Index

A

Accumulate() (in module Histogram) Add() (in module Histogram) add_option() (Experiment.OptionParser method) addAnnotation() (Mali.SequenceCollection method) AddComplementIntervalls() (in module Intervalls) (in module IntervallsWeighted) addComplementIntervals() (in module Intervals) addElement() (SVGdraw.animate method) (SVGdraw.SVGelement method) (SVGdraw.animateColor method) (SVGdraw.animateMotion method) (SVGdraw.animateTransform method) (SVGdraw.circle method) (SVGdraw.cursor method) (SVGdraw.defs method) (SVGdraw.description method) (SVGdraw.ellipse method) (SVGdraw.group method) (SVGdraw.image method) (SVGdraw.line method) (SVGdraw.lineargradient method) (SVGdraw.link method) (SVGdraw.marker method) (SVGdraw.path method) (SVGdraw.pattern method) (SVGdraw.point method) (SVGdraw.polygon method) (SVGdraw.polyline method) (SVGdraw.radialgradient method) (SVGdraw.rect method) (SVGdraw.script method) (SVGdraw.set method) (SVGdraw.stop method) (SVGdraw.style method) (SVGdraw.svg method) (SVGdraw.switch method) (SVGdraw.symbol method) (SVGdraw.text method) (SVGdraw.textpath method) (SVGdraw.title method) (SVGdraw.tref method) (SVGdraw.tspan method) (SVGdraw.use method) (SVGdraw.view method) addEntry() (Mali.SequenceCollection method) AddRelativeAndCumulativeDistributions() (in module Histogram) AGP (module) Alignment2Exons() (in module Exons) animate (class in SVGdraw)

animateColor (class in SVGdraw) animateMotion (class in SVGdraw) animateTransform (class in SVGdraw) AppendCommaOption (class in Experiment) apply() (Mali.SequenceCollection method) asAggregate() (PipelineTracks.Sample method) (PipelineTracks.Sample3 method) asFile() (PipelineTracks.Sample method) (PipelineTracks.Sample3 method) asR() (PipelineTracks.Sample method) (PipelineTracks.Sample3 method) asTable() (Experiment.Counter method) (PipelineTracks.Sample method) (PipelineTracks.Sample3 method) AString (class in AString) (module) axt

B

bam bed benchmark() (in module Experiment) benchmarkRandomFragment() (in module SaryFasta) bezier() (SVGdraw.pathdata method)

bigwig BlastAlignments (module) BlatTest (module) buildColumnMap() (Mali.SequenceCollection method)

C

cachedfunction (in module Experiment) cachedmethod() (in module Experiment) Calculate() (in module Histogram) (in module Histogram2D) CalculateConst() (in module Histogram) CalculateFromTable() (in module Histogram) CalculateOverlap() (in module Intervalls) calculateOverlap() (in module Intervals) CalculateStats() (in module Exons) CBioPortal (module) CDGSError cgat_html_add_toc (module) check_values() (Experiment.OptionParser method) CheckContainedAinB() (in module Exons) CheckCoverage() (in module Exons) CheckCoverageAinB() (in module Exons) checkLength() (Mali.SequenceCollection method) CheckOverlap() (in module Exons) circle (class in SVGdraw) clear() (IOTools.nested_dict method) clipByAnnotation() (Mali.SequenceCollection method) clone() (PipelineTracks.Sample method) (PipelineTracks.Sample3 method) close() (IOTools.FilePool method) (IOTools.FilePoolMemory method) closepath() (SVGdraw.pathdata method) Cluster (module) ClusterByExonIdentity() (in module Exons) ClusterByExonOverlap() (in module Exons) ClusterError ClusterOrthologsByGenes() (in module Orthologs) code (Tophat.Tracking attribute) code directory combinations() (in module SetTools) Combine() (in module Histogram) combine() (in module Intervals) combineAtDistance() (in module Intervals) CombineIntervallsDistance() (in module Intervalls) (in module IntervallsWeighted)

