Index

A

amplify (class in resimpy.pcr.Amplify) amplifyTransloc (class in resimpy.pcr.AmplifyTransloc)

amplRates() (resimpy.simulate.dispatcher.batch.General.general method) (resimpy.simulate.dispatcher.batch.UMI.umi method) (resimpy.simulate.dispatcher.batch.UMIDouble.umiDouble method)

B

binomial() (resimpy.util.random.Number.number method)

C

calling (class in resimpy.sequencing.Calling)

callingTransloc (class in resimpy.sequencing.CallingTransloc) choice() (resimpy.util.random.Number.number method)

D

design (class in resimpy.read.barcode.Design) (class in resimpy.read.seq.Design) (class in resimpy.read.spacer.Design) (class in resimpy.read.umi.Design)

E

epos() (resimpy.sequencing.Error.error method) (resimpy.sequencing.ErrorTransloc.errorTransloc method) epos2_deprecate() (resimpy.pcr.Error.error method) epos_deprecate() (resimpy.pcr.Error.error method) error (class in resimpy.pcr.Error) (class in resimpy.sequencing.Error)

errors() (resimpy.simulate.dispatcher.batch.UMI.umi method) errorTransloc (class in resimpy.pcr.ErrorTransloc) (class in resimpy.sequencing.ErrorTransloc) excel() (resimpy.util.file.read.Reader.reader method) (resimpy.util.file.write.Writer.writer method) (resimpy.util.sequence.fastq.Write.write method)

F

filter (class in resimpy.read.umi.Filter) filter1() (resimpy.util.sequence.convert.ManyToSingle.manyToSingle method) flow() (resimpy.pcr.Amplify.amplify method) (resimpy.pcr.AmplifyTransloc.amplifyTransloc method) (resimpy.sequencing.Calling.calling method) (resimpy.sequencing.CallingTransloc.callingTransloc method)

folder (class in resimpy.util.file.create.Folder)

G

gaussian() (resimpy.util.random.Sampling.sampling method) general (class in resimpy.simulate.dispatcher.batch.General) (class in resimpy.simulate.dispatcher.single.General) (class in resimpy.simulate.initiator.General) general() (resimpy.read.barcode.Design.design method) (resimpy.read.inf.Pseudo.pseudo method) (resimpy.read.seq.Design.design method) (resimpy.read.similarity.distance.Hamming.hamming method) (resimpy.read.spacer.Design.design method) (resimpy.read.umi.Design.design method)

generic() (resimpy.util.file.read.Reader.reader method) (resimpy.util.file.write.Writer.writer method) (resimpy.util.sequence.fastq.Write.write method) get() (resimpy.util.sequence.symbol.Single.single method) getEleTrimmed() (resimpy.util.sequence.symbol.Single.single method) getLisTrimmed() (resimpy.util.sequence.symbol.Single.single method) getTargetId() (resimpy.util.sequence.convert.ManyToSingle.manyToSingle method)

H

hamming (class in resimpy.read.similarity.distance.Hamming)

L

library (class in resimpy.read.umi.Library)

M

manyToSingle (class in resimpy.util.sequence.convert.ManyToSingle) method() (resimpy.read.umi.Filter.filter method) module resimpy resimpy.gmat resimpy.gspl resimpy.Path resimpy.pcr resimpy.pcr.Amplify resimpy.pcr.AmplifyTransloc resimpy.pcr.Error resimpy.pcr.ErrorTransloc resimpy.read resimpy.read.barcode resimpy.read.barcode.Design resimpy.read.inf resimpy.read.inf.Pseudo resimpy.read.primer resimpy.read.seq resimpy.read.seq.Design resimpy.read.seq.RuleOut resimpy.read.similarity resimpy.read.similarity.distance resimpy.read.similarity.distance.Hamming resimpy.read.spacer resimpy.read.spacer.Design resimpy.read.umi resimpy.read.umi.Design resimpy.read.umi.Filter resimpy.read.umi.Library resimpy.read.umi.RuleOut resimpy.sequencing resimpy.sequencing.Calling resimpy.sequencing.CallingTransloc resimpy.sequencing.Error resimpy.sequencing.ErrorTransloc resimpy.simulate resimpy.simulate.dispatcher resimpy.simulate.dispatcher.batch resimpy.simulate.dispatcher.batch.General resimpy.simulate.dispatcher.batch.UMI resimpy.simulate.dispatcher.batch.UMIDouble resimpy.simulate.dispatcher.single resimpy.simulate.dispatcher.single.General resimpy.simulate.dispatcher.single.UMI resimpy.simulate.dispatcher.single.UMIDouble resimpy.simulate.initiator resimpy.simulate.initiator.General resimpy.simulate.initiator.UMI resimpy.simulate.initiator.UMIDouble resimpy.util resimpy.util.file resimpy.util.file.create resimpy.util.file.create.Folder resimpy.util.file.read resimpy.util.file.read.Reader resimpy.util.file.write resimpy.util.file.write.Writer resimpy.util.random resimpy.util.random.Number resimpy.util.random.Ordering resimpy.util.random.Sampling resimpy.util.sequence resimpy.util.sequence.convert resimpy.util.sequence.convert.ManyToSingle resimpy.util.sequence.fasta resimpy.util.sequence.fastq resimpy.util.sequence.fastq.Write resimpy.util.sequence.symbol resimpy.util.sequence.symbol.Single

