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Refactor ini files to be arguments #20

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Refactor ini files to be arguments #20

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ad88d7e
Added functions to read config and colname ini files
brendanreardon May 29, 2024
aadfefc
Updated oncotree string names. Removed config and colnames global var…
brendanreardon May 29, 2024
cfa2cb8
Added properties to Writer class
brendanreardon May 29, 2024
561ad57
Renamed oncotree fields
brendanreardon May 29, 2024
93ebc22
Revised properties
brendanreardon May 29, 2024
638ee8d
Missed some conversion for oncotree keys
brendanreardon May 30, 2024
1d24cd4
Readded extended interpolation
brendanreardon May 30, 2024
cb87646
Refactored writer to not need colnames.ini as global variable
brendanreardon May 30, 2024
dc62dcb
Revised how writer classes are instantiated
brendanreardon May 30, 2024
5c7077b
Removed deconstructSigs wrapper
brendanreardon May 30, 2024
0bac0fb
In progress changes
brendanreardon May 30, 2024
b9e7f2a
Writer is having an issue with one output
brendanreardon May 30, 2024
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8 changes: 4 additions & 4 deletions moalmanac/annotator.py
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Original file line number Diff line number Diff line change
Expand Up @@ -27,8 +27,8 @@ class Annotator:
resistance_score_bin = COLNAMES[bin_section]['resistance_score_bin']
prognostic_score_bin = COLNAMES[bin_section]['prognostic_score_bin']
acmg_bin = COLNAMES[bin_section]['acmg']
cancerhotspots_bin = COLNAMES[bin_section]['cancerhotspots']
cancerhotspots3d_bin = COLNAMES[bin_section]['cancerhotspots3d']
cancerhotspots_bin = COLNAMES[bin_section]['cancer_hotspots']
cancerhotspots3d_bin = COLNAMES[bin_section]['cancer_hotspots_3d']
cgc_bin = COLNAMES[bin_section]['cgc']
clinvar_bin = COLNAMES[bin_section]['clinvar']
cosmic_bin = COLNAMES[bin_section]['cosmic']
Expand Down Expand Up @@ -1243,8 +1243,8 @@ class PreclinicalEfficacy:
section = 'preclinical'
feature_display = COLNAMES[section]['feature_display']
pvalue = COLNAMES[section]['pvalue']
efficacy = COLNAMES[section]['efficacy_obs']
lookup = COLNAMES[section]['efficacy_lookup']
efficacy = COLNAMES[section]['preclinical_efficacy_obs']
lookup = COLNAMES[section]['preclinical_efficacy_lookup']

@classmethod
def annotate(cls, actionable, efficacy, dictionary, append_lookup=True):
Expand Down
38 changes: 19 additions & 19 deletions moalmanac/colnames.ini
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Original file line number Diff line number Diff line change
Expand Up @@ -139,8 +139,8 @@ coverage = total_coverage
tumor_f = tumor_f
tumor = tumor_sample_barcode
normal = normal_sample_barcode
ontology = oncotree_term
code = oncotree_code
oncotree_term = oncotree_term
oncotree_code = oncotree_code
context = context
tumor_type = reported_tumor_type
patient_id = patient_id
Expand Down Expand Up @@ -340,8 +340,8 @@ gdsc = gdsc
ln_ic50 = ln_ic50
ic50 = ic50
tested_subfeature = tested_subfeature
efficacy_obs = preclinical_efficacy_observed
efficacy_lookup = preclinical_efficacy_lookup
preclinical_efficacy_obs = preclinical_efficacy_observed
preclinical_efficacy_lookup = preclinical_efficacy_lookup
evidence = evidence
evidence_map = evidence_map
group1 = group1
Expand Down Expand Up @@ -407,8 +407,8 @@ feature_display = ${maps:feature_display}
[burden]
patient = ${maps:patient_id}
tumor_type = ${maps:tumor_type}
ontology = ${maps:ontology}
code = ${maps:code}
oncotree_term = ${maps:oncotree_term}
oncotree_code = ${maps:oncotree_code}
bases_covered = ${maps:bases_covered}
n_nonsyn_mutations = ${maps:n_nonsyn_mutations}
mutational_burden = ${maps:mutational_burden}
Expand All @@ -430,8 +430,8 @@ number_mutations = ${maps:number_mutations}
low_number_mutations = ${maps:low_number_mutations}

[oncotree]
ontology = ${maps:ontology}
code = ${maps:code}
term = ${maps:oncotree_term}
code = ${maps:oncotree_code}

[validation_sequencing]
feature_type = ${maps:feature_type}
Expand Down Expand Up @@ -555,8 +555,8 @@ exac_sas_an = ${maps:exac_sas_an}
exac_oth_an = ${maps:exac_oth_an}
mutational_burden = ${maps:mutational_burden}
tumor_type = ${maps:tumor_type}
ontology = ${maps:ontology}
code = ${maps:code}
oncotree_term = ${maps:oncotree_term}
oncotree_code = ${maps:oncotree_code}
context = ${maps:context}
clinvar = ${maps:clinvar}
query = ${maps:query}
Expand Down Expand Up @@ -593,8 +593,8 @@ sensitive_score_bin = sensitive_score_bin
resistance_score_bin = resistance_score_bin
prognostic_score_bin = prognostic_score_bin
acmg = acmg_bin
cancerhotspots = cancerhotspots_bin
cancerhotspots3d = cancerhotspots3D_bin
cancer_hotspots = cancer_hotspots_bin
cancer_hotspots_3d = cancer_hotspots_3D_bin
cgc = cgc_bin
clinvar = clinvar_bin
cosmic = cosmic_bin
Expand All @@ -605,12 +605,12 @@ msi = msi_bin
exac_common = ${maps:exac_common}

