Index

A

AA_TO_CODONS (in module dms_variants.constants) AA_TO_CODONS_WITHGAP (in module dms_variants.constants) aas (dms_variants.codonvarianttable.CodonVariantTable attribute) AAS_NOSTOP (in module dms_variants.constants) AAS_WITHSTOP (in module dms_variants.constants) AAS_WITHSTOP_WITHGAP (in module dms_variants.constants) AbstractEpistasis (class in dms_variants.globalepistasis) add_frac_counts() (dms_variants.codonvarianttable.CodonVariantTable class method)

add_full_seqs() (dms_variants.codonvarianttable.CodonVariantTable method) add_phenotypes_to_df() (dms_variants.globalepistasis.AbstractEpistasis method) add_sample_counts_df() (dms_variants.codonvarianttable.CodonVariantTable method) addMergedLibraries() (dms_variants.codonvarianttable.CodonVariantTable static method) addSampleCounts() (dms_variants.codonvarianttable.CodonVariantTable method) aic (dms_variants.globalepistasis.AbstractEpistasis property) alpha_ms() (dms_variants.globalepistasis.MonotonicSplineEpistasis method) avgCountsPerVariant() (dms_variants.codonvarianttable.CodonVariantTable method)

B

barcode_variant_df (dms_variants.codonvarianttable.CodonVariantTable attribute) bc_orientation (dms_variants.illuminabarcodeparser.IlluminaBarcodeParser attribute) bclen (dms_variants.illuminabarcodeparser.IlluminaBarcodeParser attribute)

binarymap (dms_variants.globalepistasis.AbstractEpistasis property) bottleneck (dms_variants.globalepistasis.BottleneckLikelihood property) BottleneckLikelihood (class in dms_variants.globalepistasis)

C

c_alpha() (dms_variants.globalepistasis.MonotonicSplineEpistasis method) CauchyLikelihood (class in dms_variants.globalepistasis) CBPALETTE (in module dms_variants.constants) chastity_filter (dms_variants.illuminabarcodeparser.IlluminaBarcodeParser attribute) classifyVariants() (dms_variants.codonvarianttable.CodonVariantTable static method) codon_muts() (in module dms_variants.simulate) CODON_TO_AA (in module dms_variants.constants)

CODON_TO_AA_WITHGAP (in module dms_variants.constants) codons (dms_variants.codonvarianttable.CodonVariantTable attribute) CODONS (in module dms_variants.constants) CODONS_NOSTOP (in module dms_variants.constants) CODONS_WITHGAP (in module dms_variants.constants) codonToAAMuts() (dms_variants.codonvarianttable.CodonVariantTable class method) CodonVariantTable (class in dms_variants.codonvarianttable) cumul_rows_by_count() (in module dms_variants.utils)

D

dI_dx() (dms_variants.ispline.Isplines method) dItotal_dw_lower() (dms_variants.ispline.Isplines_total method) dItotal_dweights() (dms_variants.ispline.Isplines_total method) dItotal_dx() (dms_variants.ispline.Isplines_total method) dM_dx() (dms_variants.ispline.Msplines method) dms_variants module dms_variants.barcodes module dms_variants.bottlenecks module dms_variants.codonvarianttable module dms_variants.constants module dms_variants.fastq module

dms_variants.globalepistasis module dms_variants.illuminabarcodeparser module dms_variants.ispline module dms_variants.pdb_utils module dms_variants.plotnine_themes module dms_variants.simulate module dms_variants.utils module downstream (dms_variants.illuminabarcodeparser.IlluminaBarcodeParser attribute) downstream2 (dms_variants.illuminabarcodeparser.IlluminaBarcodeParser attribute) downstream2_mismatch (dms_variants.illuminabarcodeparser.IlluminaBarcodeParser attribute) downstream_mismatch (dms_variants.illuminabarcodeparser.IlluminaBarcodeParser attribute)

E

enrichments() (dms_variants.globalepistasis.AbstractEpistasis method) epistasis_func() (dms_variants.globalepistasis.AbstractEpistasis method) (dms_variants.globalepistasis.MonotonicSplineEpistasis method) (dms_variants.globalepistasis.NoEpistasis method)

epistasis_func_params_dict (dms_variants.globalepistasis.AbstractEpistasis property) EpistasisFittingError EpistasisFittingWarning escape_scores() (dms_variants.codonvarianttable.CodonVariantTable method) estimateBottleneck() (in module dms_variants.bottlenecks)