N

nbinomial() (resimpy.util.random.Number.number method) np() (resimpy.pcr.Amplify.amplify method) (resimpy.pcr.AmplifyTransloc.amplifyTransloc method) (resimpy.sequencing.Calling.calling method) (resimpy.sequencing.CallingTransloc.callingTransloc method)

number (class in resimpy.util.random.Number)

O

ondemand() (resimpy.simulate.dispatcher.single.UMI.umi method) ondemandAmplRates() (resimpy.simulate.dispatcher.single.General.general method) (resimpy.simulate.dispatcher.single.UMIDouble.umiDouble method) ondemandPCRErrs() (resimpy.simulate.dispatcher.single.General.general method) (resimpy.simulate.dispatcher.single.UMIDouble.umiDouble method) ondemandPCRNums() (resimpy.simulate.dispatcher.single.General.general method) (resimpy.simulate.dispatcher.single.UMIDouble.umiDouble method)

ondemandSeqErrs() (resimpy.simulate.dispatcher.single.General.general method) (resimpy.simulate.dispatcher.single.UMIDouble.umiDouble method) ondemandUMILens() (resimpy.simulate.dispatcher.single.General.general method) (resimpy.simulate.dispatcher.single.UMIDouble.umiDouble method) ordering (class in resimpy.util.random.Ordering) osmkdir() (resimpy.util.file.create.Folder.folder method)

P

paired() (resimpy.read.umi.Filter.filter method) paste() (resimpy.simulate.initiator.General.general method) (resimpy.simulate.initiator.UMI.umi method) (resimpy.simulate.initiator.UMIDouble.umiDouble method) pcrErrs() (resimpy.simulate.dispatcher.batch.General.general method) (resimpy.simulate.dispatcher.batch.UMI.umi method) (resimpy.simulate.dispatcher.batch.UMIDouble.umiDouble method) pcrNums() (resimpy.simulate.dispatcher.batch.General.general method) (resimpy.simulate.dispatcher.batch.UMI.umi method) (resimpy.simulate.dispatcher.batch.UMIDouble.umiDouble method) permute() (resimpy.util.random.Ordering.ordering method) poisson() (resimpy.util.random.Sampling.sampling method) pooling() (resimpy.simulate.initiator.General.general method) (resimpy.simulate.initiator.UMI.umi method) (resimpy.simulate.initiator.UMIDouble.umiDouble method)

postable() (resimpy.pcr.Error.error method) (resimpy.pcr.ErrorTransloc.errorTransloc method) (resimpy.sequencing.Error.error method) (resimpy.sequencing.ErrorTransloc.errorTransloc method) postable_deprecate() (resimpy.pcr.Error.error method) postableIndexBySameLen() (resimpy.pcr.Error.error method) (resimpy.pcr.ErrorTransloc.errorTransloc method) (resimpy.sequencing.Error.error method) (resimpy.sequencing.ErrorTransloc.errorTransloc method) postableLambda() (resimpy.pcr.Error.error method) (resimpy.pcr.ErrorTransloc.errorTransloc method) (resimpy.sequencing.Error.error method) (resimpy.sequencing.ErrorTransloc.errorTransloc method) pseudo (class in resimpy.read.inf.Pseudo)

R

reader (class in resimpy.util.file.read.Reader) reoccur() (resimpy.read.barcode.Design.design method) (resimpy.read.umi.Design.design method) resimpy module resimpy.gmat module resimpy.gspl module resimpy.Path module resimpy.pcr module resimpy.pcr.Amplify module resimpy.pcr.AmplifyTransloc module resimpy.pcr.Error module resimpy.pcr.ErrorTransloc module resimpy.read module resimpy.read.barcode module resimpy.read.barcode.Design module resimpy.read.inf module resimpy.read.inf.Pseudo module resimpy.read.primer module resimpy.read.seq module resimpy.read.seq.Design module resimpy.read.seq.RuleOut module resimpy.read.similarity module resimpy.read.similarity.distance module resimpy.read.similarity.distance.Hamming module resimpy.read.spacer module resimpy.read.spacer.Design module resimpy.read.umi module resimpy.read.umi.Design module resimpy.read.umi.Filter module resimpy.read.umi.Library module resimpy.read.umi.RuleOut module resimpy.sequencing module resimpy.sequencing.Calling module resimpy.sequencing.CallingTransloc module resimpy.sequencing.Error module resimpy.sequencing.ErrorTransloc module resimpy.simulate module

