Index

A

aafreqsFromAlignment() (in module dms_tools2.prefs) aaSubstitutions() (dms_tools2.seqnumbering.TranscriptConverter method) additional() (dms_tools2.minimap2.Alignment property) adjustErrorCounts() (in module dms_tools2.utils) Alignment (class in dms_tools2.minimap2) alignSeqs() (in module dms_tools2.pacbio) alignSubamplicon() (in module dms_tools2.utils)

almost_duplicated() (in module dms_tools2.barcodes) annotateCodonCounts() (in module dms_tools2.utils) atomDist() (in module dms_tools2.protstruct) AugmentedPairGrid (class in dms_tools2.plot) avgMutDiffSel() (in module dms_tools2.diffsel) avgMutFracSurvive() (in module dms_tools2.fracsurvive) avgPrefs() (in module dms_tools2.prefs) ax_lims_clip_outliers() (dms_tools2.plot.AugmentedPairGrid method)

B

barcodeInfoToCodonVariantTable() (in module dms_tools2.utils) batch_bcsubampParser() (in module dms_tools2.parseargs) batch_diffselParser() (in module dms_tools2.parseargs) batch_fracsurviveParser() (in module dms_tools2.parseargs) batch_prefsParser() (in module dms_tools2.parseargs)

bcsubampParentParser() (in module dms_tools2.parseargs) bcsubampParser() (in module dms_tools2.parseargs) beta_diversity() (in module dms_tools2.diffsel) breaksAndLabels() (in module dms_tools2.plot) buildReadConsensus() (in module dms_tools2.utils)

C

call() (dms_tools2.minimap2.MutationCaller method) (dms_tools2.minimap2.TargetVariants method) (dms_tools2.pacbio.TerminiVariantTagCaller method) callConsensus() (dms_tools2.minimap2.MutationConsensus method) CCS (class in dms_tools2.pacbio) checkAlignment() (in module dms_tools2.minimap2) checkName() (in module dms_tools2.parseargs) checkTagNucleotides() (dms_tools2.pacbio.TerminiVariantTagCaller method) cigar_str() (dms_tools2.minimap2.Alignment property) cigarToQueryAndTarget() (in module dms_tools2.minimap2)

codon_to_nt_counts() (in module dms_tools2.utils) codonEvolAccessibility() (in module dms_tools2.utils) codonToAACounts() (in module dms_tools2.utils) COLOR_BLIND_PALETTE (in module dms_tools2.plot) COLOR_BLIND_PALETTE_GRAY (in module dms_tools2.plot) comparePrefs() (in module dms_tools2.compareprefs) computeMutDiffSel() (in module dms_tools2.diffsel) computeMutFracSurvive() (in module dms_tools2.fracsurvive) computeRMS() (in module dms_tools2.compareprefs) convertCountsFormat() (in module dms_tools2.utils)

D

deletions() (dms_tools2.minimap2.Mutations method) df_read_filecols() (in module dms_tools2.diffsel) diffselParentParser() (in module dms_tools2.parseargs) diffselParser() (in module dms_tools2.parseargs) distMatrix() (in module dms_tools2.protstruct) divJensenShannon() (in module dms_tools2.compareprefs) dms_tools2 (module) dms_tools2.barcodes (module) dms_tools2.compareprefs (module) dms_tools2.diffsel (module) dms_tools2.dssp (module)

dms_tools2.fracsurvive (module) dms_tools2.ipython_utils (module) dms_tools2.minimap2 (module) dms_tools2.pacbio (module) dms_tools2.parseargs (module) dms_tools2.plot (module) dms_tools2.prefs (module) dms_tools2.protstruct (module) dms_tools2.seqnumbering (module) dms_tools2.sra (module) dms_tools2.syn_selection (module) dms_tools2.utils (module)

F

fastqFromSRA() (in module dms_tools2.sra) findSigSel() (in module dms_tools2.plot) fracsurviveParentParser() (in module dms_tools2.parseargs)

fracsurviveParser() (in module dms_tools2.parseargs) from_str() (dms_tools2.minimap2.Mutations class method) from_white_cmap() (in module dms_tools2.plot)

G

getSubstitutions() (in module dms_tools2.utils)

H

hist_bins_intsafe() (in module dms_tools2.plot)

I

i_mRNAtoChromosome() (dms_tools2.seqnumbering.TranscriptConverter method) IlluminaBarcodeParser (class in dms_tools2.barcodes) incrementCounts() (in module dms_tools2.utils) inferPrefsByRatio() (in module dms_tools2.prefs) inferSitePrefs() (in module dms_tools2.prefs)

initLogger() (in module dms_tools2.utils) insertions() (dms_tools2.minimap2.Mutations method) intronsToGaps() (in module dms_tools2.minimap2) iTargetToQuery() (in module dms_tools2.minimap2) iteratePairedFASTQ() (in module dms_tools2.utils)