F

f_post (dms_variants.globalepistasis.BottleneckLikelihood property) f_pre (dms_variants.globalepistasis.BottleneckLikelihood property) filter_by_subs_observed() (in module dms_variants.codonvarianttable)

fit() (dms_variants.globalepistasis.AbstractEpistasis method) fit_models() (in module dms_variants.globalepistasis) from_variant_count_df() (dms_variants.codonvarianttable.CodonVariantTable class method) func_scores() (dms_variants.codonvarianttable.CodonVariantTable method)

G

GaussianLikelihood (class in dms_variants.globalepistasis)

geneseq (dms_variants.codonvarianttable.CodonVariantTable attribute)

I

I() (dms_variants.ispline.Isplines method) IlluminaBarcodeParser (class in dms_variants.illuminabarcodeparser) integer_breaks() (in module dms_variants.utils) inverse_simpson_index() (in module dms_variants.barcodes)

Isplines (class in dms_variants.ispline) Isplines_total (class in dms_variants.ispline) iterate_fastq() (in module dms_variants.fastq) iterate_fastq_pair() (in module dms_variants.fastq) Itotal() (dms_variants.ispline.Isplines_total method)

J

j (dms_variants.ispline.Isplines property)

K

knots (dms_variants.ispline.Msplines attribute)

L

latent_effects_df (dms_variants.globalepistasis.AbstractEpistasis property) latent_phenotype_wt() (dms_variants.globalepistasis.AbstractEpistasis method) latentPhenotype() (dms_variants.simulate.MultiLatentSigmoidPhenotypeSimulator method) (dms_variants.simulate.SigmoidPhenotypeSimulator method) latentToObserved() (dms_variants.simulate.SigmoidPhenotypeSimulator method) latex_sci_not() (in module dms_variants.utils) libraries (dms_variants.codonvarianttable.CodonVariantTable attribute) likelihood_calc_params_dict (dms_variants.globalepistasis.AbstractEpistasis property)

list_all_valid_barcodes (dms_variants.illuminabarcodeparser.IlluminaBarcodeParser attribute) loglik (dms_variants.globalepistasis.AbstractEpistasis property) (dms_variants.globalepistasis.BottleneckLikelihood property) (dms_variants.globalepistasis.CauchyLikelihood property) (dms_variants.globalepistasis.GaussianLikelihood property) lower (dms_variants.ispline.Isplines attribute) (dms_variants.ispline.Isplines_total attribute) (dms_variants.ispline.Msplines attribute)

M

M() (dms_variants.ispline.Msplines method) mesh (dms_variants.ispline.Isplines attribute) (dms_variants.ispline.Isplines_total attribute) (dms_variants.ispline.Msplines attribute) minq (dms_variants.illuminabarcodeparser.IlluminaBarcodeParser attribute) module dms_variants dms_variants.barcodes dms_variants.bottlenecks dms_variants.codonvarianttable dms_variants.constants dms_variants.fastq dms_variants.globalepistasis dms_variants.illuminabarcodeparser dms_variants.ispline dms_variants.pdb_utils dms_variants.plotnine_themes dms_variants.simulate dms_variants.utils

MonotonicSplineEpistasis (class in dms_variants.globalepistasis) MonotonicSplineEpistasisBottleneckLikelihood (class in dms_variants.globalepistasis) MonotonicSplineEpistasisCauchyLikelihood (class in dms_variants.globalepistasis) MonotonicSplineEpistasisGaussianLikelihood (class in dms_variants.globalepistasis) Msplines (class in dms_variants.ispline) MultiLatentSigmoidPhenotypeSimulator (class in dms_variants.simulate) mutate_seq() (in module dms_variants.simulate) mutCounts() (dms_variants.codonvarianttable.CodonVariantTable method) muteffects (dms_variants.simulate.SigmoidPhenotypeSimulator attribute)

N

n (dms_variants.ispline.Isplines attribute) (dms_variants.ispline.Isplines_total attribute) (dms_variants.ispline.Msplines attribute) n_latent_phenotypes (dms_variants.globalepistasis.AbstractEpistasis property) (dms_variants.simulate.MultiLatentSigmoidPhenotypeSimulator attribute) n_variants_df() (dms_variants.codonvarianttable.CodonVariantTable method) NoEpistasis (class in dms_variants.globalepistasis) NoEpistasisBottleneckLikelihood (class in dms_variants.globalepistasis)

NoEpistasisCauchyLikelihood (class in dms_variants.globalepistasis) NoEpistasisGaussianLikelihood (class in dms_variants.globalepistasis) nparams (dms_variants.globalepistasis.AbstractEpistasis property) NT_COMPLEMENT (in module dms_variants.constants) NT_TO_REGEXP (in module dms_variants.constants) NTS (in module dms_variants.constants) NTS_AMBIGUOUS (in module dms_variants.constants) NTS_WITHGAP (in module dms_variants.constants) numCodonMutsByType() (dms_variants.codonvarianttable.CodonVariantTable method)

