Index

A

AABinarySequence (class in tools.BinarySequence) add() (tools.parsers.FastaTools.FastaFile method) (tools.parsers.FastqTools.FastqFile method) addField() (tools.parsers.CSVTools.CSVFile method)

addSource() (pyGeno.SNPFiltering.Sequence_modifiers method) AgnosticSNP (class in pyGeno.SNP) aux_insertTree() (in module tools.SegmentTree) aux_moveTree() (in module tools.SegmentTree)

B

backUpDB() (in module importation.Genomes) BinarySequence (class in tools.BinarySequence)

bootstrap module

C

CasavaSNP (class in pyGeno.SNP) catCSVs() (in module tools.parsers.CSVTools) Chromosome (class in pyGeno.Chromosome) Chromosome_Raba (class in pyGeno.Chromosome) ChrosomeSequence (class in pyGeno.Chromosome) close() (tools.parsers.VCFTools.VCFFile method) (tools.ProgressBar.ProgressBar method)

closeStreamToFile() (tools.parsers.CSVTools.CSVFile method) commit() (tools.parsers.CSVTools.CSVEntry method) commitLine() (tools.parsers.CSVTools.CSVFile method) complement() (in module tools.UsefulFunctions) complementTab() (in module tools.UsefulFunctions) count() (pyGeno.pyGenoObjectBases.pyGenoRabaObjectWrapper method) CSVEntry (class in tools.parsers.CSVTools) CSVFile (class in tools.parsers.CSVTools)

D

dbSNPSNP (class in pyGeno.SNP) decode() (tools.BinarySequence.BinarySequence method) decodePolymorphicNucleotide() (in module tools.UsefulFunctions) decodePolymorphicNucleotide_str() (in module tools.UsefulFunctions)

DefaultSNPFilter (class in pyGeno.SNPFiltering) deleteGenome() (in module importation.Genomes) deleteSNPs() (in module importation.SNPs) dropGlobalIndex() (pyGeno.pyGenoObjectBases.pyGenoRabaObjectWrapper class method)

E

emptyChildren() (tools.SegmentTree.SegmentTree method) EmptyLine encode() (tools.BinarySequence.BinarySequence method)

encodePolymorphicNucleotide() (in module tools.UsefulFunctions) ensureGlobalIndex() (pyGeno.pyGenoObjectBases.pyGenoRabaObjectWrapper class method) Exon (class in pyGeno.Exon) Exon_Raba (class in pyGeno.Exon)

F

FastaFile (class in tools.parsers.FastaTools) FastqEntry (class in tools.parsers.FastqTools) FastqFile (class in tools.parsers.FastqTools) filter() (pyGeno.SNPFiltering.DefaultSNPFilter method) find() (pyGeno.Exon.Exon method) (pyGeno.Protein.Protein method) (pyGeno.Transcript.Transcript method) (tools.BinarySequence.BinarySequence method) findAll() (in module tools.UsefulFunctions) (pyGeno.Exon.Exon method) (pyGeno.Protein.Protein method) (pyGeno.Transcript.Transcript method) (tools.BinarySequence.BinarySequence method) findAllByBiSearch() (tools.BinarySequence.BinarySequence method)

findAllIncDNA() (pyGeno.Transcript.Transcript method) findAllInCDS() (pyGeno.Exon.Exon method) findAllInUTR3() (pyGeno.Transcript.Transcript method) findAllInUTR5() (pyGeno.Transcript.Transcript method) findByBiSearch() (tools.BinarySequence.BinarySequence method) findIncDNA() (pyGeno.Transcript.Transcript method) findInCDS() (pyGeno.Exon.Exon method) findInUTR3() (pyGeno.Transcript.Transcript method) findInUTR5() (pyGeno.Transcript.Transcript method) findPolymorphisms() (tools.BinarySequence.BinarySequence method) findString() (pyGeno.Protein.Protein method) findStringAll() (pyGeno.Protein.Protein method) flatten() (tools.SegmentTree.SegmentTree method) flushIndexes() (pyGeno.pyGenoObjectBases.pyGenoRabaObjectWrapper class method) forceSet() (tools.SecureMmap.SecureMmap method)

