Summary of Python Modules¶
config module¶
updateConfig(section, option, value) |
Update configuration file |
getConfig() |
To get the present configuration. |
printConfig() |
Print configuration file |
cleanScratch() |
Clean scratch directory. |
ccmap module¶
ccmap.CCMAP.copy([fill]) |
To create a new copy of CCMAP object |
ccmap.CCMAP.get_ticks([binsize]) |
To get xticks and yticks for the matrix |
ccmap.CCMAP.make_readable() |
Enable reading the numpy array binary file. |
ccmap.CCMAP.make_unreadable() |
Disable reading the numpy array binary file from local file system |
ccmap.CCMAP.make_writable() |
Create new numpy array binary file on local file system and enable reading/writing to this file |
ccmap.CCMAP.make_editable() |
Enable editing numpy array binary file |
ccmap.jsonify(ccMapObj) |
Changes data type of attributes in CCMAP object for json module. |
ccmap.dejsonify(ccMapObj[, json_dict]) |
Change back the data type of attributes in CCMAP object. |
ccmap.save_ccmap(ccMapObj, outfile[, …]) |
Save CCMAP object on file |
ccmap.load_ccmap(infile[, workDir]) |
Load CCMAP object from an input file |
ccmap.export_cmap(ccmap, outfile[, …]) |
To export .ccmap as text file |
ccmap.checkCCMapObjectOrFile(ccMap[, workDir]) |
Check whether ccmap is a object or file |
ccmap.downSampleCCMap(cmap[, level, method, …]) |
Downsample or coarsen the contact map |
ccmap.getOutputShapeFor2DMapDownsampling(…) |
Helper function to determine output shape of map for downsampling |
ccmap.downSample2DMap(inMatrix[, outMatrix, …]) |
Downsample or coarsen the matrix |
ccmapHelpers module¶
ccmapHelpers.MemoryMappedArray |
Convenient wrapper for numpy memory mapped array file |
ccmapHelpers.MemoryMappedArray.copy |
Copy this numpy memory mapped array and generate new |
ccmapHelpers.MemoryMappedArray.copy_from |
Copy values from source MemoryMappedArray |
ccmapHelpers.MemoryMappedArray.copy_to |
Copy values to destination MemoryMappedArray |
ccmapHelpers.get_nonzeros_index(matrix[, …]) |
To get a numpy array of bool values for all rows/columns which have NO missing data |
ccmapHelpers.remove_zeros(matrix[, …]) |
To remove rows/columns with missing data (zero values) |
util module¶
util.resolutionToBinsize(resolution) |
Return the bin size from the resolution unit |
util.binsizeToResolution(binsize) |
Return the resolution unit from the bin size |
util.sorted_nicely(inputList) |
Sorts the given given list in the way that is expected. |
util.locate_significant_digit_after_decimal(value) |
Get location at which significant digit start after decimal |
util.kth_diag_indices(k, a) |
Get diagonal indices of 2D array ‘a’ offset by ‘k’ |
util.detectOutliers1D(points[, thresh]) |
Returns a boolean array with True if points are outliers and False otherwise. |
util.getRandomName([size, chars]) |
Random name generator |
util.MapNotFoundError(value) |
|
util.ResolutionNotFoundError(value) |
gcmap module¶
gcmap.GCMAP(hdf5[, mapName, chromAtX, …]) |
To access Genome wide contact map. |
gcmap.GCMAP.checkMapExist([mapName, …]) |
Check if a map is exist in the file |
gcmap.GCMAP.changeMap([mapName, chromAtX, …]) |
Change the map for another chromosome |
gcmap.GCMAP.changeResolution(resolution) |
Try to change contact map of a given resolution. |
gcmap.GCMAP.toFinerResolution() |
Try to change contact map to next finer resolution |
gcmap.GCMAP.toCoarserResolution() |
Try to change contact map to next coarser resolution |
gcmap.GCMAP.loadSmallestMap([resolution]) |
Load smallest sized contact map |
gcmap.GCMAP.genMapNameList([sortBy]) |
Generate list of contact maps available in gcmap file |
gcmap.GCMAP.performDownSampling([method]) |
Downsample recursively and store the maps |
gcmap.GCMAP.downsampleMapToResolution(resolution) |
Downsample the current map to a particular resolution |
