TB File Browser

Forked from cosmic-files

For now, SSH connections must be configured using a private and public key pair (password authentication is not supported).

Databases

References

hsp65:
Web-accessible database of hsp65 sequences from Mycobacterium reference strains.

Jody Phelan:
TBProfiler
tbdb (used by TBProfiler by default)
ntm-db (for abscessus_resistance_variants.csv)

tbdb:
Catalogue of mutations in Mycobacterium tuberculosis complex and their association with drug resistance, 2nd ed

ntm-db:
Clinical Whole Genome Sequencing for Clarithromycin and Amikacin Resistance Prediction and Subspecies Identification of Mycobacterium abscessus
Global phylogenomic analyses of Mycobacterium abscessus provide context for non cystic fibrosis infections and the evolution of antibiotic resistance
Multidrug tolerance conferred by loss-of-function mutations in anti-sigma factor RshA of Mycobacterium abscessus

Doc

NTM

rrl M. abscessus macrolides:

impl RrlSnpCall {
    /// "wt", "NA", or the observed mutant base as a char string.
    pub fn call_tag(&self) -> String {
        match self.query_base {
            None => "NA".to_string(),
            Some(b) if b == self.wt_base => format!("{} (wt)", self.wt_base as char),
            Some(b) if b == self.resistance_base => format!("{} (resistance)", self.resistance_base as char),
            Some(b) => format!("{} (mutation)", b as char),
        }
    }
}

TBProfiler:

Unique confidence values of TBProfiler (examples/tbgetconfidencetypes.rs):

• Assoc w R
• Assoc w R - Interim
• Not assoc w R
• Not assoc w R - Interim
• Uncertain significance

fn confidence_rank(conf: &str) -> u8 {  
    match conf {  
        "Assoc w R" => 0,  
        "Assoc w R - Interim" => 1,  
        "Uncertain significance" => 2,  
        "Not assoc w R - Interim" => 3,  
        "Not assoc w R" => 4,  
        _ => 5, // unknown / fallback  
    }  
}  
  
fn is_susceptible: rank >= 2

Dateien

Dev

On branch tbprofiler run on Windows with: $env:RUST_LOG="info"; cargo run