Index

A | B | C | D | E | F | G | H | I | J | L | M | N | P | R | S | T | U | V

A

AABinarySequence (class in tools.BinarySequence)
add() (tools.parsers.FastaTools.FastaFile method)
(tools.parsers.FastqTools.FastqFile method)
addField() (tools.parsers.CSVTools.CSVFile method)
addSource() (SNPFiltering.Sequence_modifiers method)
AgnosticSNP (class in 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 SNP)
catCSVs() (in module tools.parsers.CSVTools)
Chromosome (class in Chromosome)
(module)
Chromosome_Raba (class in Chromosome)
ChrosomeSequence (class in 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)
count() (pyGenoObjectBases.pyGenoRabaObjectWrapper method)
CSVEntry (class in tools.parsers.CSVTools)
CSVFile (class in tools.parsers.CSVTools)

D

dbSNPSNP (class in SNP)
decode() (tools.BinarySequence.BinarySequence method)
decodePolymorphicNucleotide() (in module tools.UsefulFunctions)
decodePolymorphicNucleotide_str() (in module tools.UsefulFunctions)
DefaultSNPFilter (class in SNPFiltering)
deleteGenome() (in module importation.Genomes)
deleteSNPs() (in module importation.SNPs)
dropGlobalIndex() (pyGenoObjectBases.pyGenoRabaObjectWrapper class method)

E

emptyChildren() (tools.SegmentTree.SegmentTree method)
EmptyLine
encode() (tools.BinarySequence.BinarySequence method)
encodePolymorphicNucleotide() (in module tools.UsefulFunctions)
ensureGlobalIndex() (pyGenoObjectBases.pyGenoRabaObjectWrapper class method)
Exon (class in Exon)
(module)
Exon_Raba (class in Exon)

F

FastaFile (class in tools.parsers.FastaTools)
FastqEntry (class in tools.parsers.FastqTools)
FastqFile (class in tools.parsers.FastqTools)
filter() (SNPFiltering.DefaultSNPFilter method)
find() (Exon.Exon method)
(Protein.Protein method)
(Transcript.Transcript method)
(tools.BinarySequence.BinarySequence method)
findAll() (Exon.Exon method)
(Protein.Protein method)
(Transcript.Transcript method)
(in module tools.UsefulFunctions)
(tools.BinarySequence.BinarySequence method)
findAllIncDNA() (Transcript.Transcript method)
findAllInCDS() (Exon.Exon method)
findAllInUTR3() (Transcript.Transcript method)
findAllInUTR5() (Transcript.Transcript method)
findIncDNA() (Transcript.Transcript method)
findInCDS() (Exon.Exon method)
findInUTR3() (Transcript.Transcript method)
findInUTR5() (Transcript.Transcript method)
findPolymorphisms() (tools.BinarySequence.BinarySequence method)
findString() (Protein.Protein method)
findStringAll() (Protein.Protein method)
flatten() (tools.SegmentTree.SegmentTree method)
flushIndexes() (pyGenoObjectBases.pyGenoRabaObjectWrapper class method)
forceSet() (tools.SecureMmap.SecureMmap method)

G

Gene (class in Gene)
(module)
Gene_Raba (class in Gene)
Genome (class in Genome)
(module)
Genome_Raba (class in Genome)
get() (pyGenoObjectBases.pyGenoRabaObjectWrapper method)
(tools.parsers.FastaTools.FastaFile method)
(tools.parsers.FastqTools.FastqFile method)
(tools.parsers.GTFTools.GTFFile method)
getcDNALength() (Transcript.Transcript method)
getCDSLength() (Exon.Exon method)
getCodon() (Transcript.Transcript method)
getDefaultSequence() (Protein.Protein method)
(tools.BinarySequence.BinarySequence method)
getFirstLevel() (tools.SegmentTree.SegmentTree method)
getGenomeList() (in module Genome)
getIndexedLength() (tools.SegmentTree.SegmentTree method)
getIndexes() (pyGenoObjectBases.pyGenoRabaObjectWrapper class method)
getNbCodons() (Transcript.Transcript method)
getNbVariants() (tools.BinarySequence.BinarySequence method)
getNucleotideCodon() (in module tools.UsefulFunctions)
(Transcript.Transcript method)
getPolymorphisms() (Protein.Protein method)
(tools.BinarySequence.BinarySequence method)
getSequenceCombinaisons() (in module tools.UsefulFunctions)
getSequenceVariants() (tools.BinarySequence.BinarySequence method)
getSNPSetsList() (in module SNP)
getUTR3Length() (Transcript.Transcript method)
getUTR5Length() (Transcript.Transcript method)
getX1() (tools.SegmentTree.SegmentTree method)
getX2() (tools.SegmentTree.SegmentTree method)
GTFFile (class in tools.parsers.GTFTools)

H

hasCDS() (Exon.Exon method)
help() (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() (Transcript.Transcript method)
iterGet() (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

move() (tools.SegmentTree.SegmentTree method)

N

newEntry() (tools.parsers.FastqTools.FastqFile method)
newLine() (tools.parsers.CSVTools.CSVFile method)
nextExon() (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() (Exon.Exon method)
polymorphicCodonCombinaisons() (in module tools.UsefulFunctions)
previousExon() (Exon.Exon method)
printDatawraps() (in module bootstrap)
printRemoteDatawraps() (in module bootstrap)
ProgressBar (class in tools.ProgressBar)
Protein (class in Protein)
(module)
Protein_Raba (class in Protein)
pyGenoObjectBases (module)
pyGenoRabaObject (class in pyGenoObjectBases)
pyGenoRabaObjectWrapper (class in pyGenoObjectBases)
pyGenoRabaObjectWrapper_metaclass (class in 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)
RLWrapper (class in pyGenoObjectBases)

S

save() (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 SNPFiltering)
SequenceDel (class in SNPFiltering)
SequenceInsert (class in SNPFiltering)
SequenceSNP (class in SNPFiltering)
showDifferences() (in module tools.UsefulFunctions)
SNP (module)
SNP_INDEL (class in SNP)
SNPFilter (class in SNPFiltering)
SNPFiltering (module)
SNPMaster (class in 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 SNP)
toStr() (tools.parsers.CSVTools.CSVFile method)
(tools.parsers.FastaTools.FastaFile method)
Transcript (class in Transcript)
(module)
Transcript_Raba (class in Transcript)
translateDNA() (in module tools.UsefulFunctions)
translateDNA_6Frames() (in module tools.UsefulFunctions)

U

update() (tools.ProgressBar.ProgressBar method)

V

VCFEntry (class in tools.parsers.VCFTools)
VCFFile (class in tools.parsers.VCFTools)