G

Gene (class in pyGeno.Gene) Gene_Raba (class in pyGeno.Gene) Genome (class in pyGeno.Genome) Genome_Raba (class in pyGeno.Genome) get() (pyGeno.pyGenoObjectBases.pyGenoRabaObjectWrapper method) (tools.parsers.FastaTools.FastaFile method) (tools.parsers.FastqTools.FastqFile method) (tools.parsers.GTFTools.GTFFile method) get_transcripts() (tools.parsers.GTFTools.GTFFile method) getcDNALength() (pyGeno.Transcript.Transcript method) getCDSLength() (pyGeno.Exon.Exon method) getCodon() (pyGeno.Transcript.Transcript method) getDefaultSequence() (pyGeno.Protein.Protein method) (tools.BinarySequence.BinarySequence method) getFirstLevel() (tools.SegmentTree.SegmentTree method) getGenomeList() (in module pyGeno.Genome) getIndexedLength() (tools.SegmentTree.SegmentTree method) getIndexes() (pyGeno.pyGenoObjectBases.pyGenoRabaObjectWrapper class method)

getNbCodons() (pyGeno.Transcript.Transcript method) getNbVariants() (tools.BinarySequence.BinarySequence method) getNucleotideCodon() (in module tools.UsefulFunctions) (pyGeno.Transcript.Transcript method) getPolymorphisms() (pyGeno.Protein.Protein method) (tools.BinarySequence.BinarySequence method) getSequenceCombinaisons() (in module tools.UsefulFunctions) getSequencesData() (pyGeno.pyGenoObjectBases.pyGenoRabaObjectWrapper method) getSequenceVariants() (tools.BinarySequence.BinarySequence method) getSNPSetsList() (in module pyGeno.SNP) getUTR3Length() (pyGeno.Transcript.Transcript method) getUTR5Length() (pyGeno.Transcript.Transcript method) getX1() (tools.SegmentTree.SegmentTree method) getX2() (tools.SegmentTree.SegmentTree method) gtf2bed() (tools.parsers.GTFTools.GTFFile method) gtf2bed_cds() (tools.parsers.GTFTools.GTFFile method) gtf2bed_exons() (tools.parsers.GTFTools.GTFFile method) gtf2bed_transcripts() (tools.parsers.GTFTools.GTFFile method) GTFFile (class in tools.parsers.GTFTools)

H

hasCDS() (pyGeno.Exon.Exon method)

help() (pyGeno.pyGenoObjectBases.pyGenoRabaObjectWrapper class method) highlightSubsequence() (in module tools.UsefulFunctions)

I

importation.Genomes module importation.SNPs module importGenome() (in module bootstrap) (in module importation.Genomes) importRemoteGenome() (in module bootstrap) importRemoteSNPs() (in module bootstrap)

importSNPs() (in module bootstrap) (in module importation.SNPs) insert() (tools.SegmentTree.SegmentTree method) insertLine() (tools.parsers.CSVTools.CSVFile method) insertTree() (tools.SegmentTree.SegmentTree method) intersect() (tools.SegmentTree.SegmentTree method) iterCodons() (pyGeno.Transcript.Transcript method) iterGet() (pyGeno.pyGenoObjectBases.pyGenoRabaObjectWrapper method)

J

joinCSVs() (in module tools.parsers.CSVTools)

L

listDatawraps() (in module bootstrap)

listRemoteDatawraps() (in module bootstrap) log() (tools.ProgressBar.ProgressBar method)

M

module bootstrap importation.Genomes importation.SNPs pyGeno.Chromosome pyGeno.Exon pyGeno.Gene pyGeno.Genome pyGeno.Protein pyGeno.pyGenoObjectBases pyGeno.SNP pyGeno.SNPFiltering pyGeno.Transcript tools.BinarySequence tools.parsers.CasavaTools tools.parsers.CSVTools tools.parsers.FastaTools tools.parsers.FastqTools tools.parsers.GTFTools tools.parsers.VCFTools tools.ProgressBar tools.SecureMmap tools.SegmentTree tools.UsefulFunctions

move() (tools.SegmentTree.SegmentTree method)

