From 5b40001d1cabed26c8526137d0798ea2e8ebae63 Mon Sep 17 00:00:00 2001 From: Brendan Reardon Date: Fri, 25 Oct 2024 15:47:16 +0200 Subject: [PATCH] 2024-10-23 bug changes (#23) --- example_output/example.log | 903 ++++++++++++++++++ moalmanac/annotation-databases.ini | 2 +- moalmanac/config.ini | 4 +- moalmanac/logger.py | 2 + moalmanac/moalmanac.py | 16 +- moalmanac/preclinical-databases.ini | 2 +- moalmanac/run_example.py | 13 +- moalmanac/simplified_input.py | 4 +- .../report_table/table_biological.html | 14 +- .../report_table/table_prognostic.html | 52 +- .../report_table/table_resistance.html | 52 +- .../report_table/table_sensitive.html | 57 +- 12 files changed, 1017 insertions(+), 104 deletions(-) create mode 100644 example_output/example.log diff --git a/example_output/example.log b/example_output/example.log new file mode 100644 index 0000000..513305f --- /dev/null +++ b/example_output/example.log @@ -0,0 +1,903 @@ +2024-10-24 17:02:09,761 - INFO - Starting to execution of Molecular Oncology Almanac +2024-10-24 17:02:09,761 - INFO - Current working directory: /Users/brendan/GitHub/moalmanac/moalmanac +2024-10-24 17:02:09,761 - INFO - --- Inputs --- +2024-10-24 17:02:09,762 - INFO - Input data, Patient metadata: +{ + "patient_id": "example", + "reported_tumor_type": "MEL", + "stage": "Metastatic", + "description": "Test patient for development runs", + "purity": 0.85, + "ploidy": 4.02, + "WGD": true, + "microsatellite_status": "msih" +} +2024-10-24 17:02:09,763 - INFO - Input data, Input files: +{ + "snv_handle": "../example_data/example_patient.capture.somatic.snvs.maf", + "indel_handle": "../example_data/example_patient.capture.somatic.indels.maf", + "bases_covered_handle": "../example_data/example_patient.capture.somatic.coverage.txt", + "called_cn_handle": "../example_data/example_patient.capture.somatic.called.cna.txt", + "cnv_handle": "../example_data/example_patient.capture.somatic.seg.annotated", + "fusion_handle": "../example_data/example_patient.rna.star.fusions.txt", + "germline_handle": "../example_data/example_patient.capture.germline.maf", + "validation_handle": "../example_data/example_patient.rna.somatic.snvs.maf", + "mutational_signatures_path": "../example_data/example_patient.capture.sbs_contributions.txt", + "disable_matchmaking": false +} +2024-10-24 17:02:09,763 - INFO - Input data, Datasources: +{ + "root": "../datasources", + "almanac_handle": "../datasources/moalmanac/molecular-oncology-almanac.json", + "cancerhotspots_handle": "../datasources/cancerhotspots/hotspots_v2.txt", + "3dcancerhotspots_handle": "../datasources/cancerhotspots/hotspots3d.txt", + "cgc_handle": "../datasources/cancergenecensus/cancer_gene_census_v97.genes.tsv", + "cosmic_handle": "../datasources/cosmic/CosmicMutantExport_v97.lite.txt", + "gsea_pathways_handle": "../datasources/gsea_gene_sets/GSEA_cancer_gene_sets.txt", + "gsea_modules_handle": "../datasources/gsea_gene_sets/c4.cm.v6.0.symbols.txt", + "exac_handle": "../datasources/exac/exac.expanded.r1.txt", + "acmg_handle": "../datasources/acmg/acmg.secondaryfindings.v3.txt", + "clinvar_handle": "../datasources/clinvar/variant_summary.lite.txt", + "hereditary_handle": "../datasources/hereditary/hereditary.txt", + "oncotree_handle": "../datasources/oncotree/oncotree.2023-03-09.txt", + "lawrence_handle": "../datasources/lawrence/lawrence_mapped_ontology.txt" +} +2024-10-24 17:02:09,763 - INFO - Input data, Datasources for preclinical modules: +{ + "root": "../datasources", + "almanac_gdsc_mappings": "../datasources/preclinical/formatted/almanac-gdsc-mappings.json", + "summary": "../datasources/preclinical/formatted/cell-lines.summary.txt", + "variants": "../datasources/preclinical/annotated/cell-lines.somatic-variants.annotated.txt", + "copynumbers": "../datasources/preclinical/annotated/cell-lines.copy-numbers.annotated.txt", + "fusions": "../datasources/preclinical/annotated/cell-lines.fusions.annotated.txt", + "fusions1": "../datasources/preclinical/annotated/cell-lines.fusions.annotated.gene1.txt", + "fusions2": "../datasources/preclinical/annotated/cell-lines.fusions.annotated.gene2.txt", + "gdsc": "../datasources/preclinical/formatted/sanger.gdsc.txt", + "dictionary": "../datasources/preclinical/cell-lines.pkl" +} +2024-10-24 17:02:09,763 - INFO - --- Configuration settings from config.ini --- +2024-10-24 17:02:09,763 - INFO - Input data, Config section: function_toggle: +{ + "calculate_model_similarity": "on", + "calculate_preclinical_efficacy": "on", + "generate_figures": "on", + "generate_actionability_report": "on", + "include_model_similarity_in_actionability_report": "on", + "include_preclinical_efficacy_in_actionability_report": "on" +} +2024-10-24 17:02:09,763 - INFO - Input data, Config section: logging: +{ + "level": "INFO" +} +2024-10-24 17:02:09,763 - INFO - Input data, Config section: versions: +{ + "interpreter": "0.7.2", + "database": "v.2024-04-11" +} +2024-10-24 17:02:09,763 - INFO - Input data, Config section: exac: +{ + "exac_common_af_threshold": "0.001" +} +2024-10-24 17:02:09,763 - INFO - Input data, Config section: fusion: +{ + "spanningfrags_min": "5.0", + "alt_type": "Fusion", + "leftbreakpoint": "leftbreakpoint", + "rightbreakpoint": "rightbreakpoint" +} +2024-10-24 17:02:09,764 - INFO - Input data, Config section: mutations: +{ + "min_coverage": "15", + "min_af": "0.05" +} +2024-10-24 17:02:09,764 - INFO - Input data, Config section: seg: +{ + "amp_percentile": "97.5", + "del_percentile": "2.5", + "amp": "Amplification", + "del": "Deletion" +} +2024-10-24 17:02:09,764 - INFO - Input data, Config section: signatures: +{ + "min_contribution": "0.06" +} +2024-10-24 17:02:09,764 - INFO - Input data, Config section: validation_sequencing: +{ + "min_power": "0.95", + "min_af_for_annotation": "0.10" +} +2024-10-24 17:02:09,764 - INFO - Input data, Config section: feature_types: +{ + "mut": "Somatic Variant", + "germline": "Germline Variant", + "cna": "Copy Number", + "fusion": "Rearrangement", + "microsatellite": "Microsatellite Stability", + "burden": "Mutational Burden", + "signature": "Mutational Signature", + "aneuploidy": "Aneuploidy", + "knockdown": "Knockdown" +} +2024-10-24 17:02:09,764 - INFO - Logging for inputs provided complete. + +2024-10-24 17:02:09,764 - INFO - --- Output directory --- +2024-10-24 17:02:09,764 - INFO - 2024-10-24-example-outputs-all-enabled specified as output directory, creating... +2024-10-24 17:02:09,803 - INFO - 2024-10-24-example-outputs-all-enabled created. + +2024-10-24 17:02:09,803 - INFO - --- Mapping provided disease to Oncotree --- +2024-10-24 17:02:09,819 - INFO - MEL mapped to Melanoma (MEL) + +2024-10-24 17:02:09,819 - INFO - --- Importing somatic genomic data --- +2024-10-24 17:02:09,819 - INFO - Somatic variants from ../example_data/example_patient.capture.somatic.snvs.maf +2024-10-24 17:02:09,866 - INFO - ...Somatic variants, passed: 203 rows and 253 columns +2024-10-24 17:02:09,866 - INFO - ...Somatic variants, rejected: 96 rows and 253 columns +2024-10-24 17:02:09,866 - INFO - Somatic indel variants from ../example_data/example_patient.capture.somatic.indels.maf +2024-10-24 17:02:09,901 - INFO - ...somatic indel variants, passed: 1 rows and 253 columns +2024-10-24 17:02:09,901 - INFO - ...somatic indel variants, rejected: 1 rows and 253 columns +2024-10-24 17:02:09,901 - INFO - Called copy number from ../example_data/example_patient.capture.somatic.called.cna.txt +2024-10-24 17:02:09,919 - INFO - ...Copy number alterations, passed: 5 rows and 253 columns +2024-10-24 17:02:09,919 - INFO - ...Copy number alterations, rejected: 1 rows and 253 columns +2024-10-24 17:02:09,919 - INFO - Fusions from ../example_data/example_patient.rna.star.fusions.txt +2024-10-24 17:02:09,958 - INFO - ...fusions, passed: 56 rows and 253 columns +2024-10-24 17:02:09,958 - INFO - ...fusions, rejected: 122 rows and 253 columns +2024-10-24 17:02:10,018 - INFO - Overall somatic events, passed: 265 rows and 253 columns +2024-10-24 17:02:10,018 - INFO - Overall somatic events, rejected: 220 rows and 253 columns + +2024-10-24 17:02:10,018 - INFO - --- Importing germline genomic data --- +2024-10-24 17:02:10,018 - INFO - Germline variants from ../example_data/example_patient.capture.germline.maf +2024-10-24 17:02:10,063 - INFO - ...germline variants, passed: 10 rows and 253 columns +2024-10-24 17:02:10,063 - INFO - ...germline variants, rejected: 0 rows and 253 columns + +2024-10-24 17:02:10,063 - INFO - --- Annotating and evaluating somatic variants --- +2024-10-24 17:02:10,063 - INFO - Annotating somatic variants +2024-10-24 17:02:10,064 - INFO - ...with MOAlmanac's database +2024-10-24 17:02:10,090 - INFO - ...annotating inputs of type Copy Number with MOAlmanac's database +2024-10-24 17:02:10,093 - INFO - ...records of Copy Number in the database: 115 +2024-10-24 17:02:10,096 - INFO - ...records of Copy Number provided: 5 +2024-10-24 17:02:10,097 - INFO - ...annotating TP53 Deletion for therapy_sensitivity... +2024-10-24 17:02:10,098 - INFO - ......was able to match on gene, biomarker type, and direction +2024-10-24 17:02:10,107 - INFO - ......1 matches for therapy_sensitivity within the database using this criteria +2024-10-24 17:02:10,107 - INFO - ...annotating TP53 Deletion for therapy_resistance... +2024-10-24 17:02:10,108 - INFO - ......was unable to match on gene, biomarker type, and direction +2024-10-24 17:02:10,108 - INFO - ......was unable to match on gene and biomarker type +2024-10-24 17:02:10,108 - INFO - ......was only able to match on gene, no specific database records matched +2024-10-24 17:02:10,108 - INFO - ...annotating TP53 Deletion for favorable_prognosis... +2024-10-24 17:02:10,109 - INFO - ......was able to match on gene, biomarker type, and direction +2024-10-24 17:02:10,114 - INFO - ......1 matches for favorable_prognosis within the database using this criteria +2024-10-24 17:02:10,163 - INFO - ...annotating CDKN2A Deletion for therapy_sensitivity... +2024-10-24 17:02:10,164 - INFO - ......was able to match on gene, biomarker type, and direction +2024-10-24 17:02:10,172 - INFO - ......1 matches for therapy_sensitivity within the database using this criteria +2024-10-24 17:02:10,172 - INFO - ...annotating CDKN2A Deletion for therapy_resistance... +2024-10-24 17:02:10,173 - INFO - ......was unable to match on gene, biomarker type, and direction +2024-10-24 17:02:10,173 - INFO - ......was unable to match on gene and biomarker type +2024-10-24 17:02:10,173 - INFO - ......was only able to match on gene, no specific database records