API

• presto.Annotation
  • addHeader()
  • annotationConsensus()
  • collapseAnnotation()
  • collapseHeader()
  • convert454Header()
  • convertGenbankHeader()
  • convertGenericHeader()
  • convertIMGTHeader()
  • convertIlluminaHeader()
  • convertMIGECHeader()
  • convertSRAHeader()
  • copyHeader()
  • deleteHeader()
  • expandHeader()
  • flattenAnnotation()
  • getAnnotationValues()
  • getCoordKey()
  • mergeAnnotation()
  • mergeHeader()
  • parseAnnotation()
  • parseLog()
  • renameAnnotation()
  • renameHeader()
• presto.Applications
  • getMuscleVersion()
  • makeBlastnDb()
  • makeUBlastDb()
  • runBlastn()
  • runCDHit()
  • runMuscle()
  • runUBlast()
  • runUClust()
• presto.Commandline
  • CommonHelpFormatter
  • checkArgs()
  • getCommonArgParser()
  • parseCommonArgs()
• presto.IO
  • countSeqFile()
  • countSeqSets()
  • getFileType()
  • getOutputHandle()
  • printCount()
  • printDebug()
  • printError()
  • printLog()
  • printMessage()
  • printProgress()
  • printWarning()
  • readPrimerFile()
  • readReferenceFile()
  • readSeqFile()
• presto.Multiprocessing
  • SeqData
    • SeqData.id
    • SeqData.data
    • SeqData.valid
    • SeqData.__bool__()
    • SeqData.__len__()
  • SeqResult
    • SeqResult.id
    • SeqResult.data
    • SeqResult.results
    • SeqResult.valid
    • SeqResult.log
    • SeqResult.__bool__()
    • SeqResult.__len__()
    • SeqResult.data_count
  • collectPairQueue()
  • collectSeqQueue()
  • feedPairQueue()
  • feedSeqQueue()
  • manageProcesses()
  • processSeqQueue()
• presto.Sequence
  • AssemblyRecord
    • AssemblyRecord.overlap
  • AssemblyStats
  • PrimerAlignment
    • PrimerAlignment.__bool__()
    • PrimerAlignment.__len__()
  • alignAssembly()
  • calculateDiversity()
  • calculateSetError()
  • checkSeqEqual()
  • compilePrimers()
  • consensusUnify()
  • deleteSeqPositions()
  • deletionUnify()
  • extractAlignment()
  • filterLength()
  • filterMissing()
  • filterQuality()
  • filterRepeats()
  • findGapPositions()
  • frequencyConsensus()
  • getAAScoreDict()
  • getDNAScoreDict()
  • indexSeqSets()
  • joinAssembly()
  • localAlignment()
  • maskQuality()
  • maskSeq()
  • meanQuality()
  • overlapConsensus()
  • qualityConsensus()
  • referenceAssembly()
  • reverseComplement()
  • scoreAA()
  • scoreAlignment()
  • scoreDNA()
  • scoreSeqPair()
  • sequentialAssembly()
  • subsetSeqIndex()
  • subsetSeqSet()
  • translateAmbigDNA()
  • trimQuality()
  • weightSeq()