Index

A

addOption() (pyokit.interface.cli.CLI method)

B

BEDIterator() (in module pyokit.io.bedIterators)

bucketIterator() (in module pyokit.datastruct.genomicInterval)

C

CLI (class in pyokit.interface.cli) clip_end() (pyokit.datastruct.sequence.Sequence method)

collapseRegions() (in module pyokit.datastruct.genomicInterval) copy() (pyokit.datastruct.sequence.Sequence method)

D

david_results_iterator() (in module pyokit.io.david)

distance() (pyokit.datastruct.genomicInterval.GenomicInterval method)

E

effective_len (pyokit.datastruct.sequence.Sequence attribute)

end (pyokit.datastruct.sequence.Sequence attribute)

F

fastaIterator() (in module pyokit.io.fastaIterators) fastqIterator() (in module pyokit.io.fastqIterators) fastqIteratorComplex() (in module pyokit.io.fastqIterators)

fastqIteratorSimple() (in module pyokit.io.fastqIterators) from_repeat_masker_string() (in module pyokit.datastruct.retrotransposon)

G

gapped_relative_subsequence() (pyokit.datastruct.sequence.Sequence method) GeneOntologyEnrichmentResult (class in pyokit.datastruct.geneOntology) GeneOntologyTerm (class in pyokit.datastruct.geneOntology) GenomicInterval (class in pyokit.datastruct.genomicInterval)

getAllArguments() (pyokit.interface.cli.CLI method) getArgument() (pyokit.interface.cli.CLI method) getOption() (pyokit.interface.cli.CLI method) getValue() (pyokit.interface.cli.CLI method)

H

hasArgument() (pyokit.interface.cli.CLI method)

hasOption() (pyokit.interface.cli.CLI method)

I

intersectingInterval() (pyokit.datastruct.intervalTree.IntervalTree method) intersectingIntervalIterator() (pyokit.datastruct.intervalTree.IntervalTree method) intersectingPoint() (pyokit.datastruct.intervalTree.IntervalTree method) intersects() (pyokit.datastruct.genomicInterval.GenomicInterval method) IntervalTree (class in pyokit.datastruct.intervalTree) intervalTrees() (in module pyokit.io.bedIterators) is_positive_strand() (pyokit.datastruct.sequence.Sequence method) isDNA() (pyokit.datastruct.sequence.Sequence method)

isLowQuality() (pyokit.datastruct.sequence.Sequence method) isNegativeStrand() (pyokit.datastruct.genomicInterval.GenomicInterval method) isPolyA() (pyokit.datastruct.sequence.Sequence method) isPolyT() (pyokit.datastruct.sequence.Sequence method) isPositiveStrand() (pyokit.datastruct.genomicInterval.GenomicInterval method) isRequired() (pyokit.interface.cli.Option method) isRNA() (pyokit.datastruct.sequence.Sequence method) isSet() (pyokit.interface.cli.Option method)

M

maskMatch() (pyokit.datastruct.sequence.Sequence method) maskRegion() (pyokit.datastruct.sequence.Sequence method)

maskRegions() (pyokit.datastruct.sequence.Sequence method) meta_data_to_string() (pyokit.datastruct.sequence.Sequence method)

N

nsLeft() (pyokit.datastruct.sequence.Sequence method)

nsRight() (pyokit.datastruct.sequence.Sequence method)

O

Option (class in pyokit.interface.cli)

optionIsSet() (pyokit.interface.cli.CLI method)

P

pairedBEDIterator() (in module pyokit.io.bedIterators) PairwiseAlignment (class in pyokit.datastruct.multipleAlignment)

parseCommandLine() (pyokit.interface.cli.CLI method) percentNuc() (pyokit.datastruct.sequence.Sequence method)

R

regionsIntersection() (in module pyokit.datastruct.genomicInterval) relative_subsequence() (pyokit.datastruct.sequence.Sequence method)

reverseComplement() (pyokit.datastruct.sequence.Sequence method)

S

s1 (pyokit.datastruct.multipleAlignment.PairwiseAlignment attribute) s2 (pyokit.datastruct.multipleAlignment.PairwiseAlignment attribute) sameRegion() (pyokit.datastruct.genomicInterval.GenomicInterval method) Sequence (class in pyokit.datastruct.sequence) signedDistance() (pyokit.datastruct.genomicInterval.GenomicInterval method) similarity() (pyokit.datastruct.sequence.Sequence method)

sizeOfOverlap() (pyokit.datastruct.genomicInterval.GenomicInterval method) split() (pyokit.datastruct.sequence.Sequence method) start (pyokit.datastruct.sequence.Sequence attribute) subsequence() (pyokit.datastruct.sequence.Sequence method) subtract() (pyokit.datastruct.genomicInterval.GenomicInterval method)

T

to_fasta_str() (pyokit.datastruct.sequence.Sequence method) toDNA() (pyokit.datastruct.sequence.Sequence method) toRNA() (pyokit.datastruct.sequence.Sequence method)

transform_center() (pyokit.datastruct.genomicInterval.GenomicInterval method) truncate() (pyokit.datastruct.sequence.Sequence method)

U

usage() (pyokit.interface.cli.CLI method)