resimpy.simulate.dispatcher module resimpy.simulate.dispatcher.batch module resimpy.simulate.dispatcher.batch.General module resimpy.simulate.dispatcher.batch.UMI module resimpy.simulate.dispatcher.batch.UMIDouble module resimpy.simulate.dispatcher.single module resimpy.simulate.dispatcher.single.General module resimpy.simulate.dispatcher.single.UMI module resimpy.simulate.dispatcher.single.UMIDouble module resimpy.simulate.initiator module resimpy.simulate.initiator.General module resimpy.simulate.initiator.UMI module resimpy.simulate.initiator.UMIDouble module resimpy.util module resimpy.util.file module resimpy.util.file.create module resimpy.util.file.create.Folder module resimpy.util.file.read module resimpy.util.file.read.Reader module resimpy.util.file.write module resimpy.util.file.write.Writer module resimpy.util.random module resimpy.util.random.Number module resimpy.util.random.Ordering module resimpy.util.random.Sampling module resimpy.util.sequence module resimpy.util.sequence.convert module resimpy.util.sequence.convert.ManyToSingle module resimpy.util.sequence.fasta module resimpy.util.sequence.fastq module resimpy.util.sequence.fastq.Write module resimpy.util.sequence.symbol module resimpy.util.sequence.symbol.Single module root_dict() (in module resimpy.Path) ruleOut (class in resimpy.read.seq.RuleOut) (class in resimpy.read.umi.RuleOut) run() (in module resimpy.simulate.dispatcher.batch.General) (in module resimpy.simulate.dispatcher.batch.UMIDouble)

S

sampling (class in resimpy.util.random.Sampling) save() (resimpy.util.sequence.convert.ManyToSingle.manyToSingle method) seqErrs() (resimpy.simulate.dispatcher.batch.General.general method) (resimpy.simulate.dispatcher.batch.UMI.umi method) (resimpy.simulate.dispatcher.batch.UMIDouble.umiDouble method)

sequential() (resimpy.read.seq.RuleOut.ruleOut method) (resimpy.read.umi.RuleOut.ruleOut method) shuffle() (resimpy.util.random.Ordering.ordering method) single (class in resimpy.util.sequence.symbol.Single) singleStart() (resimpy.read.umi.Filter.filter method) svid() (resimpy.util.sequence.convert.ManyToSingle.manyToSingle method)

T

tactic1() (resimpy.pcr.Error.error method) (resimpy.sequencing.Error.error method) (resimpy.sequencing.ErrorTransloc.errorTransloc method) to() (in module resimpy.Path) todict() (resimpy.pcr.Error.error method) (resimpy.pcr.ErrorTransloc.errorTransloc method) (resimpy.sequencing.Error.error method) (resimpy.sequencing.ErrorTransloc.errorTransloc method) (resimpy.util.sequence.symbol.Single.single method)

todict5() (resimpy.pcr.Error.error method) (resimpy.pcr.ErrorTransloc.errorTransloc method) togz() (resimpy.util.sequence.fastq.Write.write method) trim() (resimpy.util.sequence.symbol.Single.single static method)

U

umi (class in resimpy.simulate.dispatcher.batch.UMI) (class in resimpy.simulate.dispatcher.single.UMI) (class in resimpy.simulate.initiator.UMI) umi_len (resimpy.simulate.initiator.General.general property) (resimpy.simulate.initiator.UMI.umi property) (resimpy.simulate.initiator.UMIDouble.umiDouble property) umiDouble (class in resimpy.simulate.dispatcher.batch.UMIDouble) (class in resimpy.simulate.dispatcher.single.UMIDouble) (class in resimpy.simulate.initiator.UMIDouble)

umiLens() (resimpy.simulate.dispatcher.batch.General.general method) (resimpy.simulate.dispatcher.batch.UMI.umi method) (resimpy.simulate.dispatcher.batch.UMIDouble.umiDouble method) uniform() (resimpy.util.random.Number.number method) (resimpy.util.random.Sampling.sampling method)

W

worktable() (resimpy.pcr.Error.error method) (resimpy.pcr.ErrorTransloc.errorTransloc method) write (class in resimpy.util.sequence.fastq.Write)

write() (resimpy.read.barcode.Design.design method) (resimpy.read.umi.Design.design method) writer (class in resimpy.util.file.write.Writer)