Global Variables
The following global variables are used in the tbp-parser algorithm. These variables are used to determine columns in the output files, thresholds for quality control, and various other look-up tables for the algorithm.
These variables can be overwritten using a configuration file. For more information on how to overwrite these variables, please see the Configuration File section.
Global Variables¶
The content of the global variables can be found by browsing the globals.py file on GitHub.
Some global variables are excluded as their modifications will either have no effect or will break the algorithm without further changes.
| Variable Name | Description | Format |
|---|---|---|
| ANNOTATION_TO_INTERPRETATION | A dictionary to turn TBProfiler WHO annotations into their corresponding CDPH Looker or MDL interpretations | Dict[Dict[String: String]] |
| ANTIMICROBIAL_CODE_TO_DRUG_NAME | A dictionary that matches CDPH LIMS antimicrobial codes to the corresponding drug name; used to create the LIMS report | Dict[String: String] |
| ANTIMICROBIAL_CODE_TO_DRUG_NAME_CS | A dictionary that matches the LIMS antimicrobial code to the relevant antimicrobial drug name for cycloserine; activated by the --add_cs_lims flag |
Dict[String: String] |
| ANTIMICROBIAL_CODE_TO_GENES | The dictionary that matches CDPH LIMS antimicrobial codes to the corresponding genes and their corresponding CDPH LIMS codes; used to create the LIMS report | Dict[] |
| ANTIMICROBIAL_CODE_TO_GENES_tNGS | A dictionary that matches CDPH LIMS antimicrobial codes to the corresponding genes and their corresponding CDPH LIMS codes for tNGS data; used to create the LIMS report; fills the ANTIMICROBIAL_CODE_TO_GENES |
Dict[Dict[String: String]] |
| ANTIMICROBIAL_CODE_TO_GENES_WGS | A dictionary that matches CDPH LIMS antimicrobial codes to the corresponding genes and their corresponding CDPH LIMS codes for WGS data; used to create the LIMS report; fills the ANTIMICROBIAL_CODE_TO_GENES |
Dict[Dict[String: String]] |
| ANTIMICROBIAL_CODE_TO_GENES_CS | A dictionary that adds CDPH LIMS antimicrobial codes to the corresponding genes and their corresponding CDPH LIMS codes for cycloserine; activated by the --add_cs_lims flag; used to create the LIMS report; is added to ANTIMICROBIAL_CODE_TO_GENES |
Dict[Dict[String: String]] |
| ANTIMICROBIAL_DRUG_NAME_LIST | A list of the antimicrobial drug names; used to create the Looker report | List[String] |
| ANTIMICROBIAL_DRUG_NAME_TO_GENE_NAME | A dictionary that matches the antimicrobial drugs to the genes that may confer resistance to them; see also https://github.com/jodyphelan/tbdb/blob/master/tbdb.csv; used to create the Looker report | Dict[String: List[String]] |
| COVERAGE_THRESHOLD | The coverage threshold (the minimum percent coverage of a gene/locus over the minimum depth); See also MIN_DEPTH | Int |
| ETHA237_FREQUENCY | The minimum frequency for a mutation to be considered for ethA at protein position 237 | Float |
| GENE_LIST | A list of genes that correspond to a certain set of expert rules; Rv0678 is equivalent to mmpR5 | List[String] |
| GENE_TO_ANTIMICROBIAL_DRUG_NAME | A dictionary corresponding each gene to the drug they may confer resistance to, including the genes in the TBDB watchlist. See also: https://github.com/jodyphelan/tbdb/blob/master/tbdb.csv, and https://github.com/jodyphelan/tbdb/blob/master/tbdb.watchlist.csv; used to create the Laboratorian report | Dict[String: List[String]] |
| GENE_TO_LOCUS_TAG | A dictionary that matches each gene to its corresponding locus tag; see also: https://github.com/jodyphelan/TBProfiler/blob/master/db/tbdb.bed; used to create the Laboratorian report | Dict[String: String] |
| GENE_TO_TIER | A dictionary that matches each gene to it's corresponding tier; tier information provided by CDPH; used to create the Laboratorian report | Dict[String: String] |
| GENES_FOR_LIMS | The list of genes used to generate the CDPH LIMS report; used to create the LIMS report | List[String] |
| GENES_FOR_LIMS_tNGS | The list of genes used to generate the CDPH LIMS report for tNGS data; used to create the LIMS report; fills the GENES_FOR_LIMS |
List[String] |
| GENES_FOR_LIMS_WGS | The list of genes used to generate the CDPH LIMS report for WGS data; used to create the LIMS report; fills the GENES_FOR_LIMS |
List[String] |
| GENES_FOR_LIMS_CS | The list of genes used to generate the CDPH LIMS report for cycloserine; activated by the --add_cs_lims flag; used to create the LIMS report; is added to GENES_FOR_LIMS |
List[String] |
| MIN_DEPTH | The minimum depth of a gene/locus to pass QC | Int |
| MIN_FREQUENCY | The minimum frequency of a mutation to pass QC | Float |
| MIN_READ_SUPPORT | The minimum read support of a mutation to pass QC | Int |
| OPERATOR | Used to fill the OPERATOR column in the output files |
String |
| WHOV2_PROMOTER_REGIONS | A dictionary that contains regions that require special consideration | Dict[String: List[Int] or List[List[Int]]] |
| RPOB449_FREQUENCY | The minimum frequency for a mutation to be considered for rpoB at protein position 449 | Float |
| RRL_FREQUENCY | The minimum frequency for a mutation to be considered for rrl | Float |
| RRL_READ_SUPPORT | The minimum read support for a mutation to be considered for rrl | Int |
| RRS_FREQUENCY | The minimum frequency for a mutation to be considered for rrs | Float |
| RRS_READ_SUPPORT | The minimum read support for a mutation to be considered for rrs | Int |
| SAMPLE_NAME | Used to fill the sample name column in the output files | String |
| SEQUENCING_METHOD | Used to fill the sequencing_method column in the output files | String |
| TNGS_REGIONS | The speciifc primer regions for the gene(s) that is(are) split into multiple sections | Dict[Dict[String: List[Int]]] |