Index

_

__init__ (module)

A

AdjustErrorCounts() (in module utils) AlignprefixName() (in module parsearguments) AlignRead() (in module utils)

AlignSpecs() (in module parsearguments) AlignSubamplicon() (in module utils) ArgumentParserNoArgHelp (class in parsearguments) AvgMutRate() (in module utils)

B

BarcodedSubampliconsParser() (in module parsearguments)

Base10Formatter() (in module plot) BuildReadConsensus() (in module utils)

C

ChargeColorMapping() (in module weblogo) CheckReadQuality() (in module utils) ClassifyCodonCounts() (in module utils)

CodonMutsCumulFracs() (in module utils) CommaSeparatedFASTQFiles() (in module parsearguments) CorrelateParser() (in module parsearguments)

D

DiffSelectionParser() (in module parsearguments)

E

EditSitesParser() (in module parsearguments)

error() (parsearguments.ArgumentParserNoArgHelp method) ExistingFile() (in module parsearguments)

F

file_io (module) FloatBetweenHalfAndOne() (in module parsearguments)

FloatBetweenZeroAndOne() (in module parsearguments) FloatGreaterThanZero() (in module parsearguments) FunctionalGroupColorMapping() (in module weblogo)

I

InferDiffPrefsParser() (in module parsearguments) InferPrefsParser() (in module parsearguments) InferSiteDiffPreferencesFromEnrichmentRatios() (in module mcmc) InferSiteDiffPrefs() (in module mcmc)

InferSitePreferences() (in module mcmc) InferSitePreferencesFromEnrichmentRatios() (in module mcmc) IntGreaterEqual1() (in module parsearguments) IntGreaterEqual2() (in module parsearguments) IteratePairedFASTQ() (in module file_io)

K

KyteDoolittleColorMapping() (in module weblogo)

L

LogoOverlay() (in module weblogo)

LogoPlot() (in module weblogo) LogoPlotParser() (in module parsearguments)

M

MatchSubassembledBarcodesParser() (in module parsearguments) mcmc (module)

MergeParser() (in module parsearguments) MWColorMapping() (in module weblogo)

N

NaturalSort() (in module utils)

NonNegativeInt() (in module parsearguments)

P

parsearguments (module) ParseNSMutFreqBySite() (in module utils) PDF_File() (in module parsearguments) plot (module) PlotCorrelation() (in module plot) PlotDepth() (in module plot)

PlotMutCountFracs() (in module plot) PlotPairedMutFracs() (in module plot) PlotReadStarts() (in module plot) PlotSampleBargraphs() (in module plot) Pref_or_DiffPref() (in module utils) PrefsToEnrichments() (in module utils)

R

R2AlignSpecs() (in module parsearguments) ReadDiffPrefs() (in module file_io) ReadDMSCounts() (in module file_io) ReadMultipleDMSCountsFiles() (in module file_io) ReadMultiPrefOrDiffPref() (in module file_io)

ReadPreferences() (in module file_io) ReadSubassembledVariants() (in module file_io) ReadSummaryStats() (in module file_io) RemoveStopFromDiffPrefs() (in module utils) RemoveStopFromPreferences() (in module utils) RMS() (in module utils)

S

simulate (module) SimulateDiffPrefCounts() (in module simulate) SimulateLibraryCounts() (in module simulate) SiteEntropy() (in module utils) SmartHelpFormatter (class in parsearguments) StanModelDifferentErr (class in mcmc) StanModelDiffPrefNoErr (class in mcmc) StanModelDiffPrefSameErr (class in mcmc)

StanModelNoneErr (class in mcmc) StanModelSameErr (class in mcmc) Subassemble() (in module utils) SubassembleParser() (in module parsearguments) SumCodonToAA() (in module utils) SumCounts() (in module utils) SummarizeAlignmentsParser() (in module parsearguments) SumPrefsDiffPrefs() (in module utils)

T

TrimReads() (in module utils)

U

utils (module)

V

Versions() (in module file_io)

W

weblogo (module) WriteDiffPrefs() (in module file_io)

WriteDMSCounts() (in module file_io) WritePreferences() (in module file_io)