Index

_

__init__() (analysis.run_analysis.WaspAnalysisData method) (analysis.run_analysis_sc.WaspAnalysisSC method) (counting.count_alleles_sc.CountStatsSC method) (counting.parse_gene_data.WaspGeneData method) (counting.run_counting.WaspCountFiles method) (counting.run_counting_sc.WaspCountSC method) (mapping.wasp_data_files.WaspDataFiles method)

A

adata (analysis.run_analysis_sc.AdataInputs attribute) adata_count_qc() (in module analysis.as_analysis_sc) AdataInputs (class in analysis.run_analysis_sc) align_pos_gen() (in module mapping.remap_utils) analysis.__main__ module analysis.as_analysis module analysis.as_analysis_sc module

analysis.compare_ai module analysis.run_analysis module analysis.run_analysis_sc module analysis.run_compare_ai module attribute (counting.parse_gene_data.ParsedGeneData attribute) (counting.parse_gene_data.WaspGeneData attribute)

B

bam_file (counting.run_counting.WaspCountFiles attribute) (counting.run_counting_sc.WaspCountSC attribute)

barcode_file (counting.run_counting_sc.WaspCountSC attribute)

C

check_filt_input() (in module mapping.run_mapping) clamp_rho() (in module analysis.as_analysis) compare_imbalance() (in module analysis.__main__) compare_imbalance_between_groups() (in module analysis.compare_ai) compare_imbalance_between_groups_diff_snps() (in module analysis.compare_ai) count_bc_snp_alleles() (in module counting.count_alleles_sc) count_file (analysis.run_analysis.WaspAnalysisData attribute) count_snp_alleles_rust() (in module counting.count_alleles) count_variants() (in module counting.__main__) count_variants_sc() (in module counting.__main__) counting.__main__ module

counting.count_alleles module counting.count_alleles_sc module counting.filter_variant_data module counting.parse_gene_data module counting.run_counting module counting.run_counting_sc module CountStatsSC (class in counting.count_alleles_sc)

F

feature (counting.parse_gene_data.ParsedGeneData attribute) (counting.parse_gene_data.WaspGeneData attribute) feature_file (counting.run_counting_sc.WaspCountSC attribute) filt_remapped_reads() (in module mapping.filter_remap_reads)

filter_remapped() (in module mapping.__main__) find_imbalance() (in module analysis.__main__) find_imbalance_sc() (in module analysis.__main__) find_read_aln_pos() (in module counting.count_alleles)

G

gene_df (counting.parse_gene_data.ParsedGeneData attribute) gene_file (counting.parse_gene_data.WaspGeneData attribute) get_compared_imbalance() (in module analysis.compare_ai) get_compared_imbalance_diff_snps() (in module analysis.compare_ai) get_imbalance() (in module analysis.as_analysis) get_imbalance_func() (in module analysis.compare_ai)

get_imbalance_per_group() (in module analysis.as_analysis_sc) get_imbalance_sc() (in module analysis.as_analysis_sc) get_read_het_data() (in module mapping.remap_utils) groupby (analysis.run_analysis.WaspAnalysisData attribute) groups (analysis.run_analysis_sc.AdataInputs attribute) gtf_bed (counting.run_counting.WaspCountFiles attribute) gtf_to_bed() (in module counting.filter_variant_data)

I

intersect_file (counting.run_counting.WaspCountFiles attribute) intersect_reads() (in module mapping.intersect_variant_data)

intersect_vcf_region() (in module counting.filter_variant_data) is_gene_file (counting.run_counting.WaspCountFiles attribute)

L

linear_model() (in module analysis.as_analysis)

M

main() (in module analysis.__main__) (in module counting.__main__) (in module mapping.__main__) make_count_df() (in module counting.count_alleles) make_count_matrix() (in module counting.count_alleles_sc) make_gene_data() (in module counting.parse_gene_data) make_intersect_df() (in module mapping.intersect_variant_data) make_multi_seqs() (in module mapping.remap_utils) make_multi_seqs_with_qual() (in module mapping.remap_utils) make_phased_seqs() (in module mapping.remap_utils) make_phased_seqs_with_qual() (in module mapping.remap_utils) make_reads() (in module mapping.__main__) mapping.__main__ module mapping.filter_remap_reads module mapping.intersect_variant_data module mapping.make_remap_reads module mapping.remap_utils module mapping.run_mapping module mapping.wasp_data_files module

merge_filt_bam() (in module mapping.filter_remap_reads) min_count (analysis.run_analysis.WaspAnalysisData attribute) model (analysis.run_analysis.WaspAnalysisData attribute) module analysis.__main__ analysis.as_analysis analysis.as_analysis_sc analysis.compare_ai analysis.run_analysis analysis.run_analysis_sc analysis.run_compare_ai counting.__main__ counting.count_alleles counting.count_alleles_sc counting.filter_variant_data counting.parse_gene_data counting.run_counting counting.run_counting_sc mapping.__main__ mapping.filter_remap_reads mapping.intersect_variant_data mapping.make_remap_reads mapping.remap_utils mapping.run_mapping mapping.wasp_data_files

