# HG changeset patch
# User iuc
# Date 1631775138 0
# Node ID db4fe71721140208d45c43ca0fd2fb5aae0e6a4c
"planemo upload for repository https://github.com/katholt/sonneityping commit 1b4231e8f98a234c29f57fef400f58f14645dc95"
diff -r 000000000000 -r db4fe7172114 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Thu Sep 16 06:52:18 2021 +0000
@@ -0,0 +1,9 @@
+
+
+
+
+ sonneityping
+
+
+ 20210201
+
diff -r 000000000000 -r db4fe7172114 parse_mykrobe_predict.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/parse_mykrobe_predict.xml Thu Sep 16 06:52:18 2021 +0000
@@ -0,0 +1,71 @@
+
+ for Shigella sonnei and tabulate results into a single tab-delimited file
+
+ macros.xml
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ @misc{GitHubsonneityping,
+ title = {sonneityping},
+ journal = {GitHub Repository},
+ url = {https://github.com/katholt/sonneityping},
+ }
+
+
+
+
diff -r 000000000000 -r db4fe7172114 test-data/SRR6114360.json
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/SRR6114360.json Thu Sep 16 06:52:18 2021 +0000
@@ -0,0 +1,223 @@
+{
+ "SRR6114360": {
+ "susceptibility": {
+ "quinolones": {
+ "predict": "S"
+ }
+ },
+ "phylogenetics": {
+ "phylo_group": {
+ "Ecoli_Shigella": {
+ "percent_coverage": 100.0,
+ "median_depth": 26
+ }
+ },
+ "sub_complex": {
+ "Unknown": {
+ "percent_coverage": -1,
+ "median_depth": -1
+ }
+ },
+ "species": {
+ "Shigella_sonnei": {
+ "percent_coverage": 95.163,
+ "median_depth": 22.0
+ }
+ },
+ "lineage": {
+ "lineage": [
+ "lineage3.7.30.4"
+ ],
+ "calls_summary": {
+ "lineage3.7.30.4": {
+ "good_nodes": 4,
+ "tree_depth": 4,
+ "genotypes": {
+ "lineage3": 1,
+ "lineage3.7": 1,
+ "lineage3.7.30": 1,
+ "lineage3.7.30.4": 1
+ }
+ }
+ },
+ "calls": {
+ "lineage3.7.30.4": {
+ "lineage3": {
+ "C59602T": {
+ "variant": "ref-C59602T?var_name=C59602T&num_alts=1&ref=NC_016822&enum=0&gene=NA&mut=C59602T",
+ "genotype": [
+ 1,
+ 1
+ ],
+ "genotype_likelihoods": [
+ -3282.0148702940733,
+ -99999999,
+ -19.32539954665346
+ ],
+ "info": {
+ "coverage": {
+ "reference": {
+ "percent_coverage": 0.0,
+ "median_depth": 0,
+ "min_non_zero_depth": 0,
+ "kmer_count": 0,
+ "klen": 21
+ },
+ "alternate": {
+ "percent_coverage": 100.0,
+ "median_depth": 27,
+ "min_non_zero_depth": 26,
+ "kmer_count": 541,
+ "klen": 21
+ }
+ },
+ "expected_depths": [
+ 26
+ ],
+ "contamination_depths": [],
+ "filter": [],
+ "conf": 3263
+ },
+ "_cls": "Call.VariantCall"
+ }
+ },
+ "lineage3.7": {
+ "G4080478A": {
+ "variant": "ref-G4080478A?var_name=G4080478A&num_alts=1&ref=NC_016822&enum=0&gene=NA&mut=G4080478A",
+ "genotype": [
+ 1,
+ 1
+ ],
+ "genotype_likelihoods": [
+ -3961.55750528479,
+ -99999999,
+ -39.85243726626552
+ ],
+ "info": {
+ "coverage": {
