auto_process_ngs.qc.qualimap

class auto_process_ngs.qc.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

property input

Provides access to values in the ‘Input’ section

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

property results_txt

Return path to the ‘rnaseq_qc_results.txt’ file