Index

_

__init__() (snpio.analysis.genotype_encoder.GenotypeEncoder method) (snpio.analysis.tree_parser.TreeParser method) (snpio.filtering.nremover2.NRemover2 method) (snpio.GenePopReader method) (snpio.GenotypeEncoder method) (snpio.io.genepop_reader.GenePopReader method) (snpio.io.phylip_reader.PhylipReader method) (snpio.io.structure_reader.StructureReader method) (snpio.io.vcf_reader.VCFReader method) (snpio.NRemover2 method) (snpio.PhylipReader method) (snpio.Plotting method) (snpio.plotting.plotting.Plotting method) (snpio.PopGenStatistics method) (snpio.popgenstats.pop_gen_statistics.PopGenStatistics method) (snpio.SNPioMultiQC method) (snpio.StructureReader method) (snpio.TreeParser method) (snpio.VCFReader method)

_chain_active (snpio.filtering.nremover2.NRemover2 attribute) (snpio.NRemover2 attribute) _chain_resolved (snpio.filtering.nremover2.NRemover2 attribute) (snpio.NRemover2 attribute) _filtering_helper (snpio.filtering.nremover2.NRemover2 attribute) (snpio.NRemover2 attribute) _filtering_methods (snpio.filtering.nremover2.NRemover2 attribute) (snpio.NRemover2 attribute) _get_attribute_value() (snpio.Plotting method) (snpio.plotting.plotting.Plotting method) _plot_summary_statistics_per_population() (snpio.Plotting method) (snpio.plotting.plotting.Plotting method) _plot_summary_statistics_per_sample() (snpio.Plotting method) (snpio.plotting.plotting.Plotting method) _search_mode (snpio.filtering.nremover2.NRemover2 attribute) (snpio.NRemover2 attribute) _set_logger() (snpio.Plotting method) (snpio.plotting.plotting.Plotting method)

A

alignment (snpio.filtering.nremover2.NRemover2 attribute) (snpio.NRemover2 attribute)

B

boolean_filter_methods (snpio.Plotting attribute) (snpio.plotting.plotting.Plotting attribute)

C

chunk_size (snpio.io.vcf_reader.VCFReader attribute) (snpio.VCFReader attribute)

current_threshold (snpio.filtering.nremover2.NRemover2 attribute) (snpio.NRemover2 attribute)

D

debug (snpio.analysis.tree_parser.TreeParser attribute) (snpio.filtering.nremover2.NRemover2 attribute) (snpio.io.phylip_reader.PhylipReader attribute) (snpio.io.vcf_reader.VCFReader attribute) (snpio.NRemover2 attribute) (snpio.PhylipReader attribute) (snpio.Plotting attribute) (snpio.plotting.plotting.Plotting attribute) (snpio.TreeParser attribute) (snpio.VCFReader attribute)

despine (snpio.Plotting attribute) (snpio.plotting.plotting.Plotting attribute) df_global_list (snpio.filtering.nremover2.NRemover2 attribute) (snpio.NRemover2 attribute) df_sample_list (snpio.filtering.nremover2.NRemover2 attribute) (snpio.NRemover2 attribute) dpi (snpio.Plotting attribute) (snpio.plotting.plotting.Plotting attribute)

E

exclude_pops (snpio.io.phylip_reader.PhylipReader attribute) (snpio.io.vcf_reader.VCFReader attribute) (snpio.PhylipReader attribute) (snpio.VCFReader attribute)

F

filename (snpio.io.phylip_reader.PhylipReader attribute) (snpio.io.vcf_reader.VCFReader attribute) (snpio.PhylipReader attribute) (snpio.VCFReader attribute) filetype (snpio.analysis.genotype_encoder.GenotypeEncoder attribute) (snpio.GenotypeEncoder attribute) (snpio.io.vcf_reader.VCFReader attribute) (snpio.VCFReader attribute) filter_allele_depth() (snpio.filtering.nremover2.NRemover2 method) (snpio.NRemover2 method) filter_biallelic() (snpio.filtering.nremover2.NRemover2 method) (snpio.NRemover2 method) filter_linked() (snpio.filtering.nremover2.NRemover2 method) (snpio.NRemover2 method) filter_maf() (snpio.filtering.nremover2.NRemover2 method) (snpio.NRemover2 method)

filter_missing() (snpio.filtering.nremover2.NRemover2 method) (snpio.NRemover2 method) filter_missing_pop() (snpio.filtering.nremover2.NRemover2 method) (snpio.NRemover2 method) filter_missing_sample() (snpio.filtering.nremover2.NRemover2 method) (snpio.NRemover2 method) filter_monomorphic() (snpio.filtering.nremover2.NRemover2 method) (snpio.NRemover2 method) filter_singletons() (snpio.filtering.nremover2.NRemover2 method) (snpio.NRemover2 method) force_popmap (snpio.io.phylip_reader.PhylipReader attribute) (snpio.io.vcf_reader.VCFReader attribute) (snpio.PhylipReader attribute) (snpio.VCFReader attribute)