CombineIntervallsLarge() (in module Intervalls) (in module IntervallsWeighted) CombineIntervallsOverlap() (in module Intervalls) (in module IntervallsWeighted) CommentStripper (class in CSV) CompareGeneStructures() (in module Exons) CompareSets() (in module SetTools) complement() (in module Intervals) ComplementIntervalls() (in module Intervalls) (in module IntervallsWeighted) compress() (in module RLE) compressAlignment() (in module MaliIO) contig (Tophat.Locus attribute) (WrapperMACS.Macs2Peak attribute) (WrapperMACS.MacsPeak attribute) (WrapperZinba.ZinbaPeak attribute) Convert() (in module Histogram) convertAlignlib2Mali() (in module Mali) convertCoordinates() (BlatTest.Match method) ConvertDictionary() (in module CSV) convertGaps() (in module MaliIO) convertMali2Alignlib() (in module Mali) convertValue() (in module IOTools) copy() (IOTools.nested_dict method) copyAnnotations() (Mali.SequenceCollection method) CorrespondenceAnalysis (module) count() (in module FastaIterator) Count() (in module Histogram) count() (Logfile.RuntimeInformation method) (Tophat.Locus method) (Tophat.Tracking method) (WrapperMACS.Macs2Peak method) (WrapperMACS.MacsPeak method) (WrapperZinba.ZinbaPeak method) Counter (class in Experiment) CountMissedBoundaries() (in module Exons) CountNumExons() (in module Exons) createDatabase() (in module SaryFasta) critical() (in module Experiment) cstime (Logfile.RuntimeInformation attribute) CSV (module) CSV2DB (module) Cumulate() (in module Histogram) cumulate() (in module Histogram) cursor (class in SVGdraw) cutime (Logfile.RuntimeInformation attribute)

D

Database (module) debug() (in module Experiment) decode() (in module RLE) default_factory (IOTools.nested_dict attribute) defs (class in SVGdraw) deleteFiles() (IOTools.FilePool method) (IOTools.FilePoolMemory method) DeleteSmallIntervalls() (in module Intervalls) (in module IntervallsWeighted)

DeleteSmallIntervals() (in module Intervals) description (class in SVGdraw) destroy() (Experiment.OptionParser method) DictReader (class in CSV) DictReaderLarge (class in CSV) disable_interspersed_args() (Experiment.OptionParser method) drawing (class in SVGdraw)

E

edge list, [1] ellarc() (SVGdraw.pathdata method) ellipse (class in SVGdraw) enable_interspersed_args() (Experiment.OptionParser method) encode() (in module RLE) end (Tophat.Locus attribute) (WrapperMACS.Macs2Peak attribute) (WrapperMACS.MacsPeak attribute) end_date (Logfile.RuntimeInformation attribute) environment variable PATH PYTHONPATH SGE_TASK_FIRST SGE_TASK_ID SGE_TASK_LAST SGE_TASK_STEPSIZE Error, [1], [2], [3], [4]

error() (Experiment.OptionParser method) (in module Experiment) executewait() (in module CSV2DB) (in module Database) execution host Exon (class in Exons) Exons (module) Exons2Alignment() (in module Exons) experiment Experiment (module) ExternalList (module)

F

factory (PipelineTracks.Tracks attribute) fasta Fasta (module) FastaIterator (class in FastaIterator) (module) fastq, [1] fdr (WrapperMACS.Macs2Peak attribute) (WrapperMACS.MacsPeak attribute) (WrapperZinba.ZinbaPeak attribute) FilePool (class in IOTools) FilePoolMemory (class in IOTools) Fill() (in module Histogram) fill() (in module Histogram) fillHistograms() (in module Histogram) filter() (Mali.SequenceCollection method)

