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
+                                        },
+                                        "alternate": {
+                                            "percent_coverage": 100.0,
+                                            "median_depth": 85,
+                                            "min_non_zero_depth": 82,
+                                            "kmer_count": 1695,
+                                            "klen": 21
+                                        }
+                                    },
+                                    "expected_depths": [
+                                        124
+                                    ],
+                                    "contamination_depths": [],
+                                    "filter": [],
+                                    "conf": 4784
+                                },
+                                "_cls": "Call.VariantCall"
+                            }
+                        },
+                        "lineage2.2": {
+                            "G2505085A": {
+                                "variant": "ref-G2505085A?var_name=G2505085A&num_alts=2&ref=NC_000962.3&enum=0&gene=NA&mut=G2505085A",
+                                "genotype": [
+                                    0,
+                                    1
+                                ],
+                                "genotype_likelihoods": [
+                                    -3967.5854789566783,
+                                    -20.859193826341652,
+                                    -3054.5971617777313
+                                ],
+                                "info": {
+                                    "coverage": {
+                                        "reference": {
+                                            "percent_coverage": 100.0,
+                                            "median_depth": 58,
+                                            "min_non_zero_depth": 56,
+                                            "kmer_count": 1160,
+                                            "klen": 21
+                                        },
+                                        "alternate": {
+                                            "percent_coverage": 100.0,
+                                            "median_depth": 69,
+                                            "min_non_zero_depth": 64,
+                                            "kmer_count": 1383,
+                                            "klen": 21
+                                        }
+                                    },
+                                    "expected_depths": [
+                                        124
+                                    ],
+                                    "contamination_depths": [],
+                                    "filter": [],
+                                    "conf": 3947
+                                },
+                                "_cls": "Call.VariantCall"
+                            }
+                        },
+                        "lineage2.2.10": {
+                            "G1364706A": {
+                                "variant": "ref-G1364706A?var_name=G1364706A&num_alts=2&ref=NC_000962.3&enum=0&gene=NA&mut=G1364706A",
+                                "genotype": [
+                                    0,
+                                    1
+                                ],
+                                "genotype_likelihoods": [
+                                    -2360.5217287767423,
+                                    -145.4041778818164,
+                                    -3052.427673185898
+                                ],
+                                "info": {
+                                    "coverage": {
+                                        "reference": {
+                                            "percent_coverage": 100.0,
+                                            "median_depth": 51,
+                                            "min_non_zero_depth": 47,
+                                            "kmer_count": 1017,
+                                            "klen": 21
+                                        },
+                                        "alternate": {
+                                            "percent_coverage": 100.0,
+                                            "median_depth": 42,
+                                            "min_non_zero_depth": 42,
+                                            "kmer_count": 848,
+                                            "klen": 21
+                                        }
+                                    },
+                                    "expected_depths": [
+                                        124
+                                    ],
+                                    "contamination_depths": [],
+                                    "filter": [],
+                                    "conf": 2215
+                                },
+                                "_cls": "Call.VariantCall"
+                            }
+                        }
+                    },
+                    "lineage3": {
+                        "lineage3": {
+                            "C3273107A": {
+                                "variant": "ref-C3273107A?var_name=C3273107A&num_alts=1&ref=NC_000962.3&enum=0&gene=NA&mut=C3273107A",
+                                "genotype": [
+                                    0,
+                                    1
+                                ],
+                                "genotype_likelihoods": [
+                                    -3093.863597972382,
+                                    -19.52878016336399,
+                                    -3761.204834296007
+                                ],
+                                "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