class TextFileHandler
¶
TextFileHandler (filename, shape[, binsize, …]) |
To import a genomic data from column text file format |
TextFileHandler.readData () |
Read data from input file |
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class
TextFileHandler
(filename, shape, binsize=None, title=None, workDir=None)¶ To import a genomic data from column text file format
It reads text file, make an full array for given shape and fills the missing place with zeros. These zeros could be later masked to perform any analysis.
Example file format:
15670000 0.2917373776435852 15680000 0.2292359322309494 15690000 0.023434270173311234 15700000 0.06813383102416992 15710000 0.13660947978496552 15720000 0.17478400468826294 15730000 0.20540907979011536 . . .
This class is used in browser to visualize the genomic data, which are directly imported from text file.
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filename
¶ str – Input text file
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shape
¶ int – Size of array required to built
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binsize
¶ int – Size of bins expected in input file. If
binsize = None
, binsize will be determined from the files, however, it is good to give expected binsize to check whether expected binsize match with binsize present in input text file.
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title
¶ str – Title of the input data
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workDir
¶ str – Directory where temporary files will be generated. If
None
, defualt