process_c(contig_coverage)
def analyze_coverage(self, bam): contig_coverage = [] counter = 1 for split in self.splits: split.coverage = Coverage() split.coverage.run(bam, split, ignore_orphans=self.ignore_orphans, max_coverage_depth=self.max_coverage_depth) contig_coverage.extend(split.coverage.c) counter += 1 self.coverage.process_c(contig_coverage)
def __init__(self, name): self.name = name self.sequence = None self.parent = None self.splits = [] self.length = 0 self.abundance = 0.0 self.coverage = Coverage() self.min_coverage_for_variability = 10 self.skip_SNV_profiling = False self.report_variability_full = False self.ignore_orphans = False self.max_coverage_depth = constants.max_depth_for_coverage self.codon_frequencies_dict = {}
def analyze_coverage(self, bam, progress): contig_coverage = [] num_splits = len(self.splits) counter = 1 for split in self.splits: progress.update('Coverage (split: %d of %d)' % (counter, num_splits)) split.coverage = Coverage() split.coverage.run(bam, split) contig_coverage.extend(split.coverage.c) counter += 1 self.coverage.process_c(contig_coverage)