dms_variants package

dms_variants

Python package for analyzing deep mutational scanning of barcoded variants of genes.

Submodules

• barcodes
• inverse_simpson_index()
• rarefyBarcodes()
• bottlenecks
• estimateBottleneck()
• codonvarianttable
• CodonVariantTable
  • CodonVariantTable.geneseq
  • CodonVariantTable.sites
  • CodonVariantTable.codons
  • CodonVariantTable.aas
  • CodonVariantTable.libraries
  • CodonVariantTable.barcode_variant_df
  • CodonVariantTable.variant_count_df
  • CodonVariantTable.primary_target
  • CodonVariantTable.addMergedLibraries()
  • CodonVariantTable.addSampleCounts()
  • CodonVariantTable.add_frac_counts()
  • CodonVariantTable.add_full_seqs()
  • CodonVariantTable.add_sample_counts_df()
  • CodonVariantTable.avgCountsPerVariant()
  • CodonVariantTable.classifyVariants()
  • CodonVariantTable.codonToAAMuts()
  • CodonVariantTable.escape_scores()
  • CodonVariantTable.from_variant_count_df()
  • CodonVariantTable.func_scores()
  • CodonVariantTable.mutCounts()
  • CodonVariantTable.n_variants_df()
  • CodonVariantTable.numCodonMutsByType()
  • CodonVariantTable.plotAvgCountsPerVariant()
  • CodonVariantTable.plotCountsPerVariant()
  • CodonVariantTable.plotCumulMutCoverage()
  • CodonVariantTable.plotCumulVariantCounts()
  • CodonVariantTable.plotMutFreqs()
  • CodonVariantTable.plotMutHeatmap()
  • CodonVariantTable.plotNumCodonMutsByType()
  • CodonVariantTable.plotNumMutsHistogram()
  • CodonVariantTable.plotVariantSupportHistogram()
  • CodonVariantTable.prob_escape()
  • CodonVariantTable.samples()
  • CodonVariantTable.subs_to_seq()
  • CodonVariantTable.valid_barcodes()
  • CodonVariantTable.writeCodonCounts()
• filter_by_subs_observed()
• constants
• AAS_NOSTOP
• AAS_WITHSTOP
• AAS_WITHSTOP_WITHGAP
• AA_TO_CODONS
• AA_TO_CODONS_WITHGAP
• CBPALETTE
• CODONS
• CODONS_NOSTOP
• CODONS_WITHGAP
• CODON_TO_AA
• CODON_TO_AA_WITHGAP
• NTS
• NTS_AMBIGUOUS
• NTS_WITHGAP
• NT_COMPLEMENT
• NT_TO_REGEXP
• SINGLE_NT_AA_MUTS
• fastq
• iterate_fastq()
• iterate_fastq_pair()
• qual_str_to_array()
• globalepistasis
  • Global epistasis function
    • No epistasis function
    • Monotonic spline epistasis function
    • Multiple latent phenotypes
  • Likelihood calculation
    • Gaussian likelihood
    • Cauchy likelihood
    • Bottleneck likelihood
  • The model classes
  • Details of fitting
    • Fitting workflow
    • Fitting multiple latent phenotypes
    • Conveniently fitting and comparing several models
    • Vector representation of \(\beta_{\rm{wt}}\)
    • Optimization
    • Gradients used in optimization
  • Detailed documentation of models
• AbstractEpistasis
  • AbstractEpistasis.add_phenotypes_to_df()
  • AbstractEpistasis.aic
  • AbstractEpistasis.binarymap
  • AbstractEpistasis.enrichments()
  • AbstractEpistasis.epistasis_func()
  • AbstractEpistasis.epistasis_func_params_dict
  • AbstractEpistasis.fit()
  • AbstractEpistasis.latent_effects_df
  • AbstractEpistasis.latent_phenotype_wt()
  • AbstractEpistasis.likelihood_calc_params_dict
  • AbstractEpistasis.loglik
  • AbstractEpistasis.n_latent_phenotypes
  • AbstractEpistasis.nparams
  • AbstractEpistasis.phenotypes_df
  • AbstractEpistasis.phenotypes_frombinary()
  • AbstractEpistasis.preferences()
