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brendanreardonbrendanreardon
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Update db to 2023-11-09 (#16)
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10 files changed

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-5166
lines changed

‎example_data/example_patient.capture.sbs_contributions.txt‎

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signature contribution
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SBS1 0.003389830508474576
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SBS2 0.0
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SBS3 0.0
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SBS4 0.0
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SBS5 0.22372881355932203
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SBS6 0.0
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SBS7a 0.423728813559322
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SBS7b 0.0
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SBS7c 0.0
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SBS7d 0.0
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SBS8 0.0
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SBS9 0.0
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SBS10a 0.0
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SBS10b 0.11864406779661017
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SBS10c 0.0
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SBS10d 0.0
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SBS11 0.0
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SBS12 0.0
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SBS13 0.0
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SBS14 0.0
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SBS15 0.0
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SBS16 0.0
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SBS17a 0.0
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SBS17b 0.0
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SBS18 0.0
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SBS19 0.0
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SBS20 0.0
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SBS21 0.0
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SBS22 0.0
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SBS23 0.0
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SBS24 0.0
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SBS25 0.0
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SBS26 0.0
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SBS27 0.0
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SBS28 0.0
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SBS29 0.0
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SBS30 0.2305084745762712
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SBS31 0.0
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SBS32 0.0
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SBS33 0.0
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SBS34 0.0
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SBS35 0.0
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SBS36 0.0
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SBS37 0.0
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SBS38 0.0
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SBS39 0.0
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SBS40 0.0
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SBS41 0.0
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SBS42 0.0
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SBS43 0.0
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SBS44 0.0
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SBS45 0.0
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SBS46 0.0
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SBS47 0.0
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SBS48 0.0
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SBS49 0.0
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SBS50 0.0
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SBS51 0.0
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SBS52 0.0
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SBS53 0.0
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SBS54 0.0
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SBS55 0.0
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SBS56 0.0
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SBS57 0.0
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SBS58 0.0
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SBS59 0.0
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SBS60 0.0
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SBS84 0.0
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SBS85 0.0
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SBS86 0.0
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SBS87 0.0
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SBS88 0.0
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SBS89 0.0
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SBS90 0.0
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SBS91 0.0
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SBS92 0.0
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SBS93 0.0
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SBS94 0.0
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SBS95 0.0

‎example_data/example_patient.capture.somatic.indels.maf‎

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1-
Hugo_Symbol NCBI_Build Chromosome Start_position End_position Variant_Classification Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Annotation_Transcript Protein_Change t_alt_count t_ref_count
2-
PMPCA 37 9 139312448 139312449 Intron - - G example_tumor_profile example_normal_profile ENST00000371717.3 31 92
3-
C10orf2 37 10 102748300 102748301 Frame_Shift_Del TC TC - example_tumor_profile example_normal_profile ENST00000370228.1 p.L112fs 28 294
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Hugo_Symbol NCBI_Build Chromosome Start_position End_position Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Annotation_Transcript Protein_Change t_alt_count t_ref_count
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PMPCA 37 9 139312448 139312449 Intron INS - - G example_tumor_profile example_normal_profile ENST00000371717.3 31 92
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C10orf2 37 10 102748300 102748301 Frame_Shift_Del DEL TC TC - example_tumor_profile example_normal_profile ENST00000370228.1 p.L112fs 28 294

‎example_data/example_patient.capture.somatic.snvs.maf‎

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‎moalmanac/annotator.py‎

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@@ -177,14 +177,15 @@ class Almanac:
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implication = datasources.Almanac.implication
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implication_map = datasources.Almanac.implication_map
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description = datasources.Almanac.description
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preferred_assertion = datasources.Almanac.preferred_assertion
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source_type = datasources.Almanac.source_type
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citation = datasources.Almanac.citation
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url = datasources.Almanac.url
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doi = datasources.Almanac.doi
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pmid = datasources.Almanac.pmid
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nct = datasources.Almanac.nct
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publication_date = datasources.Almanac.publication_date
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last_updated = datasources.Almanac.last_updated
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predictive_implication_map = datasources.Almanac.predictive_implication_map
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@@ -820,8 +821,8 @@ def select_better_fusion_match(cls, list_of_matches):
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@classmethod
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def sort_and_subset_matches(cls, table, results_same_ontology, results_diff_ontology):
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sort_columns = [cls.implication_map, cls.preferred_assertion]
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sort_ascending = [False, False]
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sort_columns = [cls.implication_map, cls.publication_date, cls.last_updated]
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sort_ascending = [False, False, False]
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if results_same_ontology.any():
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results_same_ontology_sorted = cls.sort_dataframe(table[results_same_ontology], sort_columns, sort_ascending)
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results_same_ontology_records = cls.convert_dataframe_to_records(results_same_ontology_sorted)

