auto_process_ngs.bcl2fastq.reporting

Provides classes and functions for reporting QC information about Fastq generation, based on data in files produced by the fastq_statistics.py utility.

The main class ProcessingQCReport takes these statistics files as input and composes an HTML report.

The detect_processing_qc_warnings function scans an HTML report from ProcessingQCReport and indicates whether the report contains any warnings.

class auto_process_ngs.bcl2fastq.reporting.ProcessingQCReport(analysis_dir, stats_file, per_lane_stats_file, per_lane_sample_stats_file, name=None)

Create a processing QC report document

Example usage:

>>> report = ProcessingQCReport(...)
>>> report.write("processing_qc_report.html")
add_per_fastq_statistics()

Add a section with the per-Fastq statistics

add_per_lane_sample_statistics()

Add a section with the per-lane sample statistics

add_per_lane_statistics()

Add a section with the per-lane statistics

add_to_toc(title, s, sub_toc=None)

Add an item to the table of contents

Parameters:

  • title (str) – title for the item in the table of contents

  • s (Object) – document item to target in the table of contents

  • sub_toc (List) – optional, sub table of contents to append for this item

finalise_warnings()

Sets up warning indications on report

This method should be called when the report content has been assembled; it performs the final actions for displaying the general warning indicator etc.

flag_warnings()

Set flag to indicate that report includes warnings

By default the flag is set to False (i.e. no warnings in the report); calling this method one or more time sets the flag to True (i.e. at least one warning in the report).

The flag is checked by the finalise_warnings method when the report is completed.

init_toc(title='Contents')

Initialise the table of contents

Parameters:

title (str) – title for the table of contents (default: “Contents”)

init_warnings()

Initialise section to indicate report has warnings

The ‘warnings’ section is hidden by default, but a call to the ‘flag_warnings’ method will cause it to be unhidden when the HTML report is generated

warning(message, size=None)

Return object for displaying a warning

Returns an object which will render to an HTML warning message (essentially a paragraph with a warning icon and the supplied message text).

Parameters:

  • message (str) – warning message to display

  • size (int) – optional, set the size for the warning icon

auto_process_ngs.bcl2fastq.reporting.detect_processing_qc_warnings(html_file)

Look for warning text in processing_qc.html file

Parameters:

html_file (str) – path to HTML report file

Returns:

True if warnings were found, False if not.

Return type:

Boolean