matched +2024-10-24 17:02:10,173 - INFO - ...annotating CDKN2A Deletion for favorable_prognosis... +2024-10-24 17:02:10,174 - INFO - ......was unable to match on gene, biomarker type, and direction +2024-10-24 17:02:10,174 - INFO - ......was unable to match on gene and biomarker type +2024-10-24 17:02:10,174 - INFO - ......was only able to match on gene, no specific database records matched +2024-10-24 17:02:10,221 - INFO - ...annotating BRAF Amplification for therapy_sensitivity... +2024-10-24 17:02:10,221 - INFO - ......was unable to match on gene, biomarker type, and direction +2024-10-24 17:02:10,221 - INFO - ......was unable to match on gene and biomarker type +2024-10-24 17:02:10,221 - INFO - ......was only able to match on gene, no specific database records matched +2024-10-24 17:02:10,221 - INFO - ...annotating BRAF Amplification for therapy_resistance... +2024-10-24 17:02:10,222 - INFO - ......was able to match on gene, biomarker type, and direction +2024-10-24 17:02:10,231 - INFO - ......1 matches for therapy_resistance within the database using this criteria +2024-10-24 17:02:10,231 - INFO - ...annotating BRAF Amplification for favorable_prognosis... +2024-10-24 17:02:10,231 - INFO - ......was unable to match on gene, biomarker type, and direction +2024-10-24 17:02:10,232 - INFO - ......was unable to match on gene and biomarker type +2024-10-24 17:02:10,232 - INFO - ......was only able to match on gene, no specific database records matched +2024-10-24 17:02:10,281 - INFO - ...annotating CDK4 Amplification for therapy_sensitivity... +2024-10-24 17:02:10,282 - INFO - ......was able to match on gene, biomarker type, and direction +2024-10-24 17:02:10,287 - INFO - ......2 matches for therapy_sensitivity within the database using this criteria +2024-10-24 17:02:10,288 - INFO - ...annotating CDK4 Amplification for therapy_resistance... +2024-10-24 17:02:10,288 - INFO - ......was unable to match on gene, biomarker type, and direction +2024-10-24 17:02:10,288 - INFO - ......was unable to match on gene and biomarker type +2024-10-24 17:02:10,288 - INFO - ......was only able to match on gene, no specific database records matched +2024-10-24 17:02:10,288 - INFO - ...annotating CDK4 Amplification for favorable_prognosis... +2024-10-24 17:02:10,289 - INFO - ......was unable to match on gene, biomarker type, and direction +2024-10-24 17:02:10,289 - INFO - ......was unable to match on gene and biomarker type +2024-10-24 17:02:10,289 - INFO - ......was only able to match on gene, no specific database records matched +2024-10-24 17:02:10,336 - INFO - ...annotating FGFR2 Deletion for therapy_sensitivity... +2024-10-24 17:02:10,337 - INFO - ......was unable to match on gene, biomarker type, and direction +2024-10-24 17:02:10,337 - INFO - ......was able to match on gene and biomarker type +2024-10-24 17:02:10,343 - INFO - ......4 matches for therapy_sensitivity within the database using this criteria +2024-10-24 17:02:10,343 - INFO - ...annotating FGFR2 Deletion for therapy_resistance... +2024-10-24 17:02:10,343 - INFO - ......was unable to match on gene, biomarker type, and direction +2024-10-24 17:02:10,343 - INFO - ......was unable to match on gene and biomarker type +2024-10-24 17:02:10,343 - INFO - ......was only able to match on gene, no specific database records matched +2024-10-24 17:02:10,343 - INFO - ...annotating FGFR2 Deletion for favorable_prognosis... +2024-10-24 17:02:10,344 - INFO - ......was unable to match on gene, biomarker type, and direction +2024-10-24 17:02:10,344 - INFO - ......was unable to match on gene and biomarker type +2024-10-24 17:02:10,344 - INFO - ......was only able to match on gene, no specific database records matched +2024-10-24 17:02:10,391 - INFO - ...annotating input Copy Numbers with MOAlmanac's database complete + +2024-10-24 17:02:10,391 - INFO - ...annotating inputs of type Rearrangement with MOAlmanac's database +2024-10-24 17:02:10,393 - INFO - ...records of Rearrangement in the database: 77 +2024-10-24 17:02:10,396 - INFO - ...records of Rearrangement provided: 1 +2024-10-24 17:02:10,397 - INFO - ...annotating COL1A1 Fusion COL1A1--CITED4 for therapy_sensitivity... +2024-10-24 17:02:10,398 - INFO - ......processing as COL1A1::CITED4... +2024-10-24 17:02:10,399 - INFO - ......was unable to match on first gene, second gene, biomarker type, and rearrangement type +2024-10-24 17:02:10,399 - INFO - ......was able to match on first gene, biomarker type, and rearrangement type +2024-10-24 17:02:10,399 - INFO - ......processing as CITED4::COL1A1... +2024-10-24 17:02:10,401 - INFO - ......was unable to match on second gene, first gene, biomarker type, and rearrangement type +2024-10-24 17:02:10,401 - INFO - ......was able to match on second gene, biomarker type, and rearrangement type +2024-10-24 17:02:10,407 - INFO - ......1 matches for therapy_sensitivity within the database using this criteria +2024-10-24 17:02:10,407 - INFO - ...annotating COL1A1 Fusion COL1A1--CITED4 for therapy_resistance... +2024-10-24 17:02:10,407 - INFO - ......processing as COL1A1::CITED4... +2024-10-24 17:02:10,409 - INFO - ......was only able to match on gene, no specific database records matched +2024-10-24 17:02:10,409 - INFO - ......processing as CITED4::COL1A1... +2024-10-24 17:02:10,410 - INFO - ......was only able to match on gene, no specific database records matched +2024-10-24 17:02:10,410 - INFO - ...annotating COL1A1 Fusion COL1A1--CITED4 for favorable_prognosis... +2024-10-24 17:02:10,410 - INFO - ......processing as COL1A1::CITED4... +2024-10-24 17:02:10,412 - INFO - ......was only able to match on gene, no specific database records matched +2024-10-24 17:02:10,412 - INFO - ......processing as CITED4::COL1A1... +2024-10-24 17:02:10,413 - INFO - ......was only able to match on gene, no specific database records matched +2024-10-24 17:02:10,460 - INFO - ...annotating input Rearrangements with MOAlmanac's database complete + +2024-10-24 17:02:10,460 - INFO - ...annotating inputs of type Somatic Variant with MOAlmanac's database +2024-10-24 17:02:10,464 - INFO - ...records of Somatic Variant in the database: 608 +2024-10-24 17:02:10,469 - INFO - ...records of Somatic Variant provided: 6 +2024-10-24 17:02:10,471 - INFO - ...annotating BRAF Missense p.V600E for therapy_sensitivity... +2024-10-24 17:02:10,472 - INFO - ......was able to match on gene, biomarker type, variant classification, and protein change +2024-10-24 17:02:10,483 - INFO - ......12 matches for therapy_sensitivity within the database using this criteria +2024-10-24 17:02:10,483 - INFO - ...annotating BRAF Missense p.V600E for therapy_resistance... +2024-10-24 17:02:10,484 - INFO - ......was able to match on gene, biomarker type, variant classification, and protein change +2024-10-24 17:02:10,490 - INFO - ......2 matches for therapy_resistance within the database using this criteria +2024-10-24 17:02:10,490 - INFO - ...annotating BRAF Missense p.V600E for favorable_prognosis... +2024-10-24 17:02:10,491 - INFO - ......was able to match on gene, biomarker type, variant classification, and protein change +2024-10-24 17:02:10,496 - INFO - ......2 matches for favorable_prognosis within the database using this criteria +2024-10-24 17:02:10,545 - INFO - ...annotating MSH2 Missense p.D887N for therapy_sensitivity... +2024-10-24 17:02:10,546 - INFO - ......was unable to match on gene, biomarker type, variant classification, and protein change +2024-10-24 17:02:10,546 - INFO - ......was unable to match on gene, biomarker type, and variant classification +2024-10-24 17:02:10,546 - INFO - ......was able to match on gene and biomarker type +2024-10-24 17:02:10,552 - INFO - ......1 matches for therapy_sensitivity within the database using this criteria +2024-10-24 17:02:10,552 - INFO - ...annotating MSH2 Missense p.D887N for therapy_resistance... +2024-10-24 17:02:10,552 - INFO - ......was unable to match on gene, biomarker type, variant classification, and protein change +2024-10-24 17:02:10,552 - INFO - ......was unable to match on gene, biomarker type, and variant classification +2024-10-24 17:02:10,553 - INFO - ......was unable to match on gene and biomarker type +2024-10-24 17:02:10,553 - INFO - ......was only able to match on gene, no specific database records matched +2024-10-24 17:02:10,553 - INFO - ...annotating MSH2 Missense p.D887N for favorable_prognosis... +2024-10-24 17:02:10,553 - INFO - ......was unable to match on gene, biomarker type, variant classification, and protein change +2024-10-24 17:02:10,554 - INFO - ......was unable to match on gene, biomarker type, and variant classification +2024-10-24 17:02:10,554 - INFO - ......was unable to match on gene and biomarker type +2024-10-24 17:02:10,554 - INFO - ......was only able to match on gene, no specific database records matched +2024-10-24 17:02:10,607 - INFO - ...annotating NTRK2 Missense p.H300Y for therapy_sensitivity... +2024-10-24 17:02:10,608 - INFO - ......was unable to match on gene, biomarker type, variant classification, and protein change +2024-10-24 17:02:10,608 - INFO - ......was unable to match on gene, biomarker type, and variant classification +2024-10-24 17:02:10,608 - INFO - ......was unable to match on gene and biomarker type +2024-10-24 17:02:10,608 - INFO - ......was only able to match on gene, no specific database records matched +2024-10-24 17:02:10,608 - INFO - ...annotating NTRK2 Missense p.H300Y for therapy_resistance... +2024-10-24 17:02:10,608 - INFO - ......was unable to match on gene, biomarker type, variant classification, and protein change +2024-10-24 17:02:10,608 - INFO - ......was unable to match on gene, biomarker type, and variant classification +2024-10-24 17:02:10,608 - INFO - ......was unable to match on gene and biomarker type +2024-10-24 17:02:10,609 - INFO - ......was only able to match on gene, no specific database records matched +2024-10-24 17:02:10,609 - INFO - ...annotating NTRK2 Missense p.H300Y for favorable_prognosis... +2024-10-24 17:02:10,609 - INFO - ......was unable to match on gene, biomarker type, variant classification, and protein change +2024-10-24 17:02:10,609 - INFO - ......was unable to match on gene, biomarker type, and variant classification +2024-10-24 17:02:10,609 - INFO - ......was unable to match on gene and biomarker type +2024-10-24 17:02:10,609 - INFO - ......was only able to match on gene, no specific database records matched +2024-10-24 17:02:10,658 - INFO - ...annotating PDGFRB Missense p.G674E for therapy_sensitivity... +2024-10-24 17:02:10,659 - INFO - ......was unable to match on gene, biomarker type, variant classification, and protein change +2024-10-24 17:02:10,659 - INFO - ......was unable to match on gene, biomarker type, and variant classification +2024-10-24 17:02:10,659 - INFO - ......was unable to match on gene and biomarker type +2024-10-24 17:02:10,659 - INFO - ......was only able to match on gene, no specific database records matched +2024-10-24 17:02:10,659 - INFO - ...annotating PDGFRB Missense p.G674E for therapy_resistance... +2024-10-24 17:02:10,660 - INFO - ......was unable to match on gene, biomarker type, variant classification, and protein change +2024-10-24 17:02:10,660 - INFO - ......was unable to match on gene, biomarker type, and variant classification +2024-10-24 17:02:10,660 - INFO - ......was unable to match on gene and biomarker type +2024-10-24 17:02:10,660 - INFO - ......was only able to match on gene, no specific database records matched +2024-10-24 17:02:10,660 - INFO - ...annotating PDGFRB Missense p.G674E for favorable_prognosis... +2024-10-24 17:02:10,660 - INFO - ......was unable to match on gene, biomarker type, variant classification, and protein change +2024-10-24 17:02:10,660 - INFO - ......was unable to match on gene, biomarker type, and variant classification +2024-10-24 17:02:10,661 - INFO - ......was unable to match on gene and biomarker type +2024-10-24 17:02:10,661 - INFO - ......was only able to match on gene, no specific database records matched +2024-10-24 17:02:10,710 - INFO - ...annotating STAG2 Missense p.F467I for therapy_sensitivity... +2024-10-24 17:02:10,711 - INFO - ......was unable to match on gene, biomarker type, variant classification, and protein change +2024-10-24 17:02:10,711 - INFO - ......was unable to match on gene, biomarker type, and variant classification +2024-10-24 17:02:10,711 - INFO - ......was unable to match on gene and biomarker type +2024-10-24 17:02:10,711 - INFO - ......was only able to match on gene, no specific database records matched +2024-10-24 17:02:10,711 - INFO - ...annotating STAG2 Missense p.F467I for therapy_resistance... +2024-10-24 17:02:10,712 - INFO - ......was unable to match on gene, biomarker type, variant classification, and protein change +2024-10-24 17:02:10,712 - INFO - ......was unable to match on gene, biomarker type, and variant classification +2024-10-24 17:02:10,712 - INFO - ......was unable to match on gene and biomarker type +2024-10-24 17:02:10,712 - INFO - ......was only able to match on gene, no specific database records matched +2024-10-24 17:02:10,712 - INFO - ...annotating STAG2 Missense p.F467I for favorable_prognosis... +2024-10-24 17:02:10,713 - INFO - ......was unable to match on gene, biomarker type, variant classification, and protein change +2024-10-24 17:02:10,713 - INFO - ......was unable to match on gene, biomarker type, and variant classification +2024-10-24 17:02:10,713 - INFO - ......was able to match on gene and biomarker type +2024-10-24 17:02:10,719 - INFO - ......3 matches for favorable_prognosis within the database using this criteria +2024-10-24 17:02:10,773 - INFO - ...annotating ZRSR2 Missense p.N261I for therapy_sensitivity... +2024-10-24 17:02:10,774 - INFO - ......was unable to match on gene, biomarker type, variant classification, and protein change +2024-10-24 17:02:10,774 - INFO - ......was unable to match on gene, biomarker type, and variant classification +2024-10-24 17:02:10,774 - INFO - ......was unable to match on gene and biomarker type +2024-10-24 17:02:10,774 - INFO - ......was only able to match on gene, no specific database records matched +2024-10-24 17:02:10,774 - INFO - ...annotating ZRSR2 Missense p.N261I for therapy_resistance... +2024-10-24 17:02:10,775 - INFO - ......was unable to match on gene, biomarker type, variant classification, and protein change +2024-10-24 17:02:10,775 - INFO - ......was unable to match on gene, biomarker type, and variant classification +2024-10-24 17:02:10,775 - INFO - ......was unable to match on gene and biomarker type +2024-10-24 17:02:10,775 - INFO - ......was only able to match on gene, no specific database records matched +2024-10-24 17:02:10,775 - INFO - ...annotating ZRSR2 Missense p.N261I for favorable_prognosis... +2024-10-24 17:02:10,776 - INFO - ......was unable to match on gene, biomarker type, variant classification, and protein change +2024-10-24 17:02:10,776 - INFO - ......was unable to match on gene, biomarker type, and variant classification +2024-10-24 17:02:10,776 - INFO - ......was able to match on gene and biomarker type +2024-10-24 17:02:10,782 - INFO - ......2 matches for favorable_prognosis within the database using this criteria +2024-10-24 17:02:10,836 - INFO - ...annotating input Somatic Variants with MOAlmanac's database complete + +2024-10-24 17:02:10,838 - INFO - ...with Cancer Hotspots +2024-10-24 17:02:10,980 - INFO - ...datasource size: 3004 rows and 5 columns +2024-10-24 17:02:10,987 - INFO - ...annotation complete, 265 records annotated +2024-10-24 17:02:10,989 - INFO - ...cancerhotspots_bin == 0 for 253 records +2024-10-24 17:02:10,989 - INFO - ...cancerhotspots_bin == 1 for 11 records +2024-10-24 17:02:10,989 - INFO - ...cancerhotspots_bin == 2 for 1 records +2024-10-24 17:02:10,989 - INFO - +2024-10-24 17:02:10,989 - INFO - ...with Cancer Hotspots 3D +2024-10-24 17:02:11,007 - INFO - ...datasource size: 9521 rows and 2 columns +2024-10-24 17:02:11,020 - INFO - ...annotation complete, 265 records annotated +2024-10-24 17:02:11,022 - INFO - ...cancerhotspots3D_bin == 0 for 247 records +2024-10-24 17:02:11,022 - INFO - ...cancerhotspots3D_bin == 1 for 16 records +2024-10-24 17:02:11,022 - INFO - ...cancerhotspots3D_bin == 2 for 2 records +2024-10-24 17:02:11,022 - INFO - +2024-10-24 17:02:11,023 - INFO - ...with Cancer Gene Census +2024-10-24 17:02:11,028 - INFO - ...datasource size: 736 rows and 1 columns +2024-10-24 17:02:11,031 - INFO - ...annotation complete, 265 records annotated +2024-10-24 17:02:11,033 - INFO - ...cgc_bin == 0 for 242 records +2024-10-24 17:02:11,033 - INFO - ...cgc_bin == 1 for 23 records +2024-10-24 17:02:11,033 - INFO - +2024-10-24 17:02:11,033 - INFO - ...with COSMIC +2024-10-24 17:02:26,256 - INFO - ...datasource size: 13147512 rows and 2 columns +2024-10-24 17:02:46,317 - INFO - ...annotation complete, 265 records annotated +2024-10-24 17:02:46,335 - INFO - ...cosmic_bin == 0 for 16 records +2024-10-24 17:02:46,336 - INFO - ...cosmic_bin == 1 for 176 records +2024-10-24 17:02:46,336 - INFO - ...cosmic_bin == 2 for 73 records +2024-10-24 17:02:46,336 - INFO - +2024-10-24 17:02:47,155 - INFO - ...with GSEA Cancer Pathways +2024-10-24 17:02:47,428 - INFO - ...datasource size: 1537 rows and 1 columns +2024-10-24 17:02:47,430 - INFO - ...annotation complete, 265 records annotated +2024-10-24 17:02:47,433 - INFO - ...gsea_pathways_bin == 0 for 248 records +2024-10-24 17:02:47,433 - INFO - ...gsea_pathways_bin == 1 for 17 records +2024-10-24 17:02:47,433 - INFO - +2024-10-24 17:02:47,434 - INFO - ...with GSEA Cancer Modules +2024-10-24 17:02:47,493 - INFO - ...datasource size: 8405 rows and 1 columns +2024-10-24 17:02:47,497 - INFO - ...annotation complete, 265 records annotated +2024-10-24 17:02:47,499 - INFO - ...gsea_modules_bin == 0 for 115 records +2024-10-24 17:02:47,499 - INFO - ...gsea_modules_bin == 1 for 150 records +2024-10-24 17:02:47,499 - INFO - +2024-10-24 17:02:47,502 - INFO - ...with ExAC +2024-10-24 17:03:16,568 - INFO - ...datasource size: 9035134 rows and 5 columns +2024-10-24 17:03:30,103 - INFO - ...exac_common == 0.0 for 265 records +2024-10-24 17:03:30,104 - INFO - +2024-10-24 17:03:30,625 - INFO - ...with gene list with containing genes related to microsatellite instability +2024-10-24 17:03:30,626 - INFO - ...genes: MSH2,MSH6,MLH1,PMS2,POLE,POLE2,ACVR2A,RNF43,JAK1,MSH3,ESRP1,PRDM2,DOCK3 +2024-10-24 17:03:30,630 - INFO - ...msi_bin == 0 for 264 records +2024-10-24 17:03:30,630 - INFO - ...msi_bin == 1 for 1 records +2024-10-24 17:03:30,631 - INFO - Annotation of somatic variants complete + +2024-10-24 17:03:30,631 - INFO - Evaluating annotated somatic variants +2024-10-24 17:03:30,647 - INFO - Evaluation of somatic variants complete + +2024-10-24 17:03:30,647 - INFO - Importing validation sequencing variants for somatic variant annotation +2024-10-24 17:03:30,720 - INFO - Annotating somatic variants with validation sequencing variants +2024-10-24 17:03:30,722 - INFO - ...merging dataframes +2024-10-24 17:03:30,739 - INFO - ...141 of 204 variants were observed in validation sequencing +2024-10-24 17:03:30,739 - INFO - ...calculating power to detect variants in validation sequencing +2024-10-24 17:03:30,756 - INFO - Annotation and evaluation of somatic variants complete + +2024-10-24 17:03:30,757 - INFO - --- Annotating and evaluating germline variants --- +2024-10-24 17:03:30,758 - INFO - Annotating germline variants +2024-10-24 17:03:30,759 - INFO - ...with MOAlmanac's database +2024-10-24 17:03:30,787 - INFO - ...annotating inputs of type Germline Variant with MOAlmanac's database +2024-10-24 17:03:30,789 - INFO - ...records of Germline Variant in the database: 113 +2024-10-24 17:03:30,792 - INFO - ...records of Germline Variant provided: 7 +2024-10-24 17:03:30,794 - INFO - ...annotating ALK Missense p.I1461V for therapy_sensitivity... +2024-10-24 17:03:30,795 - INFO - ......was unable to match on gene, biomarker type, variant classification, and protein change +2024-10-24 17:03:30,795 - INFO - ......was unable to match on gene, biomarker type, and variant classification +2024-10-24 17:03:30,795 - INFO - ......was unable to match on gene and biomarker type +2024-10-24 17:03:30,795 - INFO - ......was only able to match on gene, no specific database records matched +2024-10-24 17:03:30,795 - INFO - ...annotating ALK Missense p.I1461V for therapy_resistance... +2024-10-24 17:03:30,796 - INFO - ......was unable to match on gene, biomarker type, variant classification, and protein change +2024-10-24 17:03:30,796 - INFO - ......was unable to match on gene, biomarker type, and variant classification +2024-10-24 17:03:30,796 - INFO - ......was unable to match on gene and biomarker type +2024-10-24 17:03:30,796 - INFO - ......was only able to match on gene, no specific database records matched +2024-10-24 17:03:30,796 - INFO - ...annotating ALK Missense p.I1461V for favorable_prognosis... +2024-10-24 17:03:30,797 - INFO - ......was unable to match on gene, biomarker type, variant classification, and protein change +2024-10-24 17:03:30,797 - INFO - ......was unable to match on gene, biomarker type, and variant classification +2024-10-24 17:03:30,797 - INFO - ......was unable to match on gene and biomarker type +2024-10-24 17:03:30,797 - INFO - ......was only able to match on gene, no specific database records matched +2024-10-24 17:03:30,844 - INFO - ...annotating MSH6 Missense p.G39E for therapy_sensitivity... +2024-10-24 17:03:30,845 - INFO - ......was unable to match on gene, biomarker type, variant classification, and protein change +2024-10-24 17:03:30,845 - INFO - ......was unable to match on gene, biomarker type, and variant classification +2024-10-24 17:03:30,845 - INFO - ......was able to match on gene and biomarker type +2024-10-24 17:03:30,852 - INFO - ......1 matches for therapy_sensitivity within the database using this criteria +2024-10-24 17:03:30,852 - INFO - ...annotating MSH6 Missense p.G39E for therapy_resistance... +2024-10-24 17:03:30,853 - INFO - ......was unable to match on gene, biomarker type, variant classification, and protein change +2024-10-24 17:03:30,853 - INFO - ......was unable to match on gene, biomarker type, and variant classification +2024-10-24 17:03:30,853 - INFO - ......was unable to match on gene and biomarker type +2024-10-24 17:03:30,853 - INFO - ......was only able to match on gene, no specific database records matched +2024-10-24 17:03:30,853 - INFO - ...annotating MSH6 Missense p.G39E for favorable_prognosis... +2024-10-24 17:03:30,854 - INFO - ......was unable to match on gene, biomarker type, variant classification, and protein change +2024-10-24 17:03:30,854 - INFO - ......was unable to match on gene, biomarker type, and variant classification +2024-10-24 17:03:30,854 - INFO - ......was able to match on gene and biomarker type +2024-10-24 17:03:30,859 - INFO - ......1 matches for favorable_prognosis within the database using this criteria +2024-10-24 17:03:30,909 - INFO - ...annotating BRAF Nonsense p.R509* for therapy_sensitivity... +2024-10-24 17:03:30,910 - INFO - ......was unable to match on gene, biomarker type, variant classification, and protein change +2024-10-24 17:03:30,910 - INFO - ......was unable to match on gene, biomarker type, and variant classification +2024-10-24 17:03:30,910 - INFO - ......was unable to match on gene and biomarker type +2024-10-24 17:03:30,910 - INFO - ......was only able to match on gene, no specific database records matched +2024-10-24 17:03:30,910 - INFO - ...annotating BRAF Nonsense p.R509* for therapy_resistance... +2024-10-24 17:03:30,911 - INFO - ......was unable to match on gene, biomarker type, variant classification, and protein change +2024-10-24 17:03:30,911 - INFO - ......was unable to match on gene, biomarker type, and variant classification +2024-10-24 17:03:30,911 - INFO - ......was unable to match on gene and biomarker type +2024-10-24 17:03:30,911 - INFO - ......was only able to match on gene, no specific database records matched +2024-10-24 17:03:30,911 - INFO - ...annotating BRAF Nonsense p.R509* for favorable_prognosis... +2024-10-24 17:03:30,912 - INFO - ......was unable to match on gene, biomarker type, variant classification, and protein change +2024-10-24 17:03:30,912 - INFO - ......was unable to match on gene, biomarker type, and variant classification +2024-10-24 17:03:30,912 - INFO - ......was unable to match on gene and biomarker type +2024-10-24 17:03:30,912 - INFO - ......was only able to match on gene, no specific database records matched +2024-10-24 17:03:30,962 - INFO - ...annotating TP53 Missense p.P72R for therapy_sensitivity... +2024-10-24 17:03:30,964 - INFO - ......was unable to match on gene, biomarker type, variant classification, and protein change +2024-10-24 17:03:30,964 - INFO - ......was unable to match on gene, biomarker type, and variant classification +2024-10-24 17:03:30,964 - INFO - ......was unable to match on gene and biomarker type +2024-10-24 17:03:30,964 - INFO - ......was only able to match on gene, no specific database records matched +2024-10-24 17:03:30,964 - INFO - ...annotating TP53 Missense p.P72R for therapy_resistance... +2024-10-24 17:03:30,965 - INFO - ......was unable to match on gene, biomarker type, variant classification, and protein change +2024-10-24 17:03:30,965 - INFO - ......was unable to match on gene, biomarker type, and variant classification +2024-10-24 17:03:30,965 - INFO - ......was unable to match on gene and biomarker type +2024-10-24 17:03:30,965 - INFO - ......was only able to match on gene, no specific database records matched +2024-10-24 17:03:30,965 - INFO - ...annotating TP53 Missense p.P72R for favorable_prognosis... +2024-10-24 17:03:30,966 - INFO - ......was unable to match on gene, biomarker type, variant classification, and protein change +2024-10-24 17:03:30,966 - INFO - ......was unable to match on gene, biomarker type, and variant classification +2024-10-24 17:03:30,966 - INFO - ......was unable to match on gene and biomarker type +2024-10-24 17:03:30,966 - INFO - ......was only able to match on gene, no specific database records matched +2024-10-24 17:03:31,016 - INFO - ...annotating BRCA2 Missense p.N372H for therapy_sensitivity... +2024-10-24 17:03:31,017 - INFO - ......was unable to match on gene, biomarker type, variant classification, and protein change +2024-10-24 17:03:31,017 - INFO - ......was unable to match on gene, biomarker type, and variant classification +2024-10-24 17:03:31,017 - INFO - ......was able to match on gene and biomarker type +2024-10-24 17:03:31,025 - INFO - ......13 matches for therapy_sensitivity within the database using this criteria +2024-10-24 17:03:31,025 - INFO - ...annotating BRCA2 Missense p.N372H for therapy_resistance... +2024-10-24 17:03:31,026 - INFO - ......was unable to match on gene, biomarker type, variant classification, and protein change +2024-10-24 17:03:31,026 - INFO - ......was unable to match on gene, biomarker type, and variant classification +2024-10-24 17:03:31,026 - INFO - ......was unable to match on gene and biomarker type +2024-10-24 17:03:31,026 - INFO - ......was only able to match on gene, no specific database records matched +2024-10-24 17:03:31,026 - INFO - ...annotating BRCA2 Missense p.N372H for favorable_prognosis... +2024-10-24 17:03:31,027 - INFO - ......was unable to match on gene, biomarker type, variant classification, and protein change +2024-10-24 17:03:31,027 - INFO - ......was unable to match on gene, biomarker type, and variant classification +2024-10-24 17:03:31,027 - INFO - ......was unable to match on gene and biomarker type +2024-10-24 17:03:31,027 - INFO - ......was only able to match on gene, no specific database records matched +2024-10-24 17:03:31,079 - INFO - ...annotating BRCA2 Frameshift p.S1982fs for therapy_sensitivity... +2024-10-24 17:03:31,080 - INFO - ......was unable to match on gene, biomarker type, variant classification, and protein change +2024-10-24 17:03:31,080 - INFO - ......was unable to match on gene, biomarker type, and variant classification +2024-10-24 17:03:31,081 - INFO - ......was able to match on gene and biomarker type +2024-10-24 17:03:31,087 - INFO - ......13 matches for therapy_sensitivity within the database using this criteria +2024-10-24 17:03:31,087 - INFO - ...annotating BRCA2 Frameshift p.S1982fs for therapy_resistance... +2024-10-24 17:03:31,088 - INFO - ......was unable to match on gene, biomarker type, variant classification, and protein change +2024-10-24 17:03:31,088 - INFO - ......was unable to match on gene, biomarker type, and variant classification +2024-10-24 17:03:31,088 - INFO - ......was unable to match on gene and biomarker type +2024-10-24 17:03:31,088 - INFO - ......was only able to match on gene, no specific database records matched +2024-10-24 17:03:31,088 - INFO - ...annotating BRCA2 Frameshift p.S1982fs for favorable_prognosis... +2024-10-24 17:03:31,088 - INFO - ......was unable to match on gene, biomarker type, variant classification, and protein change +2024-10-24 17:03:31,089 - INFO - ......was unable to match on gene, biomarker type, and variant classification +2024-10-24 17:03:31,089 - INFO - ......was unable to match on gene and biomarker type +2024-10-24 17:03:31,089 - INFO - ......was only able to match on gene, no specific database records matched +2024-10-24 17:03:31,138 - INFO - ...annotating BCR Missense p.N796S for therapy_sensitivity... +2024-10-24 17:03:31,139 - INFO - ......was unable to match on gene, biomarker type, variant classification, and protein change +2024-10-24 17:03:31,139 - INFO - ......was unable to match on gene, biomarker type, and variant classification +2024-10-24 17:03:31,139 - INFO - ......was unable to match on gene and biomarker type +2024-10-24 17:03:31,139 - INFO - ......was only able to match on gene, no specific database records matched +2024-10-24 17:03:31,139 - INFO - ...annotating BCR Missense p.N796S for therapy_resistance... +2024-10-24 17:03:31,140 - INFO - ......was unable to match on gene, biomarker type, variant classification, and protein change +2024-10-24 17:03:31,140 - INFO - ......was unable to match on gene, biomarker type, and variant classification +2024-10-24 17:03:31,140 - INFO - ......was unable to match on gene and biomarker type +2024-10-24 17:03:31,140 - INFO - ......was only able to match on gene, no specific database records matched +2024-10-24 17:03:31,140 - INFO - ...annotating BCR Missense p.N796S for favorable_prognosis... +2024-10-24 17:03:31,140 - INFO - ......was unable to match on gene, biomarker type, variant classification, and protein change +2024-10-24 17:03:31,141 - INFO - ......was unable to match on gene, biomarker type, and variant classification +2024-10-24 17:03:31,141 - INFO - ......was unable to match on gene and biomarker type +2024-10-24 17:03:31,141 - INFO - ......was only able to match on gene, no specific database records matched +2024-10-24 17:03:31,186 - INFO - ...annotating input Germline Variants with MOAlmanac's database complete + +2024-10-24 17:03:31,188 - INFO - ...with Cancer Hotspots +2024-10-24 17:03:31,245 - INFO - ...datasource size: 3004 rows and 5 columns +2024-10-24 17:03:31,250 - INFO - ...annotation complete, 10 records annotated +2024-10-24 17:03:31,251 - INFO - ...cancerhotspots_bin == 0 for 4 records +2024-10-24 17:03:31,251 - INFO - ...cancerhotspots_bin == 1 for 6 records +2024-10-24 17:03:31,251 - INFO - +2024-10-24 17:03:31,251 - INFO - ...with Cancer Gene Census +2024-10-24 17:03:31,256 - INFO - ...datasource size: 736 rows and 1 columns +2024-10-24 