L

latexSciNot() (in module dms_tools2.plot)

logoplotParser() (in module dms_tools2.parseargs) lowQtoN() (in module dms_tools2.utils)

M

map() (dms_tools2.minimap2.Mapper method) Mapper (class in dms_tools2.minimap2) matchAndAlignCCS() (in module dms_tools2.pacbio) matchSeqs() (in module dms_tools2.pacbio) MAX_ASA_TIEN (in module dms_tools2.dssp)

mutateSeq() (in module dms_tools2.minimap2) MutationCaller (class in dms_tools2.minimap2) MutationConsensus (class in dms_tools2.minimap2) Mutations (class in dms_tools2.minimap2) mutToSiteDiffSel() (in module dms_tools2.diffsel) mutToSiteFracSurvive() (in module dms_tools2.fracsurvive)

N

ntIdentity() (dms_tools2.seqnumbering.TranscriptConverter method) nucleotides() (dms_tools2.pacbio.TerminiVariantTag property)

numAligned() (in module dms_tools2.minimap2) numExactMatches() (in module dms_tools2.minimap2)

O

OPTIONS_CODON_DMS (in module dms_tools2.minimap2)

OPTIONS_VIRUS_W_DEL (in module dms_tools2.minimap2)

P

parentParser() (in module dms_tools2.parseargs) parse() (dms_tools2.barcodes.IlluminaBarcodeParser method) parsePAF() (in module dms_tools2.minimap2) parserDescription() (in module dms_tools2.parseargs) plotBCStats() (in module dms_tools2.plot) plotCodonMutTypes() (in module dms_tools2.plot) plotColCorrs() (in module dms_tools2.plot) plotCorrMatrix() (in module dms_tools2.plot) plotCumulMutCounts() (in module dms_tools2.plot) plotDepth() (in module dms_tools2.plot) plotFacetedNeutCurves() (in module dms_tools2.plot) plotMutFreq() (in module dms_tools2.plot)

plotRarefactionCurves() (in module dms_tools2.plot) plotReadsPerBC() (in module dms_tools2.plot) plotReadStats() (in module dms_tools2.plot) plotSiteDiffSel() (in module dms_tools2.plot) prefDistance() (in module dms_tools2.compareprefs) prefsEntropy() (in module dms_tools2.prefs) prefsParentParser() (in module dms_tools2.parseargs) prefsParser() (in module dms_tools2.parseargs) prefsToMutEffects() (in module dms_tools2.prefs) prefsToMutFromWtEffects() (in module dms_tools2.prefs) PRIOR_MIN_VALUE (in module dms_tools2.prefs) processDSSP() (in module dms_tools2.dssp)

Q

q_en() (dms_tools2.minimap2.Alignment property) q_len() (dms_tools2.minimap2.Alignment property)

q_st() (dms_tools2.minimap2.Alignment property) qvalsToAccuracy() (in module dms_tools2.pacbio)

R

r_en() (dms_tools2.minimap2.Alignment property) r_len() (dms_tools2.minimap2.Alignment property) r_st() (dms_tools2.minimap2.Alignment property) rarefactionCurve() (in module dms_tools2.utils) re_expandIUPAC() (in module dms_tools2.pacbio)

removeCIGARmutations() (in module dms_tools2.minimap2) renumberSites() (in module dms_tools2.utils) rescalePrefs() (in module dms_tools2.prefs) residueDist() (in module dms_tools2.protstruct) reverseComplement() (in module dms_tools2.utils)

S

score() (dms_tools2.minimap2.Alignment property) sessionInfo() (in module dms_tools2.utils) shiftIndels() (in module dms_tools2.minimap2) showPDF() (in module dms_tools2.ipython_utils) sigFigStr() (in module dms_tools2.utils) simpleConsensus() (in module dms_tools2.barcodes) site() (dms_tools2.pacbio.TerminiVariantTag property)

StanModelDifferentErr (class in dms_tools2.prefs) StanModelNoneErr (class in dms_tools2.prefs) StanModelSameErr (class in dms_tools2.prefs) strand() (dms_tools2.minimap2.Alignment property) substitutions() (dms_tools2.minimap2.Mutations method) summarizeCCSreports() (in module dms_tools2.pacbio) syn_selection_by_codon() (in module dms_tools2.syn_selection)

T

target() (dms_tools2.minimap2.Alignment property) TargetVariants (class in dms_tools2.minimap2) termini() (dms_tools2.pacbio.TerminiVariantTag property) TerminiVariantTag (class in dms_tools2.pacbio)

TerminiVariantTagCaller (class in dms_tools2.pacbio) tidy_split() (in module dms_tools2.barcodes) tidyToWide() (in module dms_tools2.diffsel) TranscriptConverter (class in dms_tools2.seqnumbering) trimCigar() (in module dms_tools2.minimap2)

V

VALID_NTS (dms_tools2.barcodes.IlluminaBarcodeParser attribute)