auto_process_ngs.qc.apps.rseqc

Provides utility classes and functions for handling RSeQC outputs.

Provides the following classes:

  • InferExperiment: wrapper for handling outputs from ‘infer_experiment.py’

Provides the following functions:

  • fastqc_output_files: generates names of FastQC outputs files

class auto_process_ngs.qc.apps.rseqc.InferExperiment(infer_experiment_log)

Wrapper class for handling outputs from infer_experiment.py

The InferExperiment object gives access to various aspects of the outputs of the RSeQC infer_experiment.py utility.

The following properties are available:

  • log_file (str): path to the source log file

  • paired_end (bool): True if data are paired, False if data are single end

  • forward (float): fraction of ‘forward’ aligned reads

  • reverse (float): fraction of ‘reverse’ aligned reads

  • unstranded (float): fraction of aligned reads neither ‘forward’ nor ‘reverse’

property forward

Fraction of ‘forward’ aligned reads

property log_file

Path to source log file

property paired_end

True if data are paired end, False if single end

property reverse

Fraction of ‘reverse’ aligned reads

property unstranded

Fraction of aligned reads neither ‘forward’ nor ‘reverse’

auto_process_ngs.qc.apps.rseqc.logger = <Logger auto_process_ngs.qc.apps.rseqc (WARNING)>

Example output from infer_experiment.py:

This is PairEnd Data Fraction of reads failed to determine: 0.0172 Fraction of reads explained by “1++,1–,2+-,2-+”: 0.4903 Fraction of reads explained by “1+-,1-+,2++,2–”: 0.4925

auto_process_ngs.qc.apps.rseqc.rseqc_genebody_coverage_output(name, prefix=None)

Generate names of RSeQC geneBody_coverage.py output

Given a basename, the output from geneBody_coverage.py will look like:

  • {PREFIX}/{NAME}.geneBodyCoverage.curves.png

  • {PREFIX}/{NAME}.geneBodyCoverage.r

  • {PREFIX}/{NAME}.geneBodyCoverage.txt

Parameters:

  • name (str) – basename for output files

  • prefix (str) – optional directory to prepend to outputs

Returns:

geneBody_coverage.py output (without leading paths)

Return type:

tuple