17:03:31,258 - INFO - ...annotation complete, 10 records annotated +2024-10-24 17:03:31,259 - INFO - ...cgc_bin == 1 for 10 records +2024-10-24 17:03:31,259 - INFO - +2024-10-24 17:03:31,267 - INFO - ...datasource size: 82 rows and 1 columns +2024-10-24 17:03:31,269 - INFO - ...annotation complete, 10 records annotated +2024-10-24 17:03:31,270 - INFO - ...acmg_bin == 0 for 6 records +2024-10-24 17:03:31,270 - INFO - ...acmg_bin == 1 for 4 records +2024-10-24 17:03:31,270 - INFO - +2024-10-24 17:03:31,271 - INFO - ...with ClinVar +2024-10-24 17:03:34,127 - INFO - ...datasource size: 930150 rows and 8 columns +2024-10-24 17:03:37,981 - INFO - ...clinvar_bin == 0 for 4 records +2024-10-24 17:03:37,981 - INFO - ...clinvar_bin == 1 for 2 records +2024-10-24 17:03:37,981 - INFO - +2024-10-24 17:03:38,040 - INFO - ...with gene list containing genes related to hereditary cancers +2024-10-24 17:03:38,046 - INFO - ...datasource size: 84 rows and 1 columns +2024-10-24 17:03:38,048 - INFO - ...annotation complete, 10 records annotated +2024-10-24 17:03:38,049 - INFO - ...hereditary_bin == 0 for 5 records +2024-10-24 17:03:38,049 - INFO - ...hereditary_bin == 1 for 5 records +2024-10-24 17:03:38,049 - INFO - +2024-10-24 17:03:38,049 - INFO - ...with ExAC, Extended +2024-10-24 17:04:51,549 - INFO - ...datasource size: 9035134 rows and 21 columns +2024-10-24 17:05:09,670 - INFO - ...exac_common == 0.0 for 3 records +2024-10-24 17:05:09,689 - INFO - ...exac_common == 1.0 for 7 records +2024-10-24 17:05:09,690 - INFO - +2024-10-24 17:05:10,789 - INFO - ...with gene list with containing genes related to microsatellite instability +2024-10-24 17:05:10,789 - INFO - ...genes: MSH2,MSH6,MLH1,PMS2,POLE,POLE2,ACVR2A,RNF43,JAK1,MSH3,ESRP1,PRDM2,DOCK3 +2024-10-24 17:05:10,793 - INFO - ...msi_bin == 0 for 8 records +2024-10-24 17:05:10,794 - INFO - ...msi_bin == 1 for 2 records +2024-10-24 17:05:10,794 - INFO - Annotation of germline variants complete + +2024-10-24 17:05:10,796 - INFO - Evaluating annotated germline variants +2024-10-24 17:05:10,803 - INFO - Evaluation of germline variants complete + +2024-10-24 17:05:10,804 - INFO - Annotation and evaluation of germline variants complete + +2024-10-24 17:05:10,804 - INFO - --- Investigating somatic and germline overlap --- +2024-10-24 17:05:10,804 - INFO - Annoating somatic variants for germline variants in the same gene +2024-10-24 17:05:10,859 - INFO - ...3 of 265 somatic variants had germline variants in the same gene +2024-10-24 17:05:10,859 - INFO - Summarizing somatic, germline, copy number, and fusion variants per gene +2024-10-24 17:05:12,295 - INFO - Investigating somatic and germline overlap complete + +2024-10-24 17:05:12,295 - INFO - --- Importing second-order genomic features --- +2024-10-24 17:05:12,297 - INFO - COSMIC mutational signatures from ../example_data/example_patient.capture.sbs_contributions.txt +2024-10-24 17:05:12,324 - INFO - ...imported dataframe shape:: 4 rows and 253 columns +2024-10-24 17:05:12,325 - INFO - Somatic bases covered from ../example_data/example_patient.capture.somatic.coverage.txt +2024-10-24 17:05:12,362 - INFO - Somatic coding tumor mutational burden calculated +2024-10-24 17:05:12,363 - INFO - ...bases_covered: 29908096.0 +2024-10-24 17:05:12,363 - INFO - ...n_nonsyn_mutations: 204 +2024-10-24 17:05:12,363 - INFO - ...coding_mutational_burden_per_megabase: 6.821 +2024-10-24 17:05:12,363 - INFO - ...percentile_tcga: 83.75 +2024-10-24 17:05:12,363 - INFO - ...percentile_tcga_tissuetype: nan +2024-10-24 17:05:12,363 - INFO - ...high_burden?: False + +2024-10-24 17:05:12,364 - INFO - Whole-genome doubling specified +2024-10-24 17:05:12,375 - INFO - Microsatellite status specified as: msih +2024-10-24 17:05:12,389 - INFO - Importing of second-order genomic features complete + +2024-10-24 17:05:12,390 - INFO - --- Annotating and evaluating second-order genomic features --- +2024-10-24 17:05:12,390 - INFO - Annotating COSMIC mutational signatures +2024-10-24 17:05:12,391 - INFO - ...with MOAlmanac's database +2024-10-24 17:05:12,419 - INFO - ...annotating inputs of type Mutational Signature with MOAlmanac's database +2024-10-24 17:05:12,420 - INFO - ...records of Mutational Signature in the database: 20 +2024-10-24 17:05:12,422 - INFO - ...records of Mutational Signature provided: 4 +2024-10-24 17:05:12,424 - INFO - ...annotating SBS5 therapy_sensitivity... +2024-10-24 17:05:12,425 - INFO - ......was able to match on biomarker +2024-10-24 17:05:12,431 - INFO - ......1 matches for therapy_sensitivity within the database using this criteria +2024-10-24 17:05:12,431 - INFO - ...annotating SBS5 therapy_resistance... +2024-10-24 17:05:12,432 - INFO - ......was unable to match on biomarker, no specific database records matched +2024-10-24 17:05:12,432 - INFO - ...annotating SBS5 favorable_prognosis... +2024-10-24 17:05:12,433 - INFO - ......was unable to match on biomarker, no specific database records matched +2024-10-24 17:05:12,484 - INFO - ...annotating SBS7a therapy_sensitivity... +2024-10-24 17:05:12,485 - INFO - ......was unable to match on biomarker, no specific database records matched +2024-10-24 17:05:12,485 - INFO - ...annotating SBS7a therapy_resistance... +2024-10-24 17:05:12,485 - INFO - ......was unable to match on biomarker, no specific database records matched +2024-10-24 17:05:12,485 - INFO - ...annotating SBS7a favorable_prognosis... +2024-10-24 17:05:12,486 - INFO - ......was unable to match on biomarker, no specific database records matched +2024-10-24 17:05:12,534 - INFO - ...annotating SBS10b therapy_sensitivity... +2024-10-24 17:05:12,535 - INFO - ......was able to match on biomarker +2024-10-24 17:05:12,540 - INFO - ......3 matches for therapy_sensitivity within the database using this criteria +2024-10-24 17:05:12,541 - INFO - ...annotating SBS10b therapy_resistance... +2024-10-24 17:05:12,541 - INFO - ......was unable to match on biomarker, no specific database records matched +2024-10-24 17:05:12,541 - INFO - ...annotating SBS10b favorable_prognosis... +2024-10-24 17:05:12,541 - INFO - ......was unable to match on biomarker, no specific database records matched +2024-10-24 17:05:12,590 - INFO - ...annotating SBS30 therapy_sensitivity... +2024-10-24 17:05:12,591 - INFO - ......was unable to match on biomarker, no specific database records matched +2024-10-24 17:05:12,591 - INFO - ...annotating SBS30 therapy_resistance... +2024-10-24 17:05:12,591 - INFO - ......was unable to match on biomarker, no specific database records matched +2024-10-24 17:05:12,591 - INFO - ...annotating SBS30 favorable_prognosis... +2024-10-24 17:05:12,592 - INFO - ......was unable to match on biomarker, no specific database records matched +2024-10-24 17:05:12,638 - INFO - ...annotating input Mutational Signatures with MOAlmanac's database complete + +2024-10-24 17:05:12,639 - INFO - Annotation of COSMIC mutational signatures complete + +2024-10-24 17:05:12,639 - INFO - Evaluating annotated COSMIC mutational signatures +2024-10-24 17:05:12,644 - INFO - Evaluation of COSMIC mutational signatures complete + +2024-10-24 17:05:12,644 - INFO - Annotation and evaluation of COSMIC mutational signatures complete + +2024-10-24 17:05:12,644 - INFO - Annotating tumor mutational burden +2024-10-24 17:05:12,645 - INFO - ...with MOAlmanac's database +2024-10-24 17:05:12,668 - INFO - ...annotating inputs of type Mutational Burden with MOAlmanac's database +2024-10-24 17:05:12,700 - INFO - ...records of Mutational Burden in the database: 6 +2024-10-24 17:05:12,702 - INFO - ...records of Mutational Burden provided: 1 +2024-10-24 17:05:12,703 - INFO - ...annotating Not therapy_sensitivity... +2024-10-24 17:05:12,703 - INFO - ......was unable to match on biomarker, no specific database records matched +2024-10-24 17:05:12,703 - INFO - ...annotating Not therapy_resistance... +2024-10-24 17:05:12,704 - INFO - ......was unable to match on biomarker, no specific database records matched +2024-10-24 17:05:12,704 - INFO - ...annotating Not favorable_prognosis... +2024-10-24 17:05:12,704 - INFO - ......was unable to match on biomarker, no specific database records matched +2024-10-24 17:05:12,748 - INFO - ...annotating input Mutational Burdens with MOAlmanac's database complete + +2024-10-24 17:05:12,749 - INFO - Annotation of tumor mutational burden complete + +2024-10-24 17:05:12,749 - INFO - Evaluating tumor mutational burden +2024-10-24 17:05:12,760 - INFO - Evaluation of tumor mutational burden complete + +2024-10-24 17:05:12,760 - INFO - Annotation and evaluation of tumor mutational burden complete + +2024-10-24 17:05:12,761 - INFO - Annotating whole-genome doubling +2024-10-24 17:05:12,761 - INFO - ...with MOAlmanac's database +2024-10-24 17:05:12,782 - INFO - ...annotating inputs of type Aneuploidy with MOAlmanac's database +2024-10-24 17:05:12,784 - INFO - ...records of Aneuploidy in the database: 1 +2024-10-24 17:05:12,786 - INFO - ...records of Aneuploidy provided: 1 +2024-10-24 17:05:12,787 - INFO - ...annotating Whole genome doubling therapy_sensitivity... +2024-10-24 17:05:12,787 - INFO - ......was unable to match on biomarker, no specific database records matched +2024-10-24 17:05:12,787 - INFO - ...annotating Whole genome doubling therapy_resistance... +2024-10-24 17:05:12,788 - INFO - ......was unable to match on biomarker, no specific database records matched +2024-10-24 17:05:12,788 - INFO - ...annotating Whole genome doubling favorable_prognosis... +2024-10-24 17:05:12,789 - INFO - ......was able to match on biomarker +2024-10-24 17:05:12,794 - INFO - ......1 matches for favorable_prognosis within the database using this criteria +2024-10-24 17:05:12,836 - INFO - ...annotating input Aneuploidys with MOAlmanac's database complete + +2024-10-24 17:05:12,837 - INFO - Annotation of whole-genome doubling complete + +2024-10-24 17:05:12,838 - INFO - Evaluating whole-genome doubling +2024-10-24 17:05:12,848 - INFO - Evaluation of whole-genome doubling complete + +2024-10-24 17:05:12,848 - INFO - Annotation and evaluation of whole-genome doubling complete + +2024-10-24 17:05:12,848 - INFO - Evaluating somatic and germline variants for those related to microsatellite instability +2024-10-24 17:05:12,856 - INFO - ...variants related to microsatellite instability identified: 1 +2024-10-24 17:05:12,856 - INFO - Evaluation of microsatellite instability variants complete + +2024-10-24 17:05:12,856 - INFO - Annotating and evaluating microsatellite status +2024-10-24 17:05:12,856 - INFO - Annotating microsatellite