Automatic Report

The pyGenClean module creates an automatic report using LaTeX. Each of the output directory will contain a final report (named automatic_report.tex). The report, once compiled into the PDF format, includes various quality metrics. To compile the report, perform the following commands:

$ pdflatex automatic_report.tex
$ pdflatex automatic_report.tex
$ pdflatex automatic_report.tex


Executing the command three times insure that the links in the automatic report are properly formed.

Report merging

On a typical data clean up pipeline, multiple directories will be created (one for each of the parts of the pipeline). A script is provided to merge all those reports (one per data_clean_up.YYYY-MM-DD_HH.MM.SS directory) into a single report. Here is the usage of this script:

$ pyGenClean_merge_reports --help
usage: pyGenClean_merge_reports [-h] --qc-dir DIR [DIR ...]
                                [--report-title TITLE]
                                [--report-author AUTHOR]
                                [--report-number NUMBER]
                                [--report-background BACKGROUND]
                                [--out-dir FILE]

Merges automatic reports from other pyGenClean runs.

optional arguments:
  -h, --help            show this help message and exit

  --qc-dir DIR [DIR ...]
                        A list of directory containing pyGenClean runs.

Report Options:
  --report-title TITLE  The report title. [default: Genetic Data Clean Up]
  --report-author AUTHOR
                        The current project number. [default: pyGenClean]
  --report-number NUMBER
                        The current project author. [default: Simple Project]
  --report-background BACKGROUND
                        Text of file containing the background section of the

Output Directory:
  --out-dir FILE        The name of the directory that will contain the final
                        report. [default: pyGenClean_report]

To execute the report merging procedure, perform the following command:

$ pyGenClean_merge_reports --qc-dir data_clean_up.*


It is possible to change the title, the author, the number or the background of the automatic report by using the --report-title, --report-author, --report-number or --report-background options, respectively.

Once again, to compile the final report, perform the following command:

$ pdflatex pyGenClean_report.tex
$ pdflatex pyGenClean_report.tex
$ pdflatex pyGenClean_report.tex