FilterBDGP() (in module Orthologs) flatten() (in module IOTools) fold (WrapperMACS.Macs2Peak attribute) (WrapperMACS.MacsPeak attribute) frequencies2logodds() (in module MAST) fromArray() (in module Intervals) fromFile() (PipelineTracks.Sample method) (PipelineTracks.Sample3 method) fromkeys() (IOTools.nested_dict static method) fromMap() (BlatTest.Match method) fromMaq() (BlatTest.Match method) fromPair() (BlatTest.Match method) fromR() (PipelineTracks.Sample method) (PipelineTracks.Sample3 method) fromTable() (PipelineTracks.Sample method) (PipelineTracks.Sample3 method)

G

gdl GDLDraw (module) GenomicIO (module) get() (IOTools.nested_dict method) getAlphabet() (Mali.SequenceCollection method) getAnnotation() (Mali.SequenceCollection method) getBlocks() (BlatTest.Match method) GetClone() (BlastAlignments.Map method) getCodonSequence() (in module MaliIO) getColumnNames() (in module Database) getColumns() (Mali.SequenceCollection method) getConsensus() (Mali.SequenceCollection method) getConverter() (in module GenomicIO) GetDegeneracy() (in module Orthologs) GetExonBoundariesFromTable() (in module Exons) GetExonsRange() (in module Exons) getFilename() (IOTools.FilePool method) (IOTools.FilePoolMemory method) getFooter() (in module Experiment) getFrameColumnsForMaster() (in module MaliIO) getFrameColumnsForMasterPattern() (in module MaliIO) GetGenes() (in module Orthologs) GetGenomeLengths() (in module Exons) getHeader() (in module Experiment) getHID() (in module SaryFasta) GetIndices() (in module CorrespondenceAnalysis) getIntersections() (in module Intervals) getInvertedDictionary() (in module IOTools) getLastLine() (in module IOTools) getLength() (in module Intervals) (Mali.SequenceCollection method)

GetMapColumn2Type() (in module CSV) getMapFromMali() (in module MaliIO) getMapQuery2Target() (BlatTest.Match method) getMapTarget2Query() (BlatTest.Match method) getNumLines() (in module IOTools) getOutputFile() (in module Experiment) getOverlaps() (Regions.RegionFilter method) getParams() (in module Experiment) GetPeptideLengths() (in module Exons) getPercentIdentity() (in module MaliIO) GetPermutatedMatrix() (in module CorrespondenceAnalysis) getResidueNumber() (Mali.SequenceCollection method) getSamplesInTrack() (in module PipelineTracks) getSequence() (in module GenomicIO) getSubset() (in module MaliIO) getTracks() (PipelineTracks.Tracks method) getWidth() (Mali.SequenceCollection method) gff Glam2 (module) Glam2Scan (module) go goslim graph, [1] GraphTools (module) group (class in SVGdraw) group_by_distance() (in module Iterators) GroupTable() (in module CSV) gtf

H

has_finished (Logfile.RuntimeInformation attribute) has_key() (IOTools.nested_dict method) height (WrapperZinba.ZinbaPeak attribute) Histogram (module)

histogram() (in module Histogram) Histogram2D (module) hline() (SVGdraw.pathdata method) host (Logfile.RuntimeInformation attribute)

I

IGV (class in IGV) (module) image (class in SVGdraw) index() (Logfile.RuntimeInformation method) (Tophat.Locus method) (Tophat.Tracking method) (WrapperMACS.Macs2Peak method) (WrapperMACS.MacsPeak method) (WrapperZinba.ZinbaPeak method) index_exists() (in module GenomicIO) index_file() (in module GenomicIO) info() (in module Experiment) InputError insertColumns() (Mali.SequenceCollection method) intersect() (in module Intervals) Intervalls (module) IntervallsWeighted (module) Intervals (module) InvertGenomicCoordinates() (Exons.Exon method) IOTools (module) isEmpty() (in module IOTools) items() (IOTools.nested_dict method) iterate() (in module IOTools) iterate_locus() (in module Tophat)