G

GenePopReader (class in snpio) (class in snpio.io.genepop_reader) genotype_data (snpio.analysis.tree_parser.TreeParser attribute) (snpio.filtering.nremover2.NRemover2 attribute) (snpio.NRemover2 attribute) (snpio.Plotting attribute) (snpio.plotting.plotting.Plotting attribute) (snpio.TreeParser attribute)

GenotypeEncoder (class in snpio) (class in snpio.analysis.genotype_encoder)

I

include_pops (snpio.io.phylip_reader.PhylipReader attribute) (snpio.io.vcf_reader.VCFReader attribute) (snpio.PhylipReader attribute) (snpio.VCFReader attribute)

info_fields (snpio.io.vcf_reader.VCFReader attribute) (snpio.VCFReader attribute)

K

kept_per_step (snpio.filtering.nremover2.NRemover2 attribute) (snpio.NRemover2 attribute)

L

loci_indices (snpio.filtering.nremover2.NRemover2 attribute) (snpio.io.vcf_reader.VCFReader attribute) (snpio.NRemover2 attribute) (snpio.VCFReader attribute) loci_removed_per_step (snpio.filtering.nremover2.NRemover2 attribute) (snpio.NRemover2 attribute) logger (snpio.filtering.nremover2.NRemover2 attribute) (snpio.io.phylip_reader.PhylipReader attribute) (snpio.io.vcf_reader.VCFReader attribute) (snpio.NRemover2 attribute) (snpio.PhylipReader attribute) (snpio.Plotting attribute) (snpio.plotting.plotting.Plotting attribute) (snpio.VCFReader attribute)

M

maf_filter_methods (snpio.Plotting attribute) (snpio.plotting.plotting.Plotting attribute) missing_filter_methods (snpio.Plotting attribute) (snpio.plotting.plotting.Plotting attribute) missing_vals (snpio.analysis.genotype_encoder.GenotypeEncoder attribute) (snpio.GenotypeEncoder attribute) module snpio snpio.analysis.genotype_encoder snpio.analysis.tree_parser snpio.filtering.nremover2 snpio.io.genepop_reader snpio.io.phylip_reader snpio.io.structure_reader snpio.io.vcf_reader snpio.plotting.plotting snpio.popgenstats.pop_gen_statistics

mpl_params (snpio.Plotting attribute) (snpio.plotting.plotting.Plotting attribute)

N

NRemover2 (class in snpio) (class in snpio.filtering.nremover2) num_inds (snpio.io.phylip_reader.PhylipReader attribute) (snpio.PhylipReader attribute)

num_records (snpio.io.vcf_reader.VCFReader attribute) (snpio.VCFReader attribute) num_snps (snpio.io.phylip_reader.PhylipReader attribute) (snpio.PhylipReader attribute)

O

original_loci_count (snpio.filtering.nremover2.NRemover2 attribute) (snpio.NRemover2 attribute) original_loci_indices (snpio.filtering.nremover2.NRemover2 attribute) (snpio.NRemover2 attribute) original_sample_count (snpio.filtering.nremover2.NRemover2 attribute) (snpio.NRemover2 attribute)

original_sample_indices (snpio.filtering.nremover2.NRemover2 attribute) (snpio.NRemover2 attribute) output_dir (snpio.Plotting attribute) (snpio.plotting.plotting.Plotting attribute)

P

PhylipReader (class in snpio) (class in snpio.io.phylip_reader) plot_d_statistics() (snpio.Plotting method) (snpio.plotting.plotting.Plotting method) plot_dapc() (snpio.Plotting method) (snpio.plotting.plotting.Plotting method) plot_despine (snpio.io.vcf_reader.VCFReader attribute) (snpio.VCFReader attribute) plot_dpi (snpio.io.vcf_reader.VCFReader attribute) (snpio.VCFReader attribute) plot_fontsize (snpio.io.vcf_reader.VCFReader attribute) (snpio.Plotting attribute) (snpio.plotting.plotting.Plotting attribute) (snpio.VCFReader attribute) plot_format (snpio.analysis.genotype_encoder.GenotypeEncoder attribute) (snpio.GenotypeEncoder attribute) (snpio.io.phylip_reader.PhylipReader attribute) (snpio.io.vcf_reader.VCFReader attribute) (snpio.PhylipReader attribute) (snpio.Plotting attribute) (snpio.plotting.plotting.Plotting attribute) (snpio.VCFReader attribute) plot_fst_heatmap() (snpio.Plotting method) (snpio.plotting.plotting.Plotting method) plot_fst_outliers() (snpio.Plotting method) (snpio.plotting.plotting.Plotting method) plot_pca() (snpio.Plotting method) (snpio.plotting.plotting.Plotting method) plot_sankey_filtering_report() (snpio.filtering.nremover2.NRemover2 method) (snpio.NRemover2 method) (snpio.Plotting method) (snpio.plotting.plotting.Plotting method)