  • AbstractEpistasis.single_mut_effects()
• BottleneckLikelihood
  • BottleneckLikelihood.bottleneck
  • BottleneckLikelihood.f_post
  • BottleneckLikelihood.f_pre
  • BottleneckLikelihood.loglik
• CauchyLikelihood
  • CauchyLikelihood.loglik
• EpistasisFittingError
• EpistasisFittingWarning
• GaussianLikelihood
  • GaussianLikelihood.loglik
• MonotonicSplineEpistasis
  • MonotonicSplineEpistasis.alpha_ms()
  • MonotonicSplineEpistasis.c_alpha()
  • MonotonicSplineEpistasis.epistasis_func()
• MonotonicSplineEpistasisBottleneckLikelihood
• MonotonicSplineEpistasisCauchyLikelihood
• MonotonicSplineEpistasisGaussianLikelihood
• NoEpistasis
  • NoEpistasis.epistasis_func()
• NoEpistasisBottleneckLikelihood
• NoEpistasisCauchyLikelihood
• NoEpistasisGaussianLikelihood
• fit_models()
• illuminabarcodeparser
• IlluminaBarcodeParser
  • IlluminaBarcodeParser.bclen
  • IlluminaBarcodeParser.upstream
  • IlluminaBarcodeParser.upstream2
  • IlluminaBarcodeParser.downstream
  • IlluminaBarcodeParser.downstream2
  • IlluminaBarcodeParser.upstream_mismatch
  • IlluminaBarcodeParser.upstream2_mismatch
  • IlluminaBarcodeParser.downstream_mismatch
  • IlluminaBarcodeParser.downstream2_mismatch
  • IlluminaBarcodeParser.valid_barcodes
  • IlluminaBarcodeParser.bc_orientation
  • IlluminaBarcodeParser.minq
  • IlluminaBarcodeParser.chastity_filter
  • IlluminaBarcodeParser.list_all_valid_barcodes
  • IlluminaBarcodeParser.VALID_NTS
  • IlluminaBarcodeParser.parse()
• ispline
• Isplines
  • Isplines.order
  • Isplines.mesh
  • Isplines.n
  • Isplines.lower
  • Isplines.upper
  • Isplines.I()
  • Isplines.dI_dx()
  • Isplines.j
  • Isplines.x
• Isplines_total
  • Isplines_total.order
  • Isplines_total.mesh
  • Isplines_total.n
  • Isplines_total.lower
  • Isplines_total.upper
  • Isplines_total.Itotal()
  • Isplines_total.dItotal_dw_lower()
  • Isplines_total.dItotal_dweights()
  • Isplines_total.dItotal_dx()
  • Isplines_total.x
• Msplines
  • Msplines.order
  • Msplines.mesh
  • Msplines.n
  • Msplines.knots
  • Msplines.lower
  • Msplines.upper
  • Msplines.M()
  • Msplines.dM_dx()
  • Msplines.x
• pdb_utils
• reassign_b_factor()
• plotnine_themes
• theme_graygrid
• simulate
• MultiLatentSigmoidPhenotypeSimulator
  • MultiLatentSigmoidPhenotypeSimulator.n_latent_phenotypes
  • MultiLatentSigmoidPhenotypeSimulator.latentPhenotype()
  • MultiLatentSigmoidPhenotypeSimulator.observedEnrichment()
  • MultiLatentSigmoidPhenotypeSimulator.observedPhenotype()
  • MultiLatentSigmoidPhenotypeSimulator.plotMutsHistogram()
• SigmoidPhenotypeSimulator
  • SigmoidPhenotypeSimulator.wt_latent
  • SigmoidPhenotypeSimulator.muteffects
  • SigmoidPhenotypeSimulator.latentPhenotype()
  • SigmoidPhenotypeSimulator.latentToObserved()
  • SigmoidPhenotypeSimulator.observedEnrichment()
  • SigmoidPhenotypeSimulator.observedPhenotype()
  • SigmoidPhenotypeSimulator.plotLatentVsObserved()
  • SigmoidPhenotypeSimulator.plotMutsHistogram()
• codon_muts()
• mutate_seq()
• rand_seq()
• simulateSampleCounts()
• simulate_CodonVariantTable()
• utils
• cumul_rows_by_count()
• integer_breaks()
• latex_sci_not()
• reverse_complement()
• scores_to_prefs()
• single_nt_accessible()
• tidy_split()
• tidy_to_corr()
• translate()