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update tests
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tests/run_test.py

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@@ -71,8 +71,11 @@ def test_collate():
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def test_tbp_parser():
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run_cmd("git clone https://github.com/theiagen/tbp-parser.git")
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os.mkdir("tbp-parser/tb-profiler-test")
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os.chdir("tbp-parser/tb-profiler-test")
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run_cmd("samtools index bam/por5A_fastq.bam")
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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"')
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run_cmd('python ../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"')
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test_text = ','.join([l.strip().split(',')[:-2] for l in open("example-tbp-parser.looker_report.csv")][1])
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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"
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assert test_text == target_text

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