O

observedEnrichment() (dms_variants.simulate.MultiLatentSigmoidPhenotypeSimulator method) (dms_variants.simulate.SigmoidPhenotypeSimulator method) observedPhenotype() (dms_variants.simulate.MultiLatentSigmoidPhenotypeSimulator method) (dms_variants.simulate.SigmoidPhenotypeSimulator method)

order (dms_variants.ispline.Isplines attribute) (dms_variants.ispline.Isplines_total attribute) (dms_variants.ispline.Msplines attribute)

P

parse() (dms_variants.illuminabarcodeparser.IlluminaBarcodeParser method) phenotypes_df (dms_variants.globalepistasis.AbstractEpistasis property) phenotypes_frombinary() (dms_variants.globalepistasis.AbstractEpistasis method) plotAvgCountsPerVariant() (dms_variants.codonvarianttable.CodonVariantTable method) plotCountsPerVariant() (dms_variants.codonvarianttable.CodonVariantTable method) plotCumulMutCoverage() (dms_variants.codonvarianttable.CodonVariantTable method) plotCumulVariantCounts() (dms_variants.codonvarianttable.CodonVariantTable method) plotLatentVsObserved() (dms_variants.simulate.SigmoidPhenotypeSimulator method) plotMutFreqs() (dms_variants.codonvarianttable.CodonVariantTable method)

plotMutHeatmap() (dms_variants.codonvarianttable.CodonVariantTable method) plotMutsHistogram() (dms_variants.simulate.MultiLatentSigmoidPhenotypeSimulator method) (dms_variants.simulate.SigmoidPhenotypeSimulator method) plotNumCodonMutsByType() (dms_variants.codonvarianttable.CodonVariantTable method) plotNumMutsHistogram() (dms_variants.codonvarianttable.CodonVariantTable method) plotVariantSupportHistogram() (dms_variants.codonvarianttable.CodonVariantTable method) preferences() (dms_variants.globalepistasis.AbstractEpistasis method) primary_target (dms_variants.codonvarianttable.CodonVariantTable attribute) prob_escape() (dms_variants.codonvarianttable.CodonVariantTable method)

Q

qual_str_to_array() (in module dms_variants.fastq)

R

rand_seq() (in module dms_variants.simulate) rarefyBarcodes() (in module dms_variants.barcodes)

reassign_b_factor() (in module dms_variants.pdb_utils) reverse_complement() (in module dms_variants.utils)

S

samples() (dms_variants.codonvarianttable.CodonVariantTable method) scores_to_prefs() (in module dms_variants.utils) SigmoidPhenotypeSimulator (class in dms_variants.simulate) simulate_CodonVariantTable() (in module dms_variants.simulate) simulateSampleCounts() (in module dms_variants.simulate)

single_mut_effects() (dms_variants.globalepistasis.AbstractEpistasis method) SINGLE_NT_AA_MUTS (in module dms_variants.constants) single_nt_accessible() (in module dms_variants.utils) sites (dms_variants.codonvarianttable.CodonVariantTable attribute) subs_to_seq() (dms_variants.codonvarianttable.CodonVariantTable method)

T

theme_graygrid (class in dms_variants.plotnine_themes) tidy_split() (in module dms_variants.utils)

tidy_to_corr() (in module dms_variants.utils) translate() (in module dms_variants.utils)

U

upper (dms_variants.ispline.Isplines attribute) (dms_variants.ispline.Isplines_total attribute) (dms_variants.ispline.Msplines attribute)

upstream (dms_variants.illuminabarcodeparser.IlluminaBarcodeParser attribute) upstream2 (dms_variants.illuminabarcodeparser.IlluminaBarcodeParser attribute) upstream2_mismatch (dms_variants.illuminabarcodeparser.IlluminaBarcodeParser attribute) upstream_mismatch (dms_variants.illuminabarcodeparser.IlluminaBarcodeParser attribute)

V

valid_barcodes (dms_variants.illuminabarcodeparser.IlluminaBarcodeParser attribute) valid_barcodes() (dms_variants.codonvarianttable.CodonVariantTable method)

VALID_NTS (dms_variants.illuminabarcodeparser.IlluminaBarcodeParser attribute) variant_count_df (dms_variants.codonvarianttable.CodonVariantTable attribute)

W

writeCodonCounts() (dms_variants.codonvarianttable.CodonVariantTable method)

wt_latent (dms_variants.simulate.SigmoidPhenotypeSimulator attribute)

X

x (dms_variants.ispline.Isplines property) (dms_variants.ispline.Isplines_total property) (dms_variants.ispline.Msplines property)