`auto_process_ngs.qc.apps.qualimap`

Provides utility classes and functions for handling Qualimap outputs.

Provides the following classes:

Provides the following functions:

class auto_process_ngs.qc.apps.qualimap.QualimapRnaseq(qualimap_dir)

Wrapper class for handling outputs from Qualimap ‘rnaseq’

The QualimapRnaseq object gives access to various aspects of the outputs of the Qualimap rnaseq module.

The following properties are available:

html_report (str): path to the HTML report
results_text (str): path to the results .txt file
input (dict): access values in the ‘Input’ section
reads_genomic_origin (dict): access values in the ‘Reads Genomic Origin’ section
raw_coverage_profile_along_genes_total (dict): access values from the ‘coverage_profile_along_genes_(total).txt’ file

property html_report: Return path to the ‘qualimapReport.html’ HTML report

link_to_output(name, full_path=True, relpath=None)

Return link to the result of a specified Qualimap output

Parameters:

name (str) – name of the module (e.g. ‘Reads Genomic Origin’)
full_path (boolean) – optional, if True then return the full path; otherwise return just the anchor
relpath (str) – optional, if supplied then specifies the path that full paths will be made relative to (implies full_path is True)

property raw_coverage_profile_along_genes_total: Provides access to values in the ‘raw_data_qualimapReport/coverage_profile_along_genes_(total).txt’ file

property reads_genomic_origin: Provides access to values in the ‘Reads genomic origin’ section

auto_process_ngs.qc.apps.qualimap.qualimap_rnaseq_output(prefix=None)

Generate names of Qualimap ‘rnaseq’ output

The output from Qualimap ‘rnaseq’ are always:

- {PREFIX}/qualimapReport.html
- {PREFIX}/rnaseq_qc_results.txt
- {PREFIX}/...

auto_process_ngs.qc.apps.qualimap