iterate_tabular() (in module IOTools) iterate_together() (in module FastaIterator) iterate_tracking() (in module Tophat) iterateMacs2Peaks() (in module WrapperMACS) iterateMacsPeaks() (in module WrapperMACS) iteratePeaks() (in module WrapperZinba) iterator() (in module BlatTest) (in module Maq) iterator_links() (in module BlastAlignments) iterator_per_query() (in module BlatTest) iterator_pslx() (in module BlatTest) iterator_query_overlap() (in module BlatTest) iterator_target_overlap() (in module BlatTest) iterator_test() (in module BlatTest) Iterators (module) iterflattened() (IOTools.nested_dict method) iteritems() (IOTools.nested_dict method) iterkeys() (IOTools.nested_dict method) itervalues() (IOTools.nested_dict method)

J

jobid (Logfile.RuntimeInformation attribute)

joined_iterator() (in module Intervals)

K

keys() (IOTools.nested_dict method)

L

length (WrapperMACS.Macs2Peak attribute) (WrapperMACS.MacsPeak attribute) line (class in SVGdraw) line() (SVGdraw.pathdata method) lineargradient (class in SVGdraw) link (class in SVGdraw) loadFromDirectory() (PipelineTracks.Tracks method) Locus (class in Tophat)

locus_id (Tophat.Locus attribute) (Tophat.Tracking attribute) log() (in module Experiment) Logfile (module) LogFileDataLines (class in Logfile) loglevel lower() (AString.AString method) (Mali.SequenceCollection method) lowerCase() (Mali.SequenceCollection method)

M

Macs2Peak (class in WrapperMACS) MacsPeak (class in WrapperMACS) maf MakeListComprehensionFunction() (in module SetTools) Mali (module) mali_phylip2fasta (module) MaliIO (module) Map (class in BlastAlignments) mapColumns() (Mali.SequenceCollection method) MapExons() (in module Exons) mapIdentifiers() (Mali.SequenceCollection method) MapRange() (BlastAlignments.Map method) Maq (module)

markCodons() (Mali.SequenceCollection method) marker (class in SVGdraw) markTransitions() (Mali.SequenceCollection method) maskColumn() (Mali.SequenceCollection method) maskColumns() (Mali.SequenceCollection method) MAST (module) Match (class in BlatTest) (class in Glam2Scan) (class in MAST) (class in Maq) MatchExons() (in module Exons) MatlabTools (module) median (WrapperZinba.ZinbaPeak attribute) Merge() (Exons.Exon method) move() (SVGdraw.pathdata method)

N

name (WrapperMACS.Macs2Peak attribute) nested_dict (class in IOTools)

normalize() (in module Histogram)

O

openFile() (in module Experiment) (IOTools.FilePool method) (IOTools.FilePoolMemory method) (in module IOTools) openOutputFile() (in module Experiment) OptionParser (class in Experiment)

options (Logfile.RuntimeInformation attribute) Orthologs (module)

P

PamMatrices (module) PARAM_CPC_UNIREF PARAM_DATABASE PARAM_FILE_ALIGNMENTS PARAM_FILE_REPEATS PARAM_FILE_REPEATS_GC PARAM_FILE_REPEATS_RATES PARAM_FILENAME_GO (PARAM_FILENAME_GOSLIM) PARAM_FILENAME_TERRITORIES parse() (in module Glam2) (in module Glam2Scan) (in module MAST) parse_args() (Experiment.OptionParser method) parseTranscriptComparison() (in module Tophat) ParsingError, [1], [2] PATH path (class in SVGdraw) pathdata (class in SVGdraw) pattern (class in SVGdraw) pileup (WrapperMACS.Macs2Peak attribute) pipeline_quickstart (module) PipelineTracks (module) point (class in SVGdraw) polygon (class in SVGdraw) polyline (class in SVGdraw)