gcmap.GCMAP.downsampleAllMapToResolution(…) |
Downsample all maps to a particular resolution |
gcmap.loadGCMapAsCCMap(filename[, mapName, …]) |
Load a map from gcmap file as a gcMapExplorer.lib.ccmap.CCMAP. |
gcmap.addCCMap2GCMap(cmap, filename[, …]) |
Add gcMapExplorer.lib.ccmap.CCMAP to a gcmap file |
gcmap.changeGCMapCompression(infile, …[, …]) |
Change compression method in GCMAP file |
importer module¶
importer.CooMatrixHandler([inputFiles, …]) |
To import ccmap from files similar to sparse matrix in Coordinate (COO) format |
importer.CooMatrixHandler.save_ccmaps([…]) |
To Save all Hi-C maps |
importer.CooMatrixHandler.save_gcmap(outputFile) |
To Save all Hi-C maps as a gcmap file |
importer.CooMatrixHandler.setLabels(xlabels, …) |
To set xlabels and ylabels for contact maps |
importer.CooMatrixHandler.setOutputFileList(…) |
To set list of output files |
importer.PairCooMatrixHandler(inputFile[, …]) |
To import ccmap from files similar to paired sparse matrix Coordinate (COO) format |
importer.PairCooMatrixHandler.setGCMapOptions([…]) |
Set options for output gcmap file |
importer.PairCooMatrixHandler.runConversion() |
Perform conversion and save to ccmap and/or gcmap file. |
importer.HomerInputHandler([inputFiles, …]) |
To import ccmap from Hi-C maps generated by HOMER |
importer.HomerInputHandler.save_ccmaps(outdir) |
Import and save ccmap file |
importer.HomerInputHandler.save_gcmap(outputFile) |
To Save all Hi-C maps as a gcmap file |
importer.BinsNContactFilesHandler(binFile, …) |
To import Hi-C map from bin and contact file in list format |
importer.BinsNContactFilesHandler.save_ccmaps(outdir) |
Import and save ccmap file |
importer.BinsNContactFilesHandler.save_gcmap(…) |
To Save all Hi-C maps as a gcmap file |
importer.gen_map_from_locations_value(i, j, …) |
To generate CCMAP object from three lists – i, j, value |
normalizer module¶
normalizer.NormalizeKnightRuizOriginal(ccMapObj) |
Original Knight-Ruiz algorithm for matrix balancing |
normalizer.normalizeCCMapByKR(ccMap[, …]) |
Normalize a ccmap using Knight-Ruiz matrix balancing method. |
normalizer.normalizeGCMapByKR(…[, …]) |
Normalize a gcmap using Knight-Ruiz matrix balancing method. |
normalizer.normalizeCCMapByIC(ccMap[, tol, …]) |
Normalize a ccmap by Iterative correction method |
normalizer.normalizeGCMapByIC(…[, vmin, …]) |
Normalize a gcmap using Iterative Correction. |
normalizer.normalizeCCMapByMCFS(ccMap[, …]) |
Scale ccmap using Median Contact Frequency |
normalizer.normalizeGCMapByMCFS(…[, …]) |
Scale all maps in gcmap using Median Contact Frequency |
normalizer.normalizeCCMapByVCNorm(ccMap[, …]) |
Normalize ccmap using Vanilla-Coverage method |
normalizer.normalizeGCMapByVCNorm(…[, …]) |
Normalize all maps using Vanilla-Coverage method |
cmstats module¶
cmstats.correlateCMaps(ccMapObjOne, ccMapObjTwo) |
To calculate correlation between two Hi-C maps |
cmstats.correlateGCMaps(gcmapOne, gcmapTwo) |
To calculate correlation between common Hi-C maps from two gcmap files |
cmstats.getAvgContactByDistance(ccmaps[, …]) |
To calculate average contact as a function of distance |
corrMatrix module¶
corrMatrix.calculateCorrMatrix(…[, maskvalue]) |
Calculate correlation matrix from a 2D numpy array. |
corrMatrix.calculateCovMatrix(…[, maskvalue]) |
Calculate covariance matrix from a 2D numpy array. |
corrMatrix.calculateCorrelation(ndarray x, …) |
Calculate correlation between two 1D numpy array. |
corrMatrix.calculateCovariance(ndarray x, …) |
Calculate covariance between two 1D numpy array. |
corrMatrix.calculateCorrMatrixForCCMap(…) |
Calculate correlation matrix of a contact map. |
corrMatrix.calculateCorrMatrixForGCMaps(…) |
Calculate Correlation matrix for all maps present in input gcmap file It calculates correlation between all rows and columns of contact map. |
