Summary of Python Modules¶
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.resolutionToBinsize (resolution) |
Return the bin size from the resolution unit |
ccmap.binsizeToResolution (binsize) |
Return the resolution unit from the bin size |
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 (cmap, outfile[, ...]) |
To export .ccmap as text file |
ccmapHelpers module¶
ccmapHelpers.MemoryMappedArray |
Convenient wrapper for numpy memory mapped array file |
ccmapHelpers.MemoryMappedArray.copy (self) |
Copy this numpy memory mapped array and generate new |
ccmapHelpers.MemoryMappedArray.copy_from (...) |
Copy values from source MemoryMappedArray |
ccmapHelpers.MemoryMappedArray.copy_to (self, ...) |
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) |
gcmap module¶
gcmap.GCMAP (hdf5[, mapName, chromAtX, ...]) |
To access Genome wide contact map. |
gcmap.GCMAP.changeMap ([mapName, chromAtX, ...]) |
Change the map from |
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.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 |
cmstats module¶
cmstats.correlateCMaps (ccMapObjOne, ccMapObjTwo) |
To calculate correlation between two Hi-C maps |
cmstats.getAvgContactByDistance (ccmaps[, stats]) |
To calcualte average contact as a function of distance |
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 respecitve 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.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.genrateAllTempNumpyFiles () |
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. |