O

opt_combined_imbalance() (in module analysis.compare_ai) opt_linear() (in module analysis.as_analysis) opt_phased_new() (in module analysis.as_analysis) opt_prob() (in module analysis.as_analysis)

opt_unphased_dp() (in module analysis.as_analysis) out_file (analysis.run_analysis.WaspAnalysisData attribute) (counting.run_counting.WaspCountFiles attribute) (counting.run_counting_sc.WaspCountSC attribute)

P

paired_read_gen() (in module mapping.remap_utils) paired_read_gen_stat() (in module mapping.remap_utils) parent_attribute (counting.parse_gene_data.ParsedGeneData attribute) (counting.parse_gene_data.WaspGeneData attribute) parse_gene_file() (in module counting.parse_gene_data) parse_intersect_genes() (in module counting.parse_gene_data) parse_intersect_genes_new() (in module counting.parse_gene_data) parse_intersect_region() (in module counting.filter_variant_data)

parse_intersect_region_new() (in module counting.filter_variant_data) parse_opt() (in module analysis.as_analysis) ParsedGeneData (class in counting.parse_gene_data) phased (analysis.run_analysis.WaspAnalysisData attribute) (analysis.run_analysis_sc.AdataInputs attribute) process_adata_inputs() (in module analysis.run_analysis_sc) process_bam() (in module mapping.intersect_variant_data) pseudocount (analysis.run_analysis.WaspAnalysisData attribute)

R

region_col (analysis.run_analysis.WaspAnalysisData attribute) region_file (counting.run_counting.WaspCountFiles attribute) region_type (counting.run_counting.WaspCountFiles attribute) run_ai_analysis() (in module analysis.run_analysis) run_ai_analysis_sc() (in module analysis.run_analysis_sc)

run_ai_comparison() (in module analysis.run_compare_ai) run_count_variants() (in module counting.run_counting) run_count_variants_sc() (in module counting.run_counting_sc) run_make_remap_reads() (in module mapping.run_mapping) run_make_remap_reads_unified() (in module mapping.run_mapping) run_wasp_filt() (in module mapping.run_mapping)

S

sample (analysis.run_analysis_sc.AdataInputs attribute) samples (counting.run_counting.WaspCountFiles attribute) (counting.run_counting_sc.WaspCountSC attribute)

single_model() (in module analysis.as_analysis) skip_intersect (counting.run_counting.WaspCountFiles attribute) skip_vcf_to_bed (counting.run_counting.WaspCountFiles attribute) stats_to_df() (counting.count_alleles_sc.CountStatsSC method)

T

temp_loc (counting.run_counting.WaspCountFiles attribute)

tempdir_decorator() (in module counting.run_counting) (in module mapping.run_mapping)

U

update_data() (analysis.run_analysis_sc.WaspAnalysisSC method) (counting.parse_gene_data.WaspGeneData method)

use_region_names (counting.run_counting.WaspCountFiles attribute)

V

variant_file (counting.run_counting.WaspCountFiles attribute) (counting.run_counting_sc.WaspCountSC attribute) variant_prefix (counting.run_counting.WaspCountFiles attribute)

vcf_bed (counting.run_counting.WaspCountFiles attribute) vcf_to_bed() (in module counting.filter_variant_data) (in module mapping.intersect_variant_data)

W

WaspAnalysisData (class in analysis.run_analysis) WaspAnalysisSC (class in analysis.run_analysis_sc) WaspCountFiles (class in counting.run_counting) WaspCountSC (class in counting.run_counting_sc)

WaspDataFiles (class in mapping.wasp_data_files) WaspGeneData (class in counting.parse_gene_data) write_data() (mapping.wasp_data_files.WaspDataFiles method) write_read() (in module mapping.remap_utils) write_remap_bam() (in module mapping.make_remap_reads)