[report]
code = ${maps:code}
date = ${maps:date}
description = ${maps:description}
normal = ${maps:normal}
tumor = ${maps:tumor}
ontology = ${maps:ontology}
oncotree_term = ${maps:oncotree_term}
oncotree_code = ${maps:oncotree_code}
patient_id = ${maps:patient_id}
stage = ${maps:stage}
purity = ${maps:purity}
Expand All @@ -626,8 +626,8 @@ almanac_bin = ${bin_names:almanac}
sensitive_bin = ${bin_names:sensitive_score_bin}
resistance_bin = ${bin_names:resistance_score_bin}
prognostic_bin = ${bin_names:prognostic_score_bin}
cancerhotspots_bin = ${bin_names:cancerhotspots}
cancerhotspots3d_bin = ${bin_names:cancerhotspots3d}
cancer_hotspots_bin = ${bin_names:cancer_hotspots}
cancer_hotspots_3d_bin = ${bin_names:cancer_hotspots_3d}
cgc_bin = ${bin_names:cgc}
gsea_pathways_bin = ${bin_names:gsea_pathways}
gsea_cm_bin = ${bin_names:gsea_modules}
Expand Down Expand Up @@ -710,7 +710,7 @@ number_germline_mutations = ${maps:number_germline_mutations}
validation_tumor_f = ${maps:validation_tumor_f}
validation_coverage = ${maps:validation_coverage}
validation_detection_power = ${maps:validation_detection_power}
efficacy_obs = ${maps:efficacy_obs}
preclinical_efficacy_obs = ${maps:preclinical_efficacy_obs}

[preclinical]
ccle = ccle
Expand Down Expand Up @@ -762,8 +762,8 @@ gdsc = ${maps:gdsc}
ln_ic50 = ${maps:ln_ic50}
ic50 = ${maps:ic50}
tested_subfeature = ${maps:tested_subfeature}
efficacy_obs = ${maps:efficacy_obs}
efficacy_lookup = ${maps:efficacy_lookup}
preclinical_efficacy_obs = ${maps:preclinical_efficacy_obs}
preclinical_efficacy_lookup = ${maps:preclinical_efficacy_lookup}

[matchmaking]
feature = ${maps:feature}
Expand Down
4 changes: 2 additions & 2 deletions moalmanac/datasources.py
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Original file line number Diff line number Diff line change
Expand Up @@ -22,8 +22,8 @@ class Datasources:
allele2 = COLNAMES[datasources_section]['allele2']

disease = COLNAMES[datasources_section]['disease']
ontology = COLNAMES[datasources_section]['ontology']
code = COLNAMES[datasources_section]['code']
ontology = COLNAMES[datasources_section]['oncotree_term']
code = COLNAMES[datasources_section]['oncotree_code']
context = COLNAMES[datasources_section]['context']
mutational_burden = COLNAMES[datasources_section]['mutational_burden']
therapy = COLNAMES[datasources_section]['therapy']
Expand Down
4 changes: 2 additions & 2 deletions moalmanac/evaluator.py
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Original file line number Diff line number Diff line change
Expand Up @@ -27,8 +27,8 @@ class Evaluator(object):
resistance_bin = COLNAMES[bin_section]['resistance_score_bin']
prognostic_bin = COLNAMES[bin_section]['prognostic_score_bin']
acmg_bin = COLNAMES[bin_section]['acmg']
cancerhotspots_bin = COLNAMES[bin_section]['cancerhotspots']
cancerhotspots3d_bin = COLNAMES[bin_section]['cancerhotspots3d']
cancerhotspots_bin = COLNAMES[bin_section]['cancer_hotspots']
cancerhotspots3d_bin = COLNAMES[bin_section]['cancer_hotspots_3d']
cgc_bin = COLNAMES[bin_section]['cgc']
clinvar_bin = COLNAMES[bin_section]['clinvar']
cosmic_bin = COLNAMES[bin_section]['cosmic']
Expand Down
4 changes: 2 additions & 2 deletions moalmanac/features.py
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Expand Up @@ -145,8 +145,8 @@ class BurdenReader:
burden_section = 'burden'
patient_id = COLNAMES[burden_section]['patient']
tumor_type = COLNAMES[burden_section]['tumor_type']
ontology = COLNAMES[burden_section]['ontology']
code = COLNAMES[burden_section]['code']
ontology = COLNAMES[burden_section]['oncotree_term']
code = COLNAMES[burden_section]['oncotree_code']
bases_covered = COLNAMES[burden_section]['bases_covered']
n_nonsyn_mutations = COLNAMES[burden_section]['n_nonsyn_mutations']
mutational_burden = COLNAMES[burden_section]['mutational_burden']
Expand Down
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