<commit_before>[dna_substitutions]
sub_out = nucleotide/substitutions.txt
onco_out = nucleotide/onco_substitutions.txt
tsg_out = nucleotide/tsg_substitutions.txt
sub_heatmap = nucleotide/substitution.heatmap.png
sub_barplot = nucleotide/substitution.barplot.png
onco_barplot = nucleotide/onco_substitution.barplot.png
tsg_barplot = nucleotide/tsg_substitution.barplot.png

[sample_name]
gene_out = tables/sample_gene_counts.txt
mutation_out = tables/sample_mutation_counts.txt

[mutation_types]
nuc_type = nucleotide/mutation_types.txt
nuc_type_barplot = nucleotide/mutation_types.barplot.png
aa_type = amino_acid/mutation_types.txt
aa_type_barplot = amino_acid/mutation_types.barplot.png
nuc_onco_type = nucleotide/onco_mutation_types.txt
nuc_tsg_type = nucleotide/tsg_mutation_types.txt
aa_onco_type = amino_acid/onco_mutation_types.txt
aa_tsg_type = amino_acid/tsg_mutation_types.txt
nuc_onco_type_barplot = nucleotide/onco_mutation_types.barplot.png
nuc_tsg_type_barplot = nucleotide/tsg_mutation_types.barplot.png
aa_onco_type_barplot = amino_acid/onco_mutation_types.barplot.png
aa_tsg_type_barplot = amino_acid/tsg_mutation_types.barplot.png
gene_mutation_counts_by_type = gene_mutation_counts_by_type.txt
all_mut_type_barplot = all_mut_type.barplot.png

[missense]
missense = amino_acid/missense.txt
property = amino_acid/missense_property.txt
missense_heatmap = amino_acid/missense.heatmap.png
property_heatmap = amino_acid/missense_property.heatmap.png
property_barplot = amino_acid/missense_property.barplot.png

[single_gene]
primary_tissue = primary_tissue.txt
primary_tissue_barplot = primary_tissue.barplot.png
aa_type_primary_tissue = aa_type_primary_tissue.txt
nuc_type_primary_tissue = nuc_type_primary_tissue.txt
aa_type_primary_tissue_barplot = aa_type_primary_tissue.barplot.png
nuc_type_primary_tissue_barplot = nuc_type_primary_tissue.barplot.png

[stats]
pca_plot = gene_pca.scatter.png
gene_design_matrix = gene_design_matrix.txt
gene_mutation_counts = gene_mutation_counts.txt
gene_mutation_histogram = gene_mutation.histogram.png
cumulative_gene_mutation = gene_mutation.cumulative.png

[cosmic_aa]
aa_type = tables/aachange.cosmic_aa.txt
aa_type_barplot = tables/aachange.barplot.cosmic_aa.png

[cosmic_genomic]
aa_type = tables/aachange.cosmic_genomic.txt
aa_type_barplot = tables/aachange.barplot.cosmic_genomic.png
sub_out = tables/substitutions.cosmic_genomic.txt
sub_heatmap = tables/substitution.heatmap.cosmic_genomic.png
sub_barplot = tables/substitution.barplot.cosmic_genomic.png

[gene_tsv]
gene_tsv = data/genes.tsv
gene_db = data/genes.db

[classifier]
vogelstein_predictions = 'vogelstein_predictions.txt'<commit_msg>fixed typo in output.cfg<commit_after>[dna_substitutions]
sub_out = nucleotide/substitutions.txt
onco_out = nucleotide/onco_substitutions.txt
tsg_out = nucleotide/tsg_substitutions.txt
sub_heatmap = nucleotide/substitution.heatmap.png
sub_barplot = nucleotide/substitution.barplot.png
onco_barplot = nucleotide/onco_substitution.barplot.png
tsg_barplot = nucleotide/tsg_substitution.barplot.png

[sample_name]
gene_out = tables/sample_gene_counts.txt
mutation_out = tables/sample_mutation_counts.txt

[mutation_types]
nuc_type = nucleotide/mutation_types.txt
nuc_type_barplot = nucleotide/mutation_types.barplot.png
aa_type = amino_acid/mutation_types.txt
aa_type_barplot = amino_acid/mutation_types.barplot.png
nuc_onco_type = nucleotide/onco_mutation_types.txt
nuc_tsg_type = nucleotide/tsg_mutation_types.txt
aa_onco_type = amino_acid/onco_mutation_types.txt
aa_tsg_type = amino_acid/tsg_mutation_types.txt
nuc_onco_type_barplot = nucleotide/onco_mutation_types.barplot.png
nuc_tsg_type_barplot = nucleotide/tsg_mutation_types.barplot.png
aa_onco_type_barplot = amino_acid/onco_mutation_types.barplot.png
aa_tsg_type_barplot = amino_acid/tsg_mutation_types.barplot.png
gene_mutation_counts_by_type = gene_mutation_counts_by_type.txt
all_mut_type_barplot = all_mut_type.barplot.png

[missense]
missense = amino_acid/missense.txt
property = amino_acid/missense_property.txt
missense_heatmap = amino_acid/missense.heatmap.png
property_heatmap = amino_acid/missense_property.heatmap.png
property_barplot = amino_acid/missense_property.barplot.png

[single_gene]
primary_tissue = primary_tissue.txt
primary_tissue_barplot = primary_tissue.barplot.png
aa_type_primary_tissue = aa_type_primary_tissue.txt
nuc_type_primary_tissue = nuc_type_primary_tissue.txt
aa_type_primary_tissue_barplot = aa_type_primary_tissue.barplot.png
nuc_type_primary_tissue_barplot = nuc_type_primary_tissue.barplot.png

[stats]
pca_plot = gene_pca.scatter.png
gene_design_matrix = gene_design_matrix.txt
gene_mutation_counts = gene_mutation_counts.txt
gene_mutation_histogram = gene_mutation.histogram.png
cumulative_gene_mutation = gene_mutation.cumulative.png

[cosmic_aa]
aa_type = tables/aachange.cosmic_aa.txt
aa_type_barplot = tables/aachange.barplot.cosmic_aa.png

[cosmic_genomic]
aa_type = tables/aachange.cosmic_genomic.txt
aa_type_barplot = tables/aachange.barplot.cosmic_genomic.png
sub_out = tables/substitutions.cosmic_genomic.txt
sub_heatmap = tables/substitution.heatmap.cosmic_genomic.png
sub_barplot = tables/substitution.barplot.cosmic_genomic.png

[gene_tsv]
gene_tsv = data/genes.tsv
gene_db = data/genes.db

[classifier]
vogelstein_predictions = vogelstein_predictions.txt
{'fraction_non_alphanumeric': 0.07077154120518116, 'fraction_numerical': 0.0, 'mean_word_length': 8.430088495575221, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '4393659', 'n_tokens_mistral': 2173, 'n_tokens_neox': 2002, 'n_words': 218}