‎moalmanac/colnames.ini‎

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@@ -165,14 +165,15 @@ resistance = therapy_resistance
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prognosis = favorable_prognosis
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implication = predictive_implication
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implication_map = predictive_implication_map
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preferred_assertion = preferred_assertion
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connections = connections
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source_type = source_type
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citation = citation
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url = url
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doi = doi
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pmid = pmid
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nct = nct
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publication_date = publication_date
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last_updated = last_updated
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exac_common = exac_common
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exac_af = exac_af
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exac_ac = exac_ac
@@ -459,7 +460,6 @@ implication = ${maps:implication}
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implication_map = ${maps:implication_map}
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connections = ${maps:connections}
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description = ${maps:description}
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preferred_assertion = ${maps:preferred_assertion}
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sensitive_oncotree_code = ${maps:sensitive_oncotree_code}
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sensitive_oncotree_term = ${maps:sensitive_oncotree_term}
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sensitive_context = ${maps:sensitive_context}
@@ -523,6 +523,8 @@ url = ${maps:url}
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doi = ${maps:doi}
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pmid = ${maps:pmid}
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nct = ${maps:nct}
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publication_date = ${maps:publication_date}
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last_updated = ${maps:last_updated}
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chr = ${maps:chr}
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start = ${maps:start}
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end = ${maps:end}

‎moalmanac/config.ini‎

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plot_preclinical_efficacy = on
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[versions]
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interpreter = 0.4.6
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database = v.2023-02-02
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interpreter = 0.4.7
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database = v.2023-11-09
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[exac]
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exac_common_af_threshold = 0.001

‎moalmanac/datasources.py‎

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@@ -37,14 +37,15 @@ class Datasources:
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implication_map = COLNAMES[datasources_section]['implication_map']
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connections = COLNAMES[datasources_section]['connections']
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description = COLNAMES[datasources_section]['description']
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preferred_assertion = COLNAMES[datasources_section]['preferred_assertion']
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source_type = COLNAMES[datasources_section]['source_type']
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citation = COLNAMES[datasources_section]['citation']
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url = COLNAMES[datasources_section]['url']
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doi = COLNAMES[datasources_section]['doi']
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pmid = COLNAMES[datasources_section]['pmid']
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nct = COLNAMES[datasources_section]['nct']
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publication_date = COLNAMES[datasources_section]['publication_date']
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last_updated = COLNAMES[datasources_section]['last_updated']
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sensitivity_matches = COLNAMES[datasources_section]['sensitivity_matches']
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resistance_matches = COLNAMES[datasources_section]['resistance_matches']
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implication = Datasources.implication
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implication_map = Datasources.implication_map
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description = Datasources.description
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preferred_assertion = Datasources.preferred_assertion
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source_type = Datasources.source_type
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citation = Datasources.citation
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url = Datasources.url
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doi = Datasources.doi
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pmid = Datasources.pmid
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nct = Datasources.nct
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publication_date = Datasources.publication_date
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last_updated = Datasources.last_updated
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sensitivity_matches = Datasources.sensitivity_matches
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resistance_matches = Datasources.resistance_matches

‎moalmanac/datasources/moalmanac/create_almanac_db.py‎

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@@ -26,11 +26,11 @@ def create_config():
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'disease', 'context', 'oncotree_term', 'oncotree_code',
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'therapy_name', 'therapy_strategy', 'therapy_type',
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'therapy_sensitivity', 'therapy_resistance', 'favorable_prognosis',
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'predictive_implication', 'description', 'last_updated', 'preferred_assertion'
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'predictive_implication', 'description', 'last_updated'
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]
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SOURCE_FIELDS = [
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'source_type', 'citation', 'url', 'doi', 'pmid', 'nct', 'last_updated'
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'source_type', 'citation', 'url', 'doi', 'pmid', 'nct', 'publication_date', 'last_updated'
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]
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VARIANT_FIELDS = [
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]
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MUTATIONAL_SIGNATURE_FIELDS = [
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'cosmic_signature_number', 'cosmic_signature_version'
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'cosmic_signature'
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]
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MICROSATELLITE_FIELDS = [
@@ -86,7 +86,7 @@ def copy_number(cls, record):
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@classmethod
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def cosmic_mutational_signature(cls, record):
89-
return f"Cosmic signature (version {record['cosmic_signature_version']}) {record['cosmic_signature_number']}"
89+
return f"Cosmic signature {record['cosmic_signature']} (version 3.4)"
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@classmethod
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def germline_variant(cls, record):

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