+ "reference": {
+ "percent_coverage": 0.0,
+ "median_depth": 0,
+ "min_non_zero_depth": 0,
+ "kmer_count": 0,
+ "klen": 21
+ },
+ "alternate": {
+ "percent_coverage": 100.0,
+ "median_depth": 34,
+ "min_non_zero_depth": 34,
+ "kmer_count": 702,
+ "klen": 21
+ }
+ },
+ "expected_depths": [
+ 26
+ ],
+ "contamination_depths": [],
+ "filter": [],
+ "conf": 3922
+ },
+ "_cls": "Call.VariantCall"
+ }
+ },
+ "lineage3.7.30": {
+ "A1138004G": {
+ "variant": "ref-A1138004G?var_name=A1138004G&num_alts=2&ref=NC_016822&enum=0&gene=NA&mut=A1138004G",
+ "genotype": [
+ 1,
+ 1
+ ],
+ "genotype_likelihoods": [
+ -1607.6280372631725,
+ -99999999,
+ -477.52941234336663
+ ],
+ "info": {
+ "coverage": {
+ "reference": {
+ "percent_coverage": 0.0,
+ "median_depth": 0,
+ "min_non_zero_depth": 0,
+ "kmer_count": 0,
+ "klen": 21
+ },
+ "alternate": {
+ "percent_coverage": 100.0,
+ "median_depth": 1,
+ "min_non_zero_depth": 1,
+ "kmer_count": 20,
+ "klen": 21
+ }
+ },
+ "expected_depths": [
+ 26
+ ],
+ "contamination_depths": [],
+ "filter": [
+ "LOW_TOTAL_DEPTH"
+ ],
+ "conf": 1130
+ },
+ "_cls": "Call.VariantCall"
+ }
+ },
+ "lineage3.7.30.4": {
+ "G3082193A": {
+ "variant": "ref-G3082193A?var_name=G3082193A&num_alts=1&ref=NC_016822&enum=0&gene=NA&mut=G3082193A",
+ "genotype": [
+ 1,
+ 1
+ ],
+ "genotype_likelihoods": [
+ -2726.2314885023525,
+ -99999999,
+ -40.69232343956539
+ ],
+ "info": {
+ "coverage": {
+ "reference": {
+ "percent_coverage": 0.0,
+ "median_depth": 0,
+ "min_non_zero_depth": 0,
+ "kmer_count": 0,
+ "klen": 21
+ },
+ "alternate": {
+ "percent_coverage": 100.0,
+ "median_depth": 20,
+ "min_non_zero_depth": 18,
+ "kmer_count": 400,
+ "klen": 21
+ }
+ },
+ "expected_depths": [
+ 26
+ ],
+ "contamination_depths": [],
+ "filter": [],
+ "conf": 2686
+ },
+ "_cls": "Call.VariantCall"
+ }
+ }
+ }
+ }
+ }
+ },
+ "kmer": 21,
+ "probe_sets": [
+ "/home/eric/miniconda3/lib/python3.8/site-packages/mykrobe/data/sonnei/sonnei.lineage.20210201.probes.fa.gz",
+ "/home/eric/miniconda3/lib/python3.8/site-packages/mykrobe/data/sonnei/sonnei.mlst.20201010.sonnei.fa.gz",
+ "/home/eric/miniconda3/lib/python3.8/site-packages/mykrobe/data/sonnei/sonnei.probe.uidA.20201010.fa.gz",
+ "/home/eric/miniconda3/lib/python3.8/site-packages/mykrobe/data/sonnei/sonnei.qrdr.20201010.probes.fa.gz"
+ ],
+ "files": [
+ "SRR6114360_1"
+ ],
+ "version": {
+ "mykrobe-predictor": "v0.10.0",
+ "mykrobe-atlas": "v0.10.0"
+ },
+ "genotype_model": "kmer_count"
+ }
+}
\ No newline at end of file
diff -r 000000000000 -r db4fe7172114 test-data/alleles.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/alleles.txt Thu Sep 16 06:52:18 2021 +0000
@@ -0,0 +1,148 @@
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