status +2024-10-24 17:05:12,857 - INFO - ...with MOAlmanac's database +2024-10-24 17:05:12,876 - INFO - ...annotating inputs of type Microsatellite Stability with MOAlmanac's database +2024-10-24 17:05:12,878 - INFO - ...records of Microsatellite Stability in the database: 9 +2024-10-24 17:05:12,879 - INFO - ...records of Microsatellite Stability provided: 1 +2024-10-24 17:05:12,880 - INFO - ...annotating MSI-High therapy_sensitivity... +2024-10-24 17:05:12,881 - INFO - ......was able to match on biomarker +2024-10-24 17:05:12,885 - INFO - ......4 matches for therapy_sensitivity within the database using this criteria +2024-10-24 17:05:12,886 - INFO - ...annotating MSI-High therapy_resistance... +2024-10-24 17:05:12,886 - INFO - ......was able to match on biomarker +2024-10-24 17:05:12,892 - INFO - ......1 matches for therapy_resistance within the database using this criteria +2024-10-24 17:05:12,892 - INFO - ...annotating MSI-High favorable_prognosis... +2024-10-24 17:05:12,892 - INFO - ......was able to match on biomarker +2024-10-24 17:05:12,898 - INFO - ......1 matches for favorable_prognosis within the database using this criteria +2024-10-24 17:05:12,941 - INFO - ...annotating input Microsatellite Stabilitys with MOAlmanac's database complete + +2024-10-24 17:05:12,942 - INFO - Annotation of microsatellite status complete + +2024-10-24 17:05:12,942 - INFO - Evaluating microsatellite status +2024-10-24 17:05:12,953 - INFO - Evaluation of microsatellite status complete + +2024-10-24 17:05:12,953 - INFO - Annotation and evaluation of microsatellite status complete + +2024-10-24 17:05:12,953 - INFO - Annotation and evaluation of second-order genomic features complete + +2024-10-24 17:05:12,954 - INFO - --- Summarizing clinically relevant biomarkers --- +2024-10-24 17:05:13,053 - INFO - Summary of clinically relevant biomarkers complete + +2024-10-24 17:05:13,054 - INFO - --- Summarizing highlighted therapeutic strategies from clinically relevant hits --- +2024-10-24 17:05:13,064 - INFO - Summary of highlighted therapeutic strategies complete + +2024-10-24 17:05:13,070 - INFO - --- Performing comparisons to preclinical models --- +2024-10-24 17:05:13,070 - INFO - Importing preclinical databases +2024-10-24 17:05:53,285 - INFO - Importing preclinical databases complete +2024-10-24 17:05:53,285 - INFO - Calculate preclinical efficacy of clinically relevant relationships enabled, processing... +2024-10-24 17:06:00,959 - INFO - ...complete. Successfully calculated: 18 relationships +2024-10-24 17:06:00,959 - INFO - Annotating clinically relevant findings with preclinical efficacy calculations... +2024-10-24 17:06:00,967 - INFO - ...annotation complete. +2024-10-24 17:06:00,967 - INFO - Calculating preclinical efficacy of clinically relevant relationships complete. + +2024-10-24 17:06:00,967 - INFO - Performing genomic similarity to cancer cell lines enabled, processing... +2024-10-24 17:06:01,226 - INFO - ...with Cancer Hotspots +2024-10-24 17:06:01,280 - INFO - ...datasource size: 3004 rows and 5 columns +2024-10-24 17:06:01,319 - INFO - ...annotation complete, 58928 records annotated +2024-10-24 17:06:01,329 - INFO - ...cancerhotspots_bin == 0 for 37894 records +2024-10-24 17:06:01,329 - INFO - ...cancerhotspots_bin == 1 for 18920 records +2024-10-24 17:06:01,329 - INFO - ...cancerhotspots_bin == 2 for 2114 records +2024-10-24 17:06:01,330 - INFO - +2024-10-24 17:06:01,331 - INFO - ...with Cancer Hotspots 3D +2024-10-24 17:06:01,348 - INFO - ...datasource size: 9521 rows and 2 columns +2024-10-24 17:06:01,384 - INFO - ...annotation complete, 58928 records annotated +2024-10-24 17:06:01,392 - INFO - ...cancerhotspots3D_bin == 0 for 50054 records +2024-10-24 17:06:01,393 - INFO - ...cancerhotspots3D_bin == 1 for 7641 records +2024-10-24 17:06:01,393 - INFO - ...cancerhotspots3D_bin == 2 for 1233 records +2024-10-24 17:06:01,393 - INFO - +2024-10-24 17:06:01,394 - INFO - ...with Cancer Gene Census +2024-10-24 17:06:01,398 - INFO - ...datasource size: 736 rows and 1 columns +2024-10-24 17:06:01,412 - INFO - ...annotation complete, 58928 records annotated +2024-10-24 17:06:01,420 - INFO - ...cgc_bin == 0 for 4912 records +2024-10-24 17:06:01,420 - INFO - ...cgc_bin == 1 for 54016 records +2024-10-24 17:06:01,420 - INFO - +2024-10-24 17:06:01,422 - INFO - ...with COSMIC +2024-10-24 17:06:10,063 - INFO - ...datasource size: 13147512 rows and 2 columns +2024-10-24 17:06:26,216 - INFO - ...annotation complete, 58928 records annotated +2024-10-24 17:06:26,251 - INFO - ...cosmic_bin == 0 for 775 records +2024-10-24 17:06:26,251 - INFO - ...cosmic_bin == 1 for 37876 records +2024-10-24 17:06:26,251 - INFO - ...cosmic_bin == 2 for 20277 records +2024-10-24 17:06:26,263 - INFO - +2024-10-24 17:06:26,664 - INFO - ...with GSEA Cancer Pathways +2024-10-24 17:06:26,722 - INFO - ...datasource size: 1537 rows and 1 columns +2024-10-24 17:06:26,733 - INFO - ...annotation complete, 58928 records annotated +2024-10-24 17:06:26,743 - INFO - ...gsea_pathways_bin == 0 for 45129 records +2024-10-24 17:06:26,743 - INFO - ...gsea_pathways_bin == 1 for 13799 records +2024-10-24 17:06:26,743 - INFO - +2024-10-24 17:06:26,754 - INFO - ...with GSEA Cancer Modules +2024-10-24 17:06:26,780 - INFO - ...datasource size: 8405 rows and 1 columns +2024-10-24 17:06:26,795 - INFO - ...annotation complete, 58928 records annotated +2024-10-24 17:06:26,810 - INFO - ...gsea_modules_bin == 0 for 18475 records +2024-10-24 17:06:26,810 - INFO - ...gsea_modules_bin == 1 for 40453 records +2024-10-24 17:06:26,810 - INFO - +2024-10-24 17:06:26,939 - INFO - ...with Cancer Hotspots +2024-10-24 17:06:26,993 - INFO - ...datasource size: 3004 rows and 5 columns +2024-10-24 17:06:27,044 - INFO - ...annotation complete, 57556 records annotated +2024-10-24 17:06:27,053 - INFO - ...cancerhotspots_bin == 0 for 39332 records +2024-10-24 17:06:27,053 - INFO - ...cancerhotspots_bin == 1 for 18224 records +2024-10-24 17:06:27,053 - INFO - +2024-10-24 17:06:27,055 - INFO - ...with Cancer Hotspots 3D +2024-10-24 17:06:27,074 - INFO - ...datasource size: 9521 rows and 2 columns +2024-10-24 17:06:27,121 - INFO - ...annotation complete, 57556 records annotated +2024-10-24 17:06:27,130 - INFO - ...cancerhotspots3D_bin == 0 for 50818 records +2024-10-24 17:06:27,130 - INFO - ...cancerhotspots3D_bin == 1 for 6365 records +2024-10-24 17:06:27,130 - INFO - ...cancerhotspots3D_bin == 2 for 373 records +2024-10-24 17:06:27,130 - INFO - +2024-10-24 17:06:27,131 - INFO - ...with Cancer Gene Census +2024-10-24 17:06:27,138 - INFO - ...datasource size: 736 rows and 1 columns +2024-10-24 17:06:27,151 - INFO - ...annotation complete, 57556 records annotated +2024-10-24 17:06:27,159 - INFO - ...cgc_bin == 0 for 5902 records +2024-10-24 17:06:27,159 - INFO - ...cgc_bin == 1 for 51654 records +2024-10-24 17:06:27,160 - INFO - +2024-10-24 17:06:27,161 - INFO - ...with COSMIC +2024-10-24 17:06:37,051 - INFO - ...datasource size: 13147512 rows and 2 columns +2024-10-24 17:06:53,895 - INFO - ...annotation complete, 57556 records annotated +2024-10-24 17:06:53,907 - INFO - ...cosmic_bin == 0 for 1155 records +2024-10-24 17:06:53,907 - INFO - ...cosmic_bin == 1 for 56401 records +2024-10-24 17:06:53,909 - INFO - +2024-10-24 17:06:54,347 - INFO - ...with GSEA Cancer Pathways +2024-10-24 17:06:54,409 - INFO - ...datasource size: 1537 rows and 1 columns +2024-10-24 17:06:54,420 - INFO - ...annotation complete, 57556 records annotated +2024-10-24 17:06:54,431 - INFO - ...gsea_pathways_bin == 0 for 43007 records +2024-10-24 17:06:54,431 - INFO - ...gsea_pathways_bin == 1 for 14549 records +2024-10-24 17:06:54,432 - INFO - +2024-10-24 17:06:54,443 - INFO - ...with GSEA Cancer Modules +2024-10-24 17:06:54,468 - INFO - ...datasource size: 8405 rows and 1 columns +2024-10-24 17:06:54,487 - INFO - ...annotation complete, 57556 records annotated +2024-10-24 17:06:54,501 - INFO - ...gsea_modules_bin == 0 for 18532 records +2024-10-24 17:06:54,501 - INFO - ...gsea_modules_bin == 1 for 39024 records +2024-10-24 17:06:54,501 - INFO - +2024-10-24 17:07:09,933 - INFO - ...with Cancer Hotspots +2024-10-24 17:07:09,986 - INFO - ...datasource size: 3004 rows and 5 columns +2024-10-24 17:07:09,995 - INFO - ...annotation complete, 7097 records annotated +2024-10-24 17:07:09,998 - INFO - ...cancerhotspots_bin == 0 for 6802 records +2024-10-24 17:07:09,998 - INFO - ...cancerhotspots_bin == 1 for 295 records +2024-10-24 17:07:09,998 - INFO - +2024-10-24 17:07:09,999 - INFO - ...with Cancer Hotspots 3D +2024-10-24 17:07:10,014 - INFO - ...datasource size: 9521 rows and 2 columns +2024-10-24 17:07:10,025 - INFO - ...annotation complete, 7097 records annotated +2024-10-24 17:07:10,027 - INFO - ...cancerhotspots3D_bin == 0 for 6829 records +2024-10-24 17:07:10,027 - INFO - ...cancerhotspots3D_bin == 1 for 268 records +2024-10-24 17:07:10,028 - INFO - +2024-10-24 17:07:10,028 - INFO - ...with Cancer Gene Census +2024-10-24 17:07:10,033 - INFO - ...datasource size: 736 rows and 1 columns +2024-10-24 17:07:10,037 - INFO - ...annotation complete, 7097 records annotated +2024-10-24 17:07:10,039 - INFO - ...cgc_bin == 0 for 6348 records +2024-10-24 17:07:10,039 - INFO - ...cgc_bin == 1 for 749 records +2024-10-24 17:07:10,039 - INFO - +2024-10-24 17:07:10,039 - INFO - ...with COSMIC +2024-10-24 17:07:19,271 - INFO - ...datasource size: 13147512 rows and 2 columns +2024-10-24 17:07:36,113 - INFO - ...annotation complete, 7097 records annotated +2024-10-24 17:07:36,117 - INFO - ...cosmic_bin == 0 for 475 records +2024-10-24 17:07:36,118 - INFO - ...cosmic_bin == 1 for 6622 records +2024-10-24 17:07:36,118 - INFO - +2024-10-24 17:07:36,727 - INFO - ...with GSEA Cancer Pathways +2024-10-24 17:07:36,814 - INFO - ...datasource size: 1537 rows and 1 columns +2024-10-24 17:07:36,820 - INFO - ...annotation complete, 7097 records annotated +2024-10-24 17:07:36,823 - INFO - ...gsea_pathways_bin == 0 for 6639 records +2024-10-24 17:07:36,823 - INFO - ...gsea_pathways_bin == 1 for 458 records +2024-10-24 17:07:36,823 - INFO - +2024-10-24 17:07:36,824 - INFO - ...with GSEA Cancer Modules +2024-10-24 17:07:36,850 - INFO - ...datasource size: 8405 rows and 1 columns +2024-10-24 17:07:36,856 - INFO - ...annotation complete, 7097 records annotated +2024-10-24 17:07:36,860 - INFO - ...gsea_modules_bin == 0 for 3674 records +2024-10-24 17:07:36,860 - INFO - ...gsea_modules_bin == 1 for 3423 records +2024-10-24 17:07:36,860 - INFO - +2024-10-24 17:07:36,861 - INFO - ...with Cancer Hotspots +2024-10-24 