Looker report

The Looker report is intended for use in Google's Looker Data Studio for dashboarding purposes. It offers a highly condensed version of the resistance calls (using the looker_interpretation field from the laboratorian report) for a quick summary of the sample’s drug resistance profile.

Resistance columns

Each antimicrobial drug listed in the input --coverage_bed file will be represented by one column in the Looker report. The column name will be the antimicrobial drug name in lowercase. This can be customized by adding content to the FIND_AND_REPLACE dictionary in a configuration file, though please be aware that this will change every instance of that drug name in all output reports.

Drug interpretation severity is ranked as follows (from high to low): R > R-Interim > U > S-Interim > S > WT > Insufficient Coverage > NA.

Column name	Explanation	Source
antimicrobial_drug_name (e.g., rifampicin)	The highest looker_interpretation identified for that drug in the Laboratorian report	Determined by tbp-parser

Miscellaneous columns

These miscellaneous columns are also included in the Looker report to provide additional context about the sample. They can be customized by adding content to the FIND_AND_REPLACE dictionary in a configuration file.

Column name	Explanation
sample_id	The name of the sample
output_seq_method_type	The sequencing method used to generate the data; can be set with the --sequencing_method input parameter. If left blank, "Sequencing method not provided" is the default value
lineage	The lineage of the sample (the main_lin field as reported by TBProfiler); for example, lineage1.2.1.2.1
ID	The lineage of the sample in human-readable language (the same as the Lineage ID column in the LIMS report; see the relevant documentation for more information)
analysis_date	The date tbp-parser was run in YYYY-MM-DD HH:MM format
operator	The name of the person who ran tbp-parser; can be provided with the --operator input parameter. If left blank, "Operator not provided" is the default value.

Customizing column names

To overwrite any of the output column names or text in the laboratorian report, please use the following format in a configuration file or use the command-line parameter --find_and_replace:

FIND_AND_REPLACE:
  "sample_id": "My_Sample_ID_Column"
  "rifampicin": "rifampin"

Please note that this will rename every instance of that text in all output reports (every instance of "sample_id" will be renamed to "My_Sample_ID_Column" in all output files, etc.).