sctools.metrics.gatherer.GatherGeneMetrics

class sctools.metrics.gatherer.GatherGeneMetrics(bam_file: str, output_stem: str, mitochondrial_gene_ids: Set[str] = {}, compress: bool = True)[source]

..currentmodule:: sctools.metrics

This module defines classes to gather metrics across the cells or genes of an experiment and write them to gzip-compressed csv files

MetricGatherer(bam_file, output_stem[, ...])

Gathers Metrics from an experiment

GatherCellMetrics(bam_file, output_stem[, ...])

Sequence Metric Gatherers

GatherGeneMetrics(bam_file, output_stem[, ...])

Sequence Metric Gatherers

See also

sctools.metrics.aggregator, sctools.metrics.merge, sctools.metrics.writer

bam_file must be sorted by molecule (UB), cell (CB), and gene (GE), where molecule varies fastest.

>>> from sctools.metrics.gatherer import GatherCellMetrics
>>> import os, tempfile
>>> # example data
>>> bam_file = os.path.abspath(__file__) + '../test/data/test.bam'
>>> temp_dir = tempfile.mkdtemp()
>>> g = GatherCellMetrics(bam_file=bam_file, output_stem=temp_dir + 'test', compress=True)
>>> g.extract_metrics()

GatherGeneMetrics

__init__(bam_file: str, output_stem: str, mitochondrial_gene_ids: Set[str] = {}, compress: bool = True)

Methods

__init__(bam_file, output_stem[, ...])

extract_metrics([mode])

Extract gene metrics from self.bam_file

Attributes

bam_file

the bam file that metrics are generated from

extra_docs