pop() (IOTools.nested_dict method) popitem() (IOTools.nested_dict method) posterior (WrapperZinba.ZinbaPeak attribute) PostProcessExons() (in module Exons) prettyFloat() (in module IOTools) prettyPercent() (in module IOTools) prettyString() (in module IOTools) Print() (in module Histogram) (in module Histogram2D) print_help() (Experiment.OptionParser method) print_usage() (Experiment.OptionParser method) print_version() (Experiment.OptionParser method) PrintAscii() (in module Histogram) production pipeline ProfileLibrary (module) ProfileLibraryCompass (module) ProgressBar (class in ProgressBar) (module) project pipeline propagateMasks() (Mali.SequenceCollection method) propagateTransitions() (Mali.SequenceCollection method) prune() (in module Intervals) psl pvalue (WrapperMACS.Macs2Peak attribute) (WrapperMACS.MacsPeak attribute) PYTHONPATH

Q

qbezier() (SVGdraw.pathdata method) query

quoteRow() (in module CSV2DB)

R

radialgradient (class in SVGdraw) rdf Read() (Exons.Exon method) ReadBinarySparseMatrix() (in module MatlabTools) ReadExonBoundaries() (in module Exons) readFasta() (in module MaliIO) readFromFile() (Mali.SequenceCollection method) (Regions.RegionFilter method) ReadInterpretation() (in module Orthologs) ReadList() (in module IOTools) readList() (in module IOTools) ReadMap() (in module BlastAlignments) readMap() (in module IOTools) ReadMap() (in module IOTools) readMatrix() (in module IOTools) ReadMatrix() (in module MatlabTools) readMatrix() (in module MatlabTools) readMultiMap() (in module IOTools) ReadOrphans() (in module Orthologs) readPicasso() (in module MaliIO) readSequence() (in module IOTools) ReadSparseMatrix() (in module MatlabTools) ReadTable() (in module CSV) readTable() (in module IOTools) ReadTables() (in module CSV) recount() (Mali.SequenceCollection method) rect (class in SVGdraw) ref_gene_id (Tophat.Tracking attribute) ref_transcript_id (Tophat.Tracking attribute) refined_end (WrapperZinba.ZinbaPeak attribute)

refined_start (WrapperZinba.ZinbaPeak attribute) RegionFilter (class in Regions) Regions (module) relbezier() (SVGdraw.pathdata method) relellarc() (SVGdraw.pathdata method) relhline() (SVGdraw.pathdata method) relline() (SVGdraw.pathdata method) relmove() (SVGdraw.pathdata method) relqbezier() (SVGdraw.pathdata method) relsmbezier() (SVGdraw.pathdata method) relsmqbezier() (SVGdraw.pathdata method) relvline() (SVGdraw.pathdata method) removeEmptySequences() (Mali.SequenceCollection method) removeEndGaps() (Mali.SequenceCollection method) removeGappedColumns() (in module MaliIO) removeGaps() (Mali.SequenceCollection method) RemoveIntervallsContained() (in module Intervalls) (in module IntervallsWeighted) RemoveIntervallsSpanning() (in module Intervalls) (in module IntervallsWeighted) RemoveIntervalsContained() (in module Intervals) RemoveIntervalsSpanning() (in module Intervals) removePattern() (Mali.SequenceCollection method) RemoveRedundantEntries() (in module Exons) removeUnalignedEnds() (Mali.SequenceCollection method) rename() (Mali.SequenceCollection method) replicate RLE (module) run() (in module Experiment) RuntimeError RuntimeInformation (class in Logfile)

S

sam Sample (class in PipelineTracks) sample() (in module Iterators) Sample3 (class in PipelineTracks) SaryFasta (module) Scale() (in module Histogram) script (class in SVGdraw) (Logfile.RuntimeInformation attribute) SequenceCollection (class in Mali) sequences2motif() (in module MAST) set (class in SVGdraw) setAnnotation() (Mali.SequenceCollection method) setdefault() (IOTools.nested_dict method) setDefault() (PipelineTracks.Sample class method) (PipelineTracks.Sample3 class method) SetRankToPositionFlag() (in module Exons) SetTools (module) SGE_TASK_FIRST SGE_TASK_ID SGE_TASK_LAST SGE_TASK_STEPSIZE shiftAlignment() (Mali.SequenceCollection method) ShortenIntervallsOverlap() (in module Intervalls) (in module IntervallsWeighted) ShortenIntervalsOverlap() (in module Intervals) shuffle() (Mali.SequenceCollection method) smbezier() (SVGdraw.pathdata method) SmoothWrap() (in module Histogram) smqbezier() (SVGdraw.pathdata method) Sockets (module)

