class TempNumpyArrayFiles

TempNumpyArrayFiles([workDir])	To handle temporary numpy array files
TempNumpyArrayFiles.updateArraysByBigWig(…)	Update/resize all array files using given bigWig file
TempNumpyArrayFiles.updateArraysByChromSize(…)	Update/resize an array file using given chromosome and its size
TempNumpyArrayFiles.addChromSizeInfo(…)	Update chromosome sizes using new bigWig file
TempNumpyArrayFiles.generateAllTempNumpyFiles()	Generate all memory mapped numpy array files
TempNumpyArrayFiles.generateTempNumpyFile(key)	Generate a memory mapped numpy array file
TempNumpyArrayFiles.fillAllArraysWithZeros()	Fill all arrays with zeros.

class TempNumpyArrayFiles(workDir=None)

To handle temporary numpy array files

To convert a Wig file to hdf5 file, data are parsed, and further stored temporarily in these memory-mapped numpy array files. Use of numpy arrays avoid dependency from storing chromosome location/coordinates because array index is used as the location/coordinates. Additionally, chromosome could be very large and to store these arrays could be memory expensive, these arrays are stored as binary files on the disk.

Note

These generated files are either automatically deleted after execution of script or by deleting [del] TempNumpyArrayFiles instance.

chromSizeInfo

dict – Dictionary contains chromosome size. Numpy array files will be generated on the basis of these sizes.

files

dict – Dictionary for names of temporary numpy array files, where keys are chromosomes and values are respective file names.

arrays

dict – Dictionary of memory mapped numpy array (numpy.memmap), where keys are chromosomes and values are respective numpy.memmap arrays.

workDir

str – Working directory where temporary numpy array files will be generated.

_generateTempNumpyFile(key, regenerate=False)

enerate a memory mapped numpy array file

It is used to generate a memory mapped numpy array file for given chromosome for which size is already in the TempNumpyArrayFiles.chromSizeInfo dictionary.

Warning

Private method. Use it at your own risk. It is used internally in TempNumpyArrayFiles.generateTempNumpyFile().

Parameters:

• key (str) – chromosome name. Should be present as key in TempNumpyArrayFiles.chromSizeInfo.
• regenerate (bool) – Replace or regenerate new memory mapped array for given chromosome

_getBigWigInfo(filename)

Base method to Retrieve chromosome names and their sizes

• Use TempNumpyArrayFiles.addChromSizeInfo() to automatically retrieve chromosome size information from bigWig file and to store in TempNumpyArrayFiles.chromSizeInfo.

Warning

Private method. Use it at your own risk. It is used internally in TempNumpyArrayFiles.addChromSizeInfo()

Parameters:filename (str) – Input bigWig file

addChromSizeInfo(bigWigFileName)

Update chromosome sizes using new bigWig file

To update TempNumpyArrayFiles.chromSizeInfo for new bigWig files, this method can be used.

Note

This method only updates the TempNumpyArrayFiles.chromSizeInfo dictionary. It does not resize numpy array files.

Parameters:bigWigFileName (str) – Name of input bigWig file

fillAllArraysWithZeros()

Fill all arrays with zeros.

To fill all memory mapped array with zero. It is used in WigHandler so that new data extracted from Wig files can be stored in these array files.

generateAllTempNumpyFiles()

Generate all memory mapped numpy array files

It is used to generate all memory mapped numpy array files using the TempNumpyArrayFiles.chromSizeInfo dictionary.

generateTempNumpyFile(key, regenerate=False)

Generate a memory mapped numpy array file

It is used to generate a memory mapped numpy array for given chromosome for which size is already the TempNumpyArrayFiles.chromSizeInfo dictionary.

Parameters:

• key (str) – chromosome name. Should be present as key in TempNumpyArrayFiles.chromSizeInfo.
• regenerate (bool) – Replace or regenerate new memory mapped array for given chromosome

updateArraysByBigWig(bigWigFileName)

Update/resize all array files using given bigWig file

Parameters:bigWigFileName (str) – Name of input bigWig file

updateArraysByChromSize(chrom, size)

Update/resize an array file using given chromosome and its size

Parameters:

• chrom (str) – Chromosome name
• size (int) – Total size of chromosome