N

newEntry() (tools.parsers.FastqTools.FastqFile method) newLine() (tools.parsers.CSVTools.CSVFile method)

nextExon() (pyGeno.Exon.Exon method) NucBinarySequence (class in tools.BinarySequence)

P

parse() (tools.parsers.CSVTools.CSVFile method) (tools.parsers.VCFTools.VCFFile method) parseFile() (tools.parsers.FastaTools.FastaFile method) (tools.parsers.FastqTools.FastqFile method) parseStr() (tools.parsers.FastaTools.FastaFile method) (tools.parsers.FastqTools.FastqFile method) pluck() (pyGeno.Exon.Exon method) polymorphicCodonCombinaisons() (in module tools.UsefulFunctions) previousExon() (pyGeno.Exon.Exon method) printDatawraps() (in module bootstrap) printRemoteDatawraps() (in module bootstrap) ProgressBar (class in tools.ProgressBar) Protein (class in pyGeno.Protein) Protein_Raba (class in pyGeno.Protein) pyGeno.Chromosome module pyGeno.Exon module

pyGeno.Gene module pyGeno.Genome module pyGeno.Protein module pyGeno.pyGenoObjectBases module pyGeno.SNP module pyGeno.SNPFiltering module pyGeno.Transcript module pyGenoRabaObject (class in pyGeno.pyGenoObjectBases) pyGenoRabaObjectWrapper (class in pyGeno.pyGenoObjectBases) pyGenoRabaObjectWrapper_metaclass (class in pyGeno.pyGenoObjectBases)

R

removeDuplicates() (in module tools.parsers.CSVTools) removeGaps() (tools.SegmentTree.SegmentTree method) reset() (tools.parsers.CasavaTools.SNPsTxtFile method) (tools.parsers.FastaTools.FastaFile method) (tools.parsers.FastqTools.FastqFile method)

reverseComplement() (in module tools.UsefulFunctions) reverseComplementTab() (in module tools.UsefulFunctions) RLWrapper (class in pyGeno.pyGenoObjectBases)

S

save() (pyGeno.pyGenoObjectBases.pyGenoRabaObject method) (tools.parsers.CSVTools.CSVFile method) (tools.parsers.FastaTools.FastaFile method) saveLogs() (tools.ProgressBar.ProgressBar method) SecureMmap (class in tools.SecureMmap) SegmentTree (class in tools.SegmentTree) Sequence_modifiers (class in pyGeno.SNPFiltering) SequenceDel (class in pyGeno.SNPFiltering)

SequenceInsert (class in pyGeno.SNPFiltering) SequenceSNP (class in pyGeno.SNPFiltering) showDifferences() (in module tools.UsefulFunctions) SNP_INDEL (class in pyGeno.SNP) SNPFilter (class in pyGeno.SNPFiltering) SNPMaster (class in pyGeno.SNP) SNPsTxtEntry (class in tools.parsers.CasavaTools) SNPsTxtFile (class in tools.parsers.CasavaTools) streamToFile() (tools.parsers.CSVTools.CSVFile method)

T

tools.BinarySequence module tools.parsers.CasavaTools module tools.parsers.CSVTools module tools.parsers.FastaTools module tools.parsers.FastqTools module tools.parsers.GTFTools module tools.parsers.VCFTools module

tools.ProgressBar module tools.SecureMmap module tools.SegmentTree module tools.UsefulFunctions module TopHatSNP (class in pyGeno.SNP) toStr() (tools.parsers.CSVTools.CSVFile method) (tools.parsers.FastaTools.FastaFile method) Transcript (class in pyGeno.Transcript) Transcript_Raba (class in pyGeno.Transcript) translateDNA() (in module tools.UsefulFunctions) translateDNA_6Frames() (in module tools.UsefulFunctions)

U

UnknownNucleotide

update() (tools.ProgressBar.ProgressBar method)

V

VCFEntry (class in tools.parsers.VCFTools)

VCFFile (class in tools.parsers.VCFTools)