statDist module¶
statDist.calculateTransitionProbabilityMatrix(A) |
Core function to calculate transition probability matrix. |
statDist.transitionProbabilityMatrixForCCMap(ccMap) |
To calculate transition probability matrix. |
statDist.transitionProbabilityMatrixForGCMap(…) |
To calculate transition matrices using a gcmap file. |
statDist.statDistrByEigenDecompForCCMap(ccMap) |
Calculate stationary distribution from a ccmap file or object. |
statDist.statDistrByEigenDecompForGCMap(…) |
Calculate stationary distribution using transition matrices from gcmap file for given resolution. |
statDist.stationaryDistributionByEigenDecomp(…) |
To calculate stationary distribution from probability transition matrix. |
genomicsDataHandler module¶
genomicsDataHandler.HDF5Handler(filename[, …]) |
Handler for genomic data HDF5 file. |
genomicsDataHandler.HDF5Handler.setTitle(title) |
Set title of the dataset |
genomicsDataHandler.HDF5Handler.getChromList() |
To get list of all chromosomes present in hdf5 file |
genomicsDataHandler.HDF5Handler.getResolutionList(chrom) |
To get all resolutions for given chromosome from hdf5 file |
genomicsDataHandler.HDF5Handler.getDataNameList(…) |
List of all available arrays by respective coarse method name for given chromosome and resolution |
genomicsDataHandler.HDF5Handler.buildDataTree() |
Build data dictionary from the input hdf5 file |
genomicsDataHandler.BigWigHandler(filenames) |
To handle bigWig files and to convert it to h5 file |
genomicsDataHandler.BigWigHandler.getBigWigInfo() |
Retrieve chromosome names and their sizes |
genomicsDataHandler.BigWigHandler.bigWigtoWig([…]) |
To generate Wig file |
genomicsDataHandler.BigWigHandler.saveAsH5(…) |
Save data to h5 file. |
genomicsDataHandler.WigHandler(filenames[, …]) |
To convert Wig files to hdf5 file |
genomicsDataHandler.WigHandler.parseWig() |
To parse Wig files |
genomicsDataHandler.WigHandler.setChromosome(…) |
Set the target chromosome for reading and extracting from wig file |
genomicsDataHandler.WigHandler.saveAsH5(hdf5Out) |
To convert Wig files to hdf5 file |
genomicsDataHandler.WigHandler.getRawWigDataAsDictionary([…]) |
To get a entire dictionary of data from Wig file |
genomicsDataHandler.BEDHandler(filenames[, …]) |
To convert BED files to hdf5/h5 file |
genomicsDataHandler.BEDHandler.parseBed() |
To parse bed files |
genomicsDataHandler.BEDHandler.setChromosome(…) |
Set the target chromosome for reading and extracting from bed file |
genomicsDataHandler.BEDHandler.saveAsH5(hdf5Out) |
To convert bed files to hdf5 file |
genomicsDataHandler.EncodeDatasetsConverter(…) |
Download and convert datasets from ENCODE Experiments matrix |
genomicsDataHandler.EncodeDatasetsConverter.saveAsH5(outDir) |
Download the files and convert to gcMapExplorer compatible hdf5 file. |
genomicsDataHandler.TextFileHandler(…[, …]) |
To import a genomic data from column text file format |
genomicsDataHandler.TextFileHandler.readData() |
Read data from input file |
genomicsDataHandler.TempNumpyArrayFiles([…]) |
To handle temporary numpy array files |
genomicsDataHandler.TempNumpyArrayFiles.updateArraysByBigWig(…) |
Update/resize all array files using given bigWig file |
genomicsDataHandler.TempNumpyArrayFiles.updateArraysByChromSize(…) |
Update/resize an array file using given chromosome and its size |
genomicsDataHandler.TempNumpyArrayFiles.addChromSizeInfo(…) |
Update chromosome sizes using new bigWig file |
genomicsDataHandler.TempNumpyArrayFiles.generateAllTempNumpyFiles() |
Generate all memory mapped numpy array files |
genomicsDataHandler.TempNumpyArrayFiles.generateTempNumpyFile(key) |
Generate a memory mapped numpy array file |
genomicsDataHandler.TempNumpyArrayFiles.fillAllArraysWithZeros() |
Fill all arrays with zeros. |