Merge pull request #426 from jodyphelan/dev

Typo #424
jodyphelan · Feb 20, 2025 · bd94ce5 · bd94ce5
2 parents cc79ac3 + 104a591
commit bd94ce5
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Showing 3 changed files with 10 additions and 2 deletions.
diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
@@ -39,6 +39,6 @@ jobs:
     - name: Run tests
       run: |
         cd tests
-        mamba install pytest -y
+        mamba install pytest pandas importlib_resources -y
         pytest -x .
     
diff --git a/tbprofiler/rules.py b/tbprofiler/rules.py
@@ -120,7 +120,7 @@ def process_result(self, args: argparse.Namespace, result: ProfileResult):
                     if var.type=='synonymous_mutation':
                         confidence[drug] = 'Not Assoc W R - Interim'
                     else:
-                        confidence[drug] = 'Uncertain Significance'
+                        confidence[drug] = 'Uncertain significance'
                     ann = {
                         'type':'who_confidence',
                         'drug':drug,

diff --git a/tests/run_test.py b/tests/run_test.py
@@ -68,3 +68,11 @@ def test_collate():
         O.write("por5_vcf\n")
     run_cmd(f"tb-profiler collate --db {db} --samples samples.txt")
     assert open("tbprofiler.txt").read() == collate_text
+
+def test_tbp_parser():
+    run_cmd("git clone https://github.com/theiagen/tbp-parser.git")
+    run_cmd("samtools index bam/por5A_fastq.bam")
+    run_cmd('python tbp-parser/tbp_parser/tbp_parser.py results/por5A_freebayes.results.json bam/por5A_fastq.bam    -o "example-tbp-parser"    --min_depth 12     --min_frequency 0.9     --sequencing_method "Illumina NextSeq"    --operator "John Doe"')
+    test_text = ','.join([l.strip().split(',')[:-2] for l in open("example-tbp-parser.looker_report.csv")][1])
+    target_text = "por5A_freebayes,Illumina NextSeq,U,S-Interim,U,U,R,R,R,U,S,U,S,R,R,U,lineage4,DNA of Mycobacterium tuberculosis species detected"
+    assert test_text == target_text