updates lims ID

Dockerfile

@@ -3,7 +3,7 @@
 # Shelby Bennett, Erin Young, Curtis Kapsak, & Kutluhan Incekara
 
 ARG SAMTOOLS_VER="1.18"
-ARG TBP_PARSER_VER="2.2.2"
+ARG TBP_PARSER_VER="2.3.0"
 
 FROM ubuntu:jammy AS builder
 

docs/inputs/theiaprok.md

@@ -29,7 +29,7 @@ The following optional inputs are also available for user modification on Terra:
 | `merlin_magic` | **tbp_parser_coverage_regions_bed** | File | A BED file containing the regions to calculate percent coverage for | [tbdb-modified-regions.md](https://github.com/theiagen/tbp-parser/blob/main/data/tbdb-modified-regions.bed) |
 | `merlin_magic` | **tbp_parser_coverage_threshold** | Int | The minimum percentage of a region that has depth above the threshold set by `min_depth` (used for a gene/locus to pass QC) | 100 |
 | `merlin_magic` | **tbp_parser_debug** | Boolean | Set to `false` to turn off debug mode for `tbp-parser` | `true` |
-| `merlin_magic` | **tbp_parser_docker_image** | String | The Docker image to use when running `tbp-parser` | "us-docker.pkg.dev/general-theiagen/theiagen/tbp-parser:2.2.2" |
+| `merlin_magic` | **tbp_parser_docker_image** | String | The Docker image to use when running `tbp-parser` | "us-docker.pkg.dev/general-theiagen/theiagen/tbp-parser:2.3.0" |
 | `merlin_magic` | **tbp_parser_etha237_frequency** | Float | Minimum frequency for a mutation in ethA at protein position 237 to pass QC in `tbp-parser` | 0.1 |
 | `merlin_magic` | **tbp_parser_expert_rule_regions_bed** | File | A file that contains the regions where R mutations and expert rules are applied |  |
 | `merlin_magic` | **tbp_parser_min_depth** | Int | Minimum depth for a variant to pass QC in tbp_parser | 10 |

docs/usage.md

@@ -9,7 +9,7 @@ title: Getting Started
 We highly recommend using the following Docker iamge to run tbp-parser:
 
 ``` bash
-docker pull us-docker.pkg.dev/general-theiagen/theiagen/tbp-parser:2.2.2 #(1)!
+docker pull us-docker.pkg.dev/general-theiagen/theiagen/tbp-parser:2.3.0 #(1)!
 ```
 
 1. We host our Docker images on the Google Artifact Registry so that they are always availble for usage.
@@ -21,7 +21,7 @@ docker run -it --entrypoint=/bin/bash us-docker.pkg.dev/general-theiagen/theiage
 