plot_summary_statistics() (snpio.Plotting method) (snpio.plotting.plotting.Plotting method) plot_title_fontsize (snpio.Plotting attribute) (snpio.plotting.plotting.Plotting attribute) Plotting (class in snpio) (class in snpio.plotting.plotting) PopGenStatistics (class in snpio) (class in snpio.popgenstats.pop_gen_statistics) popmap (snpio.filtering.nremover2.NRemover2 attribute) (snpio.NRemover2 attribute) popmap_inverse (snpio.filtering.nremover2.NRemover2 attribute) (snpio.NRemover2 attribute) popmapfile (snpio.io.phylip_reader.PhylipReader attribute) (snpio.io.vcf_reader.VCFReader attribute) (snpio.PhylipReader attribute) (snpio.VCFReader attribute) populations (snpio.filtering.nremover2.NRemover2 attribute) (snpio.NRemover2 attribute) prefix (snpio.analysis.genotype_encoder.GenotypeEncoder attribute) (snpio.filtering.nremover2.NRemover2 attribute) (snpio.GenotypeEncoder attribute) (snpio.io.phylip_reader.PhylipReader attribute) (snpio.io.vcf_reader.VCFReader attribute) (snpio.NRemover2 attribute) (snpio.PhylipReader attribute) (snpio.Plotting attribute) (snpio.plotting.plotting.Plotting attribute) (snpio.VCFReader attribute) print_filtering_report() (snpio.filtering.nremover2.NRemover2 method) (snpio.NRemover2 method)

Q

qmatrix (snpio.analysis.tree_parser.TreeParser attribute) (snpio.TreeParser attribute)

R

random_subset_loci() (snpio.filtering.nremover2.NRemover2 method) (snpio.NRemover2 method) replace_vals (snpio.analysis.genotype_encoder.GenotypeEncoder attribute) (snpio.GenotypeEncoder attribute)

resolve() (snpio.filtering.nremover2.NRemover2 method) (snpio.NRemover2 method) resource_data (snpio.io.vcf_reader.VCFReader attribute) (snpio.VCFReader attribute)

S

sample_indices (snpio.filtering.nremover2.NRemover2 attribute) (snpio.io.vcf_reader.VCFReader attribute) (snpio.NRemover2 attribute) (snpio.VCFReader attribute) samples (snpio.analysis.genotype_encoder.GenotypeEncoder attribute) (snpio.filtering.nremover2.NRemover2 attribute) (snpio.GenotypeEncoder attribute) (snpio.io.phylip_reader.PhylipReader attribute) (snpio.io.vcf_reader.VCFReader attribute) (snpio.NRemover2 attribute) (snpio.PhylipReader attribute) (snpio.VCFReader attribute) samples_removed_per_step (snpio.filtering.nremover2.NRemover2 attribute) (snpio.NRemover2 attribute) search_thresholds() (snpio.filtering.nremover2.NRemover2 method) (snpio.NRemover2 method) show (snpio.Plotting attribute) (snpio.plotting.plotting.Plotting attribute) show_plots (snpio.io.vcf_reader.VCFReader attribute) (snpio.VCFReader attribute) siterates (snpio.analysis.tree_parser.TreeParser attribute) (snpio.TreeParser attribute) snp_data (snpio.analysis.genotype_encoder.GenotypeEncoder attribute) (snpio.GenotypeEncoder attribute) (snpio.io.phylip_reader.PhylipReader attribute) (snpio.io.vcf_reader.VCFReader attribute) (snpio.PhylipReader attribute) (snpio.VCFReader attribute)

snpio module snpio.analysis.genotype_encoder module snpio.analysis.tree_parser module snpio.filtering.nremover2 module snpio.io.genepop_reader module snpio.io.phylip_reader module snpio.io.structure_reader module snpio.io.vcf_reader module snpio.plotting.plotting module snpio.popgenstats.pop_gen_statistics module SNPioMultiQC (class in snpio) step_index (snpio.filtering.nremover2.NRemover2 attribute) (snpio.NRemover2 attribute) store_format_fields (snpio.io.vcf_reader.VCFReader attribute) (snpio.VCFReader attribute) StructureReader (class in snpio) (class in snpio.io.structure_reader)

T

thin_loci() (snpio.filtering.nremover2.NRemover2 method) (snpio.NRemover2 method) treefile (snpio.analysis.tree_parser.TreeParser attribute) (snpio.TreeParser attribute)

TreeParser (class in snpio) (class in snpio.analysis.tree_parser)

V

vcf_attributes_fn (snpio.io.vcf_reader.VCFReader attribute) (snpio.VCFReader attribute) vcf_header (snpio.io.vcf_reader.VCFReader attribute) (snpio.VCFReader attribute) VCFReader (class in snpio) (class in snpio.io.vcf_reader) verbose (snpio.analysis.genotype_encoder.GenotypeEncoder attribute) (snpio.analysis.tree_parser.TreeParser attribute) (snpio.filtering.nremover2.NRemover2 attribute) (snpio.GenotypeEncoder attribute) (snpio.io.phylip_reader.PhylipReader attribute) (snpio.io.vcf_reader.VCFReader attribute) (snpio.NRemover2 attribute) (snpio.PhylipReader attribute) (snpio.Plotting attribute) (snpio.plotting.plotting.Plotting attribute) (snpio.TreeParser attribute) (snpio.VCFReader attribute)