sort() (IGV.IGV method) source directory spannedtext (class in SVGdraw) sphinxreport splitFasta() (in module GenomicIO) sra start (Tophat.Locus attribute) (WrapperMACS.Macs2Peak attribute) (WrapperMACS.MacsPeak attribute) Start() (in module Experiment), [1] start_date (Logfile.RuntimeInformation attribute) stderr stdin stdout stime (Logfile.RuntimeInformation attribute) stop (class in SVGdraw) Stop() (in module Experiment), [1] str2val() (in module IOTools) strand (Tophat.Locus attribute) (WrapperZinba.ZinbaPeak attribute) style (class in SVGdraw) submit host SuffixArray (module) summit (WrapperMACS.Macs2Peak attribute) (WrapperMACS.MacsPeak attribute) (WrapperZinba.ZinbaPeak attribute) svg (class in SVGdraw) SVGdraw (module) SVGelement (class in SVGdraw) switch (class in SVGdraw) switchTargetStrand() (BlatTest.Match method) symbol (class in SVGdraw)

T

tags (WrapperMACS.MacsPeak attribute) takeColumns() (Mali.SequenceCollection method) target task test directory text (class in SVGdraw) textpath (class in SVGdraw) title (class in SVGdraw) toLabels() (PipelineTracks.Sample method) (PipelineTracks.Sample3 method) Tophat (module) track

Tracking (class in Tophat) Tracks (class in PipelineTracks) transcript_ids (Tophat.Locus attribute) TranscriptInfo (in module Tophat) transcripts (Tophat.Locus attribute) (Tophat.Tracking attribute) transfrag_id (Tophat.Tracking attribute) tref (class in SVGdraw) truncate() (in module Intervals) (Mali.SequenceCollection method) tspan (class in SVGdraw) tss tsv

U

unionIntersectionMatrix() (in module SetTools) unrefined_end (WrapperZinba.ZinbaPeak attribute) unrefined_start (WrapperZinba.ZinbaPeak attribute) update() (IOTools.nested_dict method) UpdatePeptideCoordinates() (in module Exons)

upper() (AString.AString method) (Mali.SequenceCollection method) upperCase() (Mali.SequenceCollection method) UsageError use (class in SVGdraw) utime (Logfile.RuntimeInformation attribute)

V

val2str() (in module IOTools) values() (IOTools.nested_dict method) vcf VCF (module) verify() (in module SaryFasta)

view (class in SVGdraw) viewitems() (IOTools.nested_dict method) viewkeys() (IOTools.nested_dict method) viewvalues() (IOTools.nested_dict method) vline() (SVGdraw.pathdata method)

W

wall (Logfile.RuntimeInformation attribute) warn() (in module Experiment) warning() (in module Experiment) which() (in module IOTools) wiggle working directory WrapperAdaptiveCAI (module) WrapperBl2Seq (module) WrapperENC (module) WrapperMACS (module) WrapperMuscle (module) WrapperZinba (module)

Write() (in module Histogram) writeClustalW() (in module MaliIO) writeFasta() (in module MaliIO) writeMast() (in module MAST) writeMatrix() (in module IOTools) WriteMatrix() (in module MatlabTools) writeMatrix() (in module MatlabTools) WriteMODELLER() (in module MaliIO) writeSets() (in module SetTools) writeTable() (in module IOTools) writeToFile() (Mali.SequenceCollection method) writeTomTom() (in module MAST)

Y

yaml

Z

ZinbaPeak (class in WrapperZinba)