17:07:36,930 - INFO - ...datasource size: 3004 rows and 5 columns +2024-10-24 17:07:36,939 - INFO - ...annotation complete, 6864 records annotated +2024-10-24 17:07:36,941 - INFO - ...cancerhotspots_bin == 0 for 6591 records +2024-10-24 17:07:36,942 - INFO - ...cancerhotspots_bin == 1 for 273 records +2024-10-24 17:07:36,942 - INFO - +2024-10-24 17:07:36,942 - INFO - ...with Cancer Hotspots 3D +2024-10-24 17:07:36,959 - INFO - ...datasource size: 9521 rows and 2 columns +2024-10-24 17:07:36,971 - INFO - ...annotation complete, 6864 records annotated +2024-10-24 17:07:36,973 - INFO - ...cancerhotspots3D_bin == 0 for 6602 records +2024-10-24 17:07:36,973 - INFO - ...cancerhotspots3D_bin == 1 for 262 records +2024-10-24 17:07:36,973 - INFO - +2024-10-24 17:07:36,974 - INFO - ...with Cancer Gene Census +2024-10-24 17:07:36,979 - INFO - ...datasource size: 736 rows and 1 columns +2024-10-24 17:07:36,983 - INFO - ...annotation complete, 6864 records annotated +2024-10-24 17:07:36,985 - INFO - ...cgc_bin == 0 for 6147 records +2024-10-24 17:07:36,985 - INFO - ...cgc_bin == 1 for 717 records +2024-10-24 17:07:36,985 - INFO - +2024-10-24 17:07:36,985 - INFO - ...with COSMIC +2024-10-24 17:07:46,129 - INFO - ...datasource size: 13147512 rows and 2 columns +2024-10-24 17:08:02,976 - INFO - ...annotation complete, 6864 records annotated +2024-10-24 17:08:02,980 - INFO - ...cosmic_bin == 0 for 445 records +2024-10-24 17:08:02,981 - INFO - ...cosmic_bin == 1 for 6419 records +2024-10-24 17:08:02,981 - INFO - +2024-10-24 17:08:03,392 - INFO - ...with GSEA Cancer Pathways +2024-10-24 17:08:03,460 - INFO - ...datasource size: 1537 rows and 1 columns +2024-10-24 17:08:03,463 - INFO - ...annotation complete, 6864 records annotated +2024-10-24 17:08:03,466 - INFO - ...gsea_pathways_bin == 0 for 6431 records +2024-10-24 17:08:03,466 - INFO - ...gsea_pathways_bin == 1 for 433 records +2024-10-24 17:08:03,466 - INFO - +2024-10-24 17:08:03,466 - INFO - ...with GSEA Cancer Modules +2024-10-24 17:08:03,492 - INFO - ...datasource size: 8405 rows and 1 columns +2024-10-24 17:08:03,498 - INFO - ...annotation complete, 6864 records annotated +2024-10-24 17:08:03,501 - INFO - ...gsea_modules_bin == 0 for 3557 records +2024-10-24 17:08:03,501 - INFO - ...gsea_modules_bin == 1 for 3307 records +2024-10-24 17:08:03,501 - INFO - +2024-10-24 17:08:03,502 - INFO - ...with Cancer Hotspots +2024-10-24 17:08:03,555 - INFO - ...datasource size: 3004 rows and 5 columns +2024-10-24 17:08:03,564 - INFO - ...annotation complete, 6859 records annotated +2024-10-24 17:08:03,567 - INFO - ...cancerhotspots_bin == 0 for 6644 records +2024-10-24 17:08:03,567 - INFO - ...cancerhotspots_bin == 1 for 215 records +2024-10-24 17:08:03,567 - INFO - +2024-10-24 17:08:03,568 - INFO - ...with Cancer Hotspots 3D +2024-10-24 17:08:03,586 - INFO - ...datasource size: 9521 rows and 2 columns +2024-10-24 17:08:03,598 - INFO - ...annotation complete, 6859 records annotated +2024-10-24 17:08:03,600 - INFO - ...cancerhotspots3D_bin == 0 for 6618 records +2024-10-24 17:08:03,600 - INFO - ...cancerhotspots3D_bin == 1 for 241 records +2024-10-24 17:08:03,601 - INFO - +2024-10-24 17:08:03,602 - INFO - ...with Cancer Gene Census +2024-10-24 17:08:03,606 - INFO - ...datasource size: 736 rows and 1 columns +2024-10-24 17:08:03,609 - INFO - ...annotation complete, 6859 records annotated +2024-10-24 17:08:03,611 - INFO - ...cgc_bin == 0 for 6300 records +2024-10-24 17:08:03,611 - INFO - ...cgc_bin == 1 for 559 records +2024-10-24 17:08:03,612 - INFO - +2024-10-24 17:08:03,612 - INFO - ...with COSMIC +2024-10-24 17:08:12,340 - INFO - ...datasource size: 13147512 rows and 2 columns +2024-10-24 17:08:28,512 - INFO - ...annotation complete, 6859 records annotated +2024-10-24 17:08:28,515 - INFO - ...cosmic_bin == 0 for 424 records +2024-10-24 17:08:28,516 - INFO - ...cosmic_bin == 1 for 6435 records +2024-10-24 17:08:28,516 - INFO - +2024-10-24 17:08:28,908 - INFO - ...with GSEA Cancer Pathways +2024-10-24 17:08:28,978 - INFO - ...datasource size: 1537 rows and 1 columns +2024-10-24 17:08:28,983 - INFO - ...annotation complete, 6859 records annotated +2024-10-24 17:08:28,985 - INFO - ...gsea_pathways_bin == 0 for 6467 records +2024-10-24 17:08:28,985 - INFO - ...gsea_pathways_bin == 1 for 392 records +2024-10-24 17:08:28,985 - INFO - +2024-10-24 17:08:28,986 - INFO - ...with GSEA Cancer Modules +2024-10-24 17:08:29,010 - INFO - ...datasource size: 8405 rows and 1 columns +2024-10-24 17:08:29,017 - INFO - ...annotation complete, 6859 records annotated +2024-10-24 17:08:29,021 - INFO - ...gsea_modules_bin == 0 for 3741 records +2024-10-24 17:08:29,021 - INFO - ...gsea_modules_bin == 1 for 3118 records +2024-10-24 17:08:29,021 - INFO - +2024-10-24 17:08:35,412 - INFO - ...genomic similarity to cancer cell lines complete. Summarizing... +2024-10-24 17:08:35,413 - INFO - ...genomic similarity to cancer cell lines summarized +2024-10-24 17:08:35,414 - INFO - Genomic similarity to cancer cell lines complete + +2024-10-24 17:08:35,414 - INFO - --- Writing outputs --- +2024-10-24 17:08:35,419 - INFO - Writing Clinically relevant observations to 2024-10-24-example-outputs-all-enabled/example.actionable.txt: 21 rows and 44 columns +2024-10-24 17:08:35,429 - INFO - Writing Germline variants in ACMG genes to 2024-10-24-example-outputs-all-enabled/example.germline.acmg.txt: 4 rows and 34 columns +2024-10-24 17:08:35,437 - INFO - Writing Germline variants in cancer related genes to 2024-10-24-example-outputs-all-enabled/example.germline.cancer_related.txt: 10 rows and 38 columns +2024-10-24 17:08:35,443 - INFO - Writing Germline variants in genes related to hereditary cancers to 2024-10-24-example-outputs-all-enabled/example.germline.hereditary_cancers.txt: 5 rows and 34 columns +2024-10-24 17:08:35,446 - INFO - Writing Integrated summary to 2024-10-24-example-outputs-all-enabled/example.integrated.summary.txt: 20 rows and 4 columns +2024-10-24 17:08:35,452 - INFO - Writing Variants in genes related to microsatellite instability to 2024-10-24-example-outputs-all-enabled/example.msi_variants.txt: 1 rows and 38 columns +2024-10-24 17:08:35,454 - INFO - Writing Tumor mutational burden to 2024-10-24-example-outputs-all-enabled/example.mutational_burden.txt: 1 rows and 10 columns +2024-10-24 17:08:35,463 - INFO - Writing Somatic variants that were scored to 2024-10-24-example-outputs-all-enabled/example.somatic.scored.txt: 265 rows and 41 columns +2024-10-24 17:08:35,475 - INFO - Writing Somatic variants that were filtered to 2024-10-24-example-outputs-all-enabled/example.somatic.filtered.txt: 220 rows and 23 columns +2024-10-24 17:08:35,478 - INFO - Writing Therapeutic strategies that were highlighted to 2024-10-24-example-outputs-all-enabled/example.therapeutic_strategies.txt: 2 rows and 11 columns +2024-10-24 17:08:35,479 - INFO - Writing Preclinical efficacy of clinically relevant relationships to 2024-10-24-example-outputs-all-enabled/example.preclinical.efficacy.txt: 18 rows and 16 columns +2024-10-24 17:08:35,481 - INFO - Writing Genomic similarity to cancer cell lines to 2024-10-24-example-outputs-all-enabled/example.matchmaker.txt: 453 rows and 3 columns + +2024-10-24 17:08:35,484 - INFO - --- Generating and writing figures --- +2024-10-24 17:08:35,485 - INFO - Plotting DNA and RNA somatic variant overlap +2024-10-24 17:08:36,003 - INFO - Figure generation completed + +2024-10-24 17:08:36,003 - INFO - --- Generating actionability report --- +2024-10-24 17:08:36,003 - INFO - Generating metadata dictionary for report +2024-10-24 17:08:36,005 - INFO - Generating report +2024-10-24 17:08:36,022 - INFO - Rendering report to: /example.report.html +2024-10-24 17:08:36,355 - INFO - Report generation completed + +2024-10-24 17:08:36,355 - INFO - Molecular Oncology Almanac process complete. Runtime: 386.5951 seconds diff --git a/moalmanac/annotation-databases.ini b/moalmanac/annotation-databases.ini index 200f099..3d313dd 100644 --- a/moalmanac/annotation-databases.ini +++ b/moalmanac/annotation-databases.ini @@ -1,4 +1,4 @@ -[databases] +[paths] root = ../datasources almanac_handle = ${root}/moalmanac/molecular-oncology-almanac.json cancerhotspots_handle = ${root}/cancerhotspots/hotspots_v2.txt diff --git a/moalmanac/config.ini b/moalmanac/config.ini index b54cc1c..8b5c7d5 100644 --- a/moalmanac/config.ini +++ b/moalmanac/config.ini @@ -8,10 +8,12 @@ include_model_similarity_in_actionability_report = on include_preclinical_efficacy_in_actionability_report = on [logging] +; Possible values for level include "NOTSET", "DEBUG", "INFO", "WARNING", "ERROR", and "CRITICAL". They are described +; within the logging module's document: https://docs.python.org/3/library/logging.html#logging-levels. level = INFO [versions] -interpreter = 0.7.1 +interpreter = 0.7.2 database = v.2024-04-11 [exac] diff --git a/moalmanac/logger.py b/moalmanac/logger.py index 4c9c5dc..4fb7cad 100644 --- a/moalmanac/logger.py +++ b/moalmanac/logger.py @@ -1,6 +1,7 @@ import json import logging + class Logger: @staticmethod def generate_filename(folder, label): @@ -16,6 +17,7 @@ def setup(cls, output_folder, file_prefix, config): level=config['logging']['level'] ) + class Messages: @staticmethod def dataframe_size(label, dataframe, add_line_break=False): diff --git a/moalmanac/moalmanac.py b/moalmanac/moalmanac.py index efac2bd..24425af 100644 --- a/moalmanac/moalmanac.py +++ b/moalmanac/moalmanac.py @@ -333,7 +333,7 @@ def somatic_variants(df, dbs, ontology, config, path_validation): logger.Messages.general(message="No passed validation sequencing variants to annotate with") else: logger.Messages.general(message="No somatic variants detected. Skipping annotation and evaluation.") - evaluated= features.Features.create_empty_dataframe() + evaluated = features.Features.create_empty_dataframe() logger.Messages.general(message="Annotation and evaluation of somatic variants complete", add_line_break=True) return evaluated @@ -706,8 +706,6 @@ def main(patient, inputs, output_folder, config, dbs, dbs_preclinical=None): if __name__ == "__main__": - start_time = time.time() - arg_parser = argparse.ArgumentParser( prog='Molecular Oncology Almanac', description='A clinical interpretation algorithm for cancer genomics.' @@ -854,21 +852,19 @@ def main(patient, inputs, output_folder, config, dbs, dbs_preclinical=None): config_ini = Ini.read(args.config, extended_interpolation=False, convert_to_dictionary=False) db_paths = Ini.read(args.dbs, extended_interpolation=True, convert_to_dictionary=True) + db_paths = db_paths['paths'] + if args.preclinical_dbs: preclinical_db_paths = Ini.read(args.preclinical_dbs, extended_interpolation=True, convert_to_dictionary=True) + preclinical_db_paths = preclinical_db_paths['paths'] else: preclinical_db_paths = None - print(db_paths) main( patient=patient_dict, inputs=inputs_dict, output_folder=output_directory, config=config_ini, - dbs=db_paths['databases'], - dbs_preclinical=preclinical_db_paths['preclinical'] + dbs=db_paths, + dbs_preclinical=preclinical_db_paths ) - - end_time = time.time() - time_statement = "Molecular Oncology Almanac runtime: %s seconds" % round((end_time - start_time), 4) - print(time_statement) diff --git a/moalmanac/preclinical-databases.ini b/moalmanac/preclinical-databases.ini index d6e2086..e59e12c 100644 --- a/moalmanac/preclinical-databases.ini +++ b/moalmanac/preclinical-databases.ini @@ -1,4 +1,4 @@ -[preclinical] +[paths] root = ../datasources almanac_gdsc_mappings = ${root}/preclinical/formatted/almanac-gdsc-mappings.json summary = ${root}/preclinical/formatted/cell-lines.summary.txt diff --git a/moalmanac/run_example.py b/moalmanac/run_example.py index 75718b4..0cb7d1d 100644 --- a/moalmanac/run_example.py +++ b/moalmanac/run_example.py @@ -45,12 +45,15 @@ } config_ini_path = "config.ini" -dbs_ini_path = "annotation-databases.ini" -dbs_preclinical_ini_path = "preclinical-databases.ini" - config_ini = Ini.read(config_ini_path, extended_interpolation=False, convert_to_dictionary=False) + +dbs_ini_path = "annotation-databases.ini" db_paths = Ini.read(dbs_ini_path, extended_interpolation=True, convert_to_dictionary=True) +db_paths = db_paths['paths'] + +dbs_preclinical_ini_path = "preclinical-databases.ini" preclinical_db_paths = Ini.read(dbs_preclinical_ini_path, extended_interpolation=True, convert_to_dictionary=True) +preclinical_db_paths = preclinical_db_paths['paths'] def execute_cmd(command): @@ -71,8 +74,8 @@ def execute_cmd(command): inputs=input_dictionary, output_folder=output_directory, config=config_ini, - dbs=db_paths['databases'], - dbs_preclinical=preclinical_db_paths['preclinical'] + dbs=db_paths, + dbs_preclinical=preclinical_db_paths ) end_time = time.time() diff --git a/moalmanac/simplified_input.py b/moalmanac/simplified_input.py index ba87257..573cca0 100644 --- a/moalmanac/simplified_input.py +++ b/moalmanac/simplified_input.py @@ -300,8 +300,8 @@ def main(patient, input_file, output_folder, config, dbs, dbs_preclinical=None): input_file=args.input, output_folder=output_directory, config=config_ini, - dbs=db_paths, - dbs_preclinical=preclinical_db_paths + dbs=db_paths['databases'], + dbs_preclinical=preclinical_db_paths['preclinical'] if preclinical_db_paths else None ) end_time = time.time() diff --git a/moalmanac/templates/report_table/table_biological.html b/moalmanac/templates/report_table/table_biological.html index 284b591..f17bb31 100644 --- a/moalmanac/templates/report_table/table_biological.html +++ b/moalmanac/templates/report_table/table_biological.html @@ -7,12 +7,14 @@

Variants and Features that may be Biologically Relevant< {% include 'report_table/columns_biological.html' %} - {% for label, group in report.alterations[report.alterations['score_bin'] == 'Biologically Relevant'].groupby('feature_type') %} - - - - - {% endfor %} + {% if not report.alterations.empty %} + {% for label, group in report.alterations[report.alterations['score_bin'] == 'Biologically Relevant'].groupby('feature_type') %} + + + + + {% endfor %} + {% endif %}
{{ label }}{{ ', '.join(group['feature_display'].sort_values().tolist()) }}
{{ label }}{{ ', '.join(group['feature_display'].sort_values().tolist()) }}
diff --git a/moalmanac/templates/report_table/table_prognostic.html b/moalmanac/templates/report_table/table_prognostic.html index e4b87e5..bb15af4 100644 --- a/moalmanac/templates/report_table/table_prognostic.html +++ b/moalmanac/templates/report_table/table_prognostic.html @@ -7,31 +7,33 @@

Variants and Features associated with Prognostic Informa {% include 'report_table/columns_prognosis.html' %} - {% for index in report.alterations[report.alterations['prognostic_predictive_implication'].notnull()].sort_values(['prognostic_predictive_implication_map', 'prognostic_score_bin_map'], ascending=[False, False]).index.tolist() %} - - - - - - {% endfor %} + {% if not report.alterations.empty %} + {% for index in report.alterations[report.alterations['prognostic_predictive_implication'].notnull()].sort_values(['prognostic_predictive_implication_map', 'prognostic_score_bin_map'], ascending=[False, False]).index.tolist() %} + + + + + + {% endfor %} + {% endif %}
{{ report.alterations.loc[index, 'prognostic_predictive_implication'] }} -
- {{ report.alterations.loc[index, 'prognostic_score_bin'] }} -
- {% include 'modals/evidence_prognosis.html' %} - 		{{ report.alterations.loc[index, 'feature_type'] }}{{ report.alterations.loc[index, 'feature_display'] }} - {% if report.alterations.loc[index, 'favorable_prognosis'] == 1.0 %} - Favorable - {% else %} - Not favorable - {% endif %} -
- {{ report.alterations.loc[index, 'prognostic_description'] }} - {% if report.alterations.loc[index, 'prognostic_url'] != "" %} - - [source] - - {% endif %} -
{{ report.alterations.loc[index, 'prognostic_predictive_implication'] }} +
+ {{ report.alterations.loc[index, 'prognostic_score_bin'] }} +
+ {% include 'modals/evidence_prognosis.html' %} + 		{{ report.alterations.loc[index, 'feature_type'] }}{{ report.alterations.loc[index, 'feature_display'] }} + {% if report.alterations.loc[index, 'favorable_prognosis'] == 1.0 %} + Favorable + {% else %} + Not favorable + {% endif %} +
+ {{ report.alterations.loc[index, 'prognostic_description'] }} + {% if report.alterations.loc[index, 'prognostic_url'] != "" %} + + [source] + + {% endif %} +
diff --git a/moalmanac/templates/report_table/table_resistance.html b/moalmanac/templates/report_table/table_resistance.html index 38085b5..f8e9bba 100644 --- a/moalmanac/templates/report_table/table_resistance.html +++ b/moalmanac/templates/report_table/table_resistance.html @@ -7,31 +7,33 @@

Variants and Features associated with Therapeutic Resist {% include 'report_table/columns_therapies.html' %} - {% for index in report.alterations[report.alterations['resistance_predictive_implication'].notnull()].sort_values(['resistance_predictive_implication_map', 'resistance_score_bin_map'], ascending=[False, False]).index.tolist() %} - - - - - - {% endfor %} + {% if not report.alterations.empty %} + {% for index in report.alterations[report.alterations['resistance_predictive_implication'].notnull()].sort_values(['resistance_predictive_implication_map', 'resistance_score_bin_map'], ascending=[False, False]).index.tolist() %} + + + + + + {% endfor %} + {% endif %}
{{ report.alterations.loc[index, 'resistance_predictive_implication'] }} -
- {{ report.alterations.loc[index, 'resistance_score_bin'] }} -
- {% include 'modals/evidence_resistance.html' %} - 		{{ report.alterations.loc[index, 'feature_type'] }}{{ report.alterations.loc[index, 'feature_display'] }} - {% if report.alterations.loc[index, 'resistance_therapy_name'] != '' %} - {{ report.alterations.loc[index, 'resistance_therapy_name'] }} - {% else %} - {{ report.alterations.loc[index, 'resistance_therapy_type'] }} - {% endif %} -
- {{ report.alterations.loc[index, 'resistance_description'] }} - {% if report.alterations.loc[index, 'resistance_url'] != "" %} - - [source] - - {% endif %} -
{{ report.alterations.loc[index, 'resistance_predictive_implication'] }} +
+ {{ report.alterations.loc[index, 'resistance_score_bin'] }} +
+ {% include 'modals/evidence_resistance.html' %} + 		{{ report.alterations.loc[index, 'feature_type'] }}{{ report.alterations.loc[index, 'feature_display'] }} + {% if report.alterations.loc[index, 'resistance_therapy_name'] != '' %} + {{ report.alterations.loc[index, 'resistance_therapy_name'] }} + {% else %} + {{ report.alterations.loc[index, 'resistance_therapy_type'] }} + {% endif %} +
+ {{ report.alterations.loc[index, 'resistance_description'] }} + {% if report.alterations.loc[index, 'resistance_url'] != "" %} + + [source] + + {% endif %} +
diff --git a/moalmanac/templates/report_table/table_sensitive.html b/moalmanac/templates/report_table/table_sensitive.html index 07036a3..0527b6f 100644 --- a/moalmanac/templates/report_table/table_sensitive.html +++ b/moalmanac/templates/report_table/table_sensitive.html @@ -7,34 +7,35 @@

Variants and Features associated with Therapeutic Sensit {% include 'report_table/columns_therapies.html' %} - {% for index in report.alterations[report.alterations['sensitive_predictive_implication'].notnull()].sort_values(['sensitive_predictive_implication_map', 'sensitive_score_bin_map'], ascending=[False, False]).index.tolist() %} - - - - - - - {% endfor %} + {% if not report.alterations.empty %} + {% for index in report.alterations[report.alterations['sensitive_predictive_implication'].notnull()].sort_values(['sensitive_predictive_implication_map', 'sensitive_score_bin_map'], ascending=[False, False]).index.tolist() %} + + + + + + {% endfor %} + {% endif %}
{{ report.alterations.loc[index, 'sensitive_predictive_implication'] }} -
- {{ report.alterations.loc[index, 'sensitive_score_bin'] }} -
- {% include 'modals/evidence_sensitive.html' %} - 		{{ report.alterations.loc[index, 'feature_type'] }}{{ report.alterations.loc[index, 'feature_display'] }} - - {% if report.alterations.loc[index, 'sensitive_therapy_name'] != '' %} - {{ report.alterations.loc[index, 'sensitive_therapy_name'] }} - {% else %} - {{ report.alterations.loc[index, 'sensitive_therapy_type'] }} - {% endif %} -
- {{ report.alterations.loc[index, 'sensitive_description'] }} - {% if report.alterations.loc[index, 'sensitive_url'] != "" %} - - [source] - - {% endif %} - {% include 'modals/efficacy.html' %} -
{{ report.alterations.loc[index, 'sensitive_predictive_implication'] }} +
+ {{ report.alterations.loc[index, 'sensitive_score_bin'] }} +
+ {% include 'modals/evidence_sensitive.html' %} + 		{{ report.alterations.loc[index, 'feature_type'] }}{{ report.alterations.loc[index, 'feature_display'] }} + + {% if report.alterations.loc[index, 'sensitive_therapy_name'] != '' %} + {{ report.alterations.loc[index, 'sensitive_therapy_name'] }} + {% else %} + {{ report.alterations.loc[index, 'sensitive_therapy_type'] }} + {% endif %} +
+ {{ report.alterations.loc[index, 'sensitive_description'] }} + {% if report.alterations.loc[index, 'sensitive_url'] != "" %} + + [source] + + {% endif %} + {% include 'modals/efficacy.html' %} +