Mercurial > repos > iuc > hamronize_summarize
diff test-data/mykrobe/mykrobe.json @ 5:88045b4d5597 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
| author | iuc |
|---|---|
| date | Tue, 05 Mar 2024 19:47:21 +0000 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mykrobe/mykrobe.json Tue Mar 05 19:47:21 2024 +0000 @@ -0,0 +1,269 @@ +{ + "SRR6916544": { + "susceptibility": { + "Rifampicin": { + "predict": "r", + "called_by": { + "rpoB_S450L-TCG761154TTG": { + "variant": null, + "genotype": [ + 0, + 1 + ], + "genotype_likelihoods": [ + -3594.140082249598, + -136.57739012799902, + -2127.6812715680494 + ], + "info": { + "coverage": { + "reference": { + "percent_coverage": 100.0, + "median_depth": 40, + "min_non_zero_depth": 32, + "kmer_count": 796, + "klen": 21 + }, + "alternate": { + "percent_coverage": 100.0, + "median_depth": 60, + "min_non_zero_depth": 58, + "kmer_count": 1150, + "klen": 20 + } + }, + "expected_depths": [ + 124 + ], + "contamination_depths": [], + "filter": [], + "conf": 3458 + }, + "_cls": "Call.VariantCall" + } + } + } + }, + "phylogenetics": { + "phylo_group": { + "Mycobacterium_tuberculosis_complex": { + "percent_coverage": 99.681, + "median_depth": 124 + } + }, + "sub_complex": { + "Unknown": { + "percent_coverage": -1, + "median_depth": -1 + } + }, + "species": { + "Mycobacterium_tuberculosis": { + "percent_coverage": 98.804, + "median_depth": 121 + } + }, + "lineage": { + "lineage": [ + "lineage2.2.10", + "lineage3" + ], + "calls_summary": { + "lineage2.2.10": { + "good_nodes": 3, + "tree_depth": 3, + "genotypes": { + "lineage2": 0.5, + "lineage2.2": 0.5, + "lineage2.2.10": 0.5 + } + }, + "lineage3": { + "good_nodes": 1, + "tree_depth": 1, + "genotypes": { + "lineage3": 0.5 + } + } + }, + "calls": { + "lineage2.2.10": { + "lineage2": { + "G497491A": { + "variant": "ref-G497491A?var_name=G497491A&num_alts=1&ref=NC_000962.3&enum=0&gene=NA&mut=G497491A", + "genotype": [ + 0, + 1 + ], + "genotype_likelihoods": [ + -4852.294042193726, + -68.00214340670391, + -4045.7527933854217 + ], + "info": { + "coverage": { + "reference": { + "percent_coverage": 100.0, + "median_depth": 76, + "min_non_zero_depth": 70, + "kmer_count": 1498, + "klen": 21 + }, + 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"info": { + "coverage": { + "reference": { + "percent_coverage": 100.0, + "median_depth": 66, + "min_non_zero_depth": 64, + "kmer_count": 1323, + "klen": 21 + }, + "alternate": { + "percent_coverage": 100.0, + "median_depth": 58, + "min_non_zero_depth": 54, + "kmer_count": 1160, + "klen": 21 + } + }, + "expected_depths": [ + 124 + ], + "contamination_depths": [], + "filter": [], + "conf": 3074 + }, + "_cls": "Call.VariantCall" + } + } + } + } + } + }, + "kmer": 21, + "probe_sets": [ + "/home/pvh/miniconda3/envs/mykrobe/lib/python3.9/site-packages/mykrobe/data/tb/tb-species-170421.fasta.gz", + "/home/pvh/miniconda3/envs/mykrobe/lib/python3.9/site-packages/mykrobe/data/tb/tb-hunt-probe-set-jan-03-2019.fasta.gz", + "/home/pvh/miniconda3/envs/mykrobe/lib/python3.9/site-packages/mykrobe/data/tb/tb.lineage.20200930.probes.fa.gz" + ], + "files": [ + "../SRR6916544_1.fastq.gz", + "../SRR6916544_2.fastq.gz" + ], + "version": { + "mykrobe-predictor": "v0.10.0", + "mykrobe-atlas": "v0.10.0" + }, + "genotype_model": "kmer_count" + } +} \ No newline at end of file