Everything
All Classes
core.AnalyseMapping.CustomRead
core.AnalyseMapping.ReadID
core.AnalyseMapping.TPRead
All Functions
core.AnalyseMapping.CheckForSameAlignments
core.AnalyseMapping.CompareAlignments
core.AnalyseMapping.ComputeRQScore
core.AnalyseMapping.CreateCompareList
core.AnalyseMapping.GetCompletePath
core.AnalyseMapping.GetOrderDictionary
core.AnalyseMapping.ReadArtificialSAMfileHTSeq
core.AnalyseMapping.ReadFromTab
core.AnalyseMapping.ReadSAMnoMem
core.AnalyseMapping.SkipHeader
core.AnalyseMapping.extendReadDic
core.AnalyseMapping.getAlignmentLength
core.AnalyseMapping.getAllID
core.AnalyseMapping.getCustomRead
core.AnalyseMapping.getHammingdistance
core.AnalyseMapping.getMisGap
core.AnalyseMapping.getNextLine
core.AnalyseMapping.getNumberOf
core.AnalyseMapping.getRanks
core.AnalyseMapping.getTPRead
core.AnalyseMapping.getmean
core.AnalyseMapping.getsum
core.AnalyseMapping.initOutFiles
core.AnalyseMapping.isSaneAlignment
core.AnalyseMapping.loadpickle
core.AnalyseMapping.readInput
core.AnalyseMapping.readReadQualities
core.AnalyseMapping.readSAMline
core.AnalyseMapping.returnIndex
core.AnalyseMapping.returnSequence
core.AnalyseMapping.savepickle
core.AnalyseMapping.writeToTabArt
core.AnalyseMapping.writeToTabRef
core.FindOrfs.build_ORF
core.FindOrfs.find_orfs
core.FindOrfs.findstop_help
core.InsertMutations.getMutation
core.InsertMutations.getdifference
core.InsertMutations.isvalidposition
core.InsertMutations.mutate_random
core.PlotData.CalculateRoc2
core.PlotData.plotOverviewHist
core.PlotData.trapezoidal_rule
core.Prep.createdic
core.Prep.isvalidtriplet
core.Prep.loadpickle
core.Prep.savepickle
core.Prep.trans_seq
core.ReadAndWrite.aa_dist_seq
core.ReadAndWrite.gethammingdistance
core.ReadAndWrite.nucleotide_dist_file
core.ReadAndWrite.nucleotide_dist_seq
core.ReadAndWrite.readdna
core.ReadAndWrite.writefile
core.ReadAndWrite.writeoverview
script-arden_analyze.TestFiles
script-arden_analyze.main
script-arden_create.Create
script-arden_create.printExample
script-arden_filter.FilterSAM
script-arden_filter.filter
script-arden_filter.getMisGapRQ
script-arden_filter.readHeader
script-arden_filter.writeFilteredReads
All Variables
core.AnalyseMapping.AlignedReadsdic
core.AnalyseMapping.__package__
core.AnalyseMapping.algnedToArt
core.AnalyseMapping.algnedToRef
core.AnalyseMapping.alngts
core.FindOrfs.__package__
core.InsertMutations.__package__
core.PlotData.__package__
core.Prep.__package__
core.Prep.genetic_code
core.ReadAndWrite.__package__
core.__package__
script-arden_analyze.__package__
script-arden_create.a
script-arden_create.b
script-arden_create.bases
script-arden_filter.__package__
script-arden_filter.counter1
script-arden_filter.counter2
[hide private]