trxtools

version 0.3.0

trxtools is set of bioinformatic tools and methods to facilitate analysis of transcriptional data.

Major focus is put on postprocessing of high-troughput sequencing data originating from the followin methods:

• CRAC/CLIP

• RNA-seq

• tRNA-seq

• NET-seq

• ChIP-seq

Some functions in the package use a specific file naming system:

'expID', 'expDate', 'protein', 'condition1', 'condition2', 'condition3'

i.e. C123_JK050420_POLR2A-FLAG_wt_arsenite30min will be used for an experiment C123 conducted by a person JK on 020420. This is puldown with POLR2A-FLAG in wt cells after arsenite30min

Reporting bugs

If you encounter a bug, please report it on the GitHub issue tracker.

Contents

• Scripts
  • Main scripts
    • SAM2profilesGenomic.py
    • SAM2profilesTranscripts.py
    • genomeNascentFolding.py
  • Supporting scripts
    • genome2WindowsGTF.py
    • csv2pickle.py
    • mergeSalmon.py
    • fasta2slidingWindows.py

• trxtools package
  • trxtools.sam module
    • trxtools.sam.SAMgeneral submodule
      • countDeletion()
      • countMiddle()
      • countRead()
      • groupCIGAR()
      • noncoded2profile()
      • noncoded2profile1()
      • parseNoncoded()
      • parseNoncodedList()
      • saveBigWig()
      • selectEnds()
      • selectPolyA()
      • selectSortPaths()
      • stripCIGAR()
      • stripSubstitutions()
      • tostripCIGARfive()
      • tostripCIGARthree()
    • trxtools.sam.SAMgenome submodule
      • chromosome2profile3end()
      • parseHeader()
      • reads2genome()
      • reads2genome3end()
      • reads2genome5end()
      • reads2genomeDeletions()
      • sam2genome()
    • trxtools.sam.SAMtranscripts submodule
      • reads2profile()
      • reads2profileDeletions()
      • sam2profiles()
      • transcript2profile()
      • transcript2profileDeletions()
  • trxtools.BigWig module
    • foldingFromBigWig()
    • geneFromBigWig()
    • getSeqData()
    • strip_BigWig_names()
  • trxtools.metaprofiles module
    • bed_split_strands()
    • binMultipleMatrices()
    • getMultipleMatrices()
    • getMultipleMatricesFromPeak()
    • get_bw_data()
    • get_multiple_matrices()
    • join_strand_matrices()
    • matrixFromBigWig()
    • matrix_from_bigwig()
    • metaprofile()
    • peak2matrice()
    • readBED()
    • read_bed()
    • regionScore()
    • selectSubsetMM()
  • trxtools.assays module
    • bulkInputIDT()
    • extruded()
    • findPrimer()
    • nonTemplateDNA()
    • sequenceConstrain()
    • stalled()
    • structureFile()
    • templateDNA()
    • testScaffold()
    • toOrder()
  • trxtools.go_enrichment module
    • get_enrichment()
  • trxtools.methods module
    • DNA_stretch_positions()
    • DNA_string_positions()
    • addCluster()
    • bashCommand()
    • bed2len()
    • calGC()
    • cleanNames()
    • define_experiments()
    • enriched()
    • expNameParser()
    • expStats()
    • filterExp()
    • find_pol3_terminators()
    • groupCRACsamples()
    • indexOrder()
    • is_inside()
    • letterContent()
    • listPaths()
    • loadGTF()
    • nested_region_cleanup()
    • normalize()
    • parseCRACname()
    • quantileCategory()
    • randomDNAall()
    • randomDNAsingle()
    • readSalmon()
    • read_DEseq()
    • read_HTSeq_output()
    • read_STARstats()
    • read_featureCount()
    • read_list()
    • read_tabFile()
    • reverse_complement()
    • reverse_complement_DNA()
    • reverse_complement_RNA()
    • rollingGC()
    • runPCA()
    • timestamp()
    • timestampRandomInt()
  • trxtools.nascent module
    • Fold
      • Fold.RNAfold()
      • Fold.RNAinvert()
      • Fold.RNAinvertStall()
      • Fold.UNAfold()
      • Fold.bashFolding()
    • Hybrid
      • Hybrid.RNAhybrid()
      • Hybrid.bashHybrid()
    • extendingWindow()
    • foldNascentElem()
    • handleInput()
    • join2d()
    • merge2d()
    • name2index()
    • nascentElems()
    • nascentElemsDataFrame()
    • nascentFolding()
    • parseFoldingName()
    • prepareNascent()
    • slidingWindow()
  • trxtools.plotting module
    • GOterm()
    • PCA()
    • boxplot1()
    • clusterClusterMap()
    • cumulativeDifference()
    • cumulativePeaks()
    • enhancedVolcano()
    • generateSubplots()
    • hplotSTARstats_readLen()
    • hplotSTARstats_reads()
    • metaprofileAndHeatmap()
    • plotAndFolding()
    • plotSTARstats()
    • plotSTARstats_chimeric()
    • plotSTARstats_mapping()
    • plotSTARstats_mistmatches()
    • plotSTARstats_readLen()
    • plotSTARstats_reads()
    • plot_as_box_plot()
    • plot_diff()
    • plot_heatmap()
    • plot_to_compare()
    • select_colors()
    • vennDiagram()
  • trxtools.profiles module
    • FoldingFromBigWig()
    • binCollect3()
    • calculateFDR()
    • compare1toRef()
    • compareMoretoRef()
    • dictBigWig()
    • findPeaks()
    • findTroughs()
    • geneFromBigWig()
    • ntotal()
    • parseConcatFile()
    • preprocess()
    • pseudocounts()
    • save_csv()
    • stripBigWignames()
  • trxtools.secondary module
    • Lstem()
    • Rstem()
    • checkVienna()
    • loopStems()
    • loops()
    • substructures()
    • test()
    • vienna2format()

• Release information
  • Reporting bugs
  • Versions
    • v0.3.0
    • v0.2.2
    • v0.2.1
  • Authors

Indices and tables

• Index

• Module Index