 # Once inside the container interactively, you can run the tbp-parser tool
 python3 /tbp-parser/tbp_parser/tbp_parser.py -v
-# v2.2.2
+# 2.3.0
 ```
 
 ### Locally with Python

docs/versioning/exhaustive.md

@@ -68,7 +68,8 @@ The following is a list of every version of `tbp-parser` and a short summary of
 - v2.2.0 - removes ciprofloxacin, fluoroquinolones, and ofloxacin from gyrA and gyrB and aminoglycosides from rrs in the `globals.GENE_TO_ANTIMICROBIAL_DRUG_NAME` dictionary; if a drug is missing in the TBProfiler JSON's gene_associated_drug field that is present in that global dictionary, it will be added for the mutation.
 - v2.2.1 - fixes a bug where rifampicin was not renamed to rifampin, which caused duplicate lines to appear in the Laboratorian report.
 - v2.2.2 - removes the high-level and low-level resistance comments from the LIMS report
-
+- v2.3.0 - reworks the lineage detection so that if TBProfiler detects a lineage, it is reported; if no lineage is reported by TBProfiler, then whether or not M.tb was detected depends on the percentage of LIMS genes above a (now lower) default percentage of 0.7
+
 ---
 
 The following diagram shows how each version is related to the others without technical details:

tbp_parser/LIMS.py

@@ -28,18 +28,18 @@ def get_id(self):
     """
     self.logger.info("LIMS:Within LIMS class get_id function")
 
+    # if the percentage of genes above the coverage threshold is greater than 70%, then we can call the lineage if TBProfiler did not designate it
+    percentage_limit = 0.7
+
     # calculate percentage of genes in the LIMS report above the coverage threshold
     self.logger.debug("LIMS:Calculating the percentage of LIMS genes above the coverage threshold")
     if self.tngs:
       number_of_lims_genes_above_coverage_threshold = sum(int(globals.COVERAGE_DICTIONARY[gene]) >= 90 for gene in globals.COVERAGE_DICTIONARY.keys())
       percentage_lims_genes_above = number_of_lims_genes_above_coverage_threshold / len(globals.COVERAGE_DICTIONARY.keys())
-      # if the percentage of genes above the coverage threshold is greater than 70%, then we can call the lineage
-      percentage_limit = 0.7
+
     else:
       number_of_lims_genes_above_coverage_threshold = sum(int(globals.COVERAGE_DICTIONARY[gene]) >= globals.COVERAGE_THRESHOLD for gene in globals.GENES_FOR_LIMS)
       percentage_lims_genes_above = number_of_lims_genes_above_coverage_threshold / len(globals.GENES_FOR_LIMS)
-      # if the percentage of genes above the coverage threshold is greater than 90%, then we can call the lineage
-      percentage_limit = 0.9      
 
     self.logger.debug("LIMS:The percentage of LIMS genes above the coverage threshold is {}".format(percentage_lims_genes_above))
 
@@ -54,37 +54,40 @@ def get_id(self):
       self.logger.debug("LIMS:The detected lineage is: '{}', and the detected sublineage is: '{}'".format(detected_lineage, detected_sublineage))
 
       sublineages = detected_sublineage.split(";")
-      if percentage_lims_genes_above >= percentage_limit:
-        self.logger.debug("LIMS:Percentage of LIMS genes above the coverage threshold is GREATER than 90%")
 
-        if self.tngs:
-          self.logger.debug("LIMS:The sequencing method is tNGS; now checking for a His57Asp mutation in pncA")
-          pncA_mutations = globals.DF_LABORATORIAN[(globals.DF_LABORATORIAN["tbprofiler_gene_name"] == "pncA")]
-          if "p.His57Asp" in pncA_mutations["tbprofiler_variant_substitution_aa"].tolist():
-            self.logger.debug("LIMS:p.His57Asp detected in pncA, lineage is likely M. bovis")
-            lineage.add("DNA of Mycobacterium bovis detected")
-          else:
-            self.logger.debug("LIMS:p.His57Asp not detected in pncA, lineage is likely M. tuberculosis")
-            lineage.add("DNA of Mycobacterium tuberculosis complex detected (not M. bovis)")
+      if self.tngs:
+        self.logger.debug("LIMS:The sequencing method is tNGS; now checking for a His57Asp mutation in pncA")
+        pncA_mutations = globals.DF_LABORATORIAN[(globals.DF_LABORATORIAN["tbprofiler_gene_name"] == "pncA")]
+        if "p.His57Asp" in pncA_mutations["tbprofiler_variant_substitution_aa"].tolist():
+          self.logger.debug("LIMS:p.His57Asp detected in pncA, lineage is likely M. bovis")
+          lineage.add("DNA of Mycobacterium bovis detected")
+        else:
+          self.logger.debug("LIMS:p.His57Asp not detected in pncA, lineage is likely M. tuberculosis")
+          lineage.add("DNA of Mycobacterium tuberculosis complex detected (not M. bovis)") 
+
+      else:  
+        self.logger.debug("LIMS:The sequencing method is WGS; now checking the TBProfiler lineage calls")
+        if "lineage" in detected_lineage:
+          lineage.add("DNA of Mycobacterium tuberculosis species detected")
+
+        for sublineage in sublineages:  
+          if "BCG" in detected_lineage or "BCG" in sublineage:
+            lineage.add("DNA of Mycobacterium bovis BCG detected")
+
+          elif ("La1" in detected_lineage or "La1" in sublineage) or ("bovis" in detected_lineage or "bovis" in sublineage):
+            lineage.add("DNA of Mycobacterium bovis (not BCG) detected")     
+
+      if len(lineage) == 0:
+        if (percentage_lims_genes_above >= percentage_limit):
+          self.logger.debug("LIMS:Percentage of LIMS genes above the coverage threshold is GREATER than 90% AND no lineage has been detected")
+          self.logger.debug("LIMS:TBProfiler was likely unable to determine the lineage, but since percentage_lims_genes_above >= percentage_limit, we will assume M.tb")
 
-        else:  
-          self.logger.debug("LIMS:The sequencing method is WGS; now checking the TBProfiler lineage calls")
-          if "lineage" in detected_lineage:
-            lineage.add("DNA of Mycobacterium tuberculosis species detected")
-
-          for sublineage in sublineages:  
-            if "BCG" in detected_lineage or "BCG" in sublineage:
-              lineage.add("DNA of Mycobacterium bovis BCG detected")
-
-            elif ("La1" in detected_lineage or "La1" in sublineage) or ("bovis" in detected_lineage or "bovis" in sublineage):
-              lineage.add("DNA of Mycobacterium bovis (not BCG) detected")     
-
           if detected_lineage == "" or detected_lineage == "NA" or len(lineage) == 0:
               lineage.add("DNA of Mycobacterium tuberculosis complex detected")
-
-      else:
-        self.logger.debug("LIMS:Percentage of LIMS genes above the coverage threshold is LESS than 90%")
-        lineage.add("DNA of Mycobacterium tuberculosis complex NOT detected")
+            
+        else:
+          self.logger.debug("LIMS:Percentage of LIMS genes above the coverage threshold is LESS than 90% AND no lineage has been detected")
+          lineage.add("DNA of Mycobacterium tuberculosis complex NOT detected")
 
       lineage = "; ".join(sorted(lineage))
 

tbp_parser/__init__.py

@@ -1 +1 @@
-__VERSION__ = "v2.2.0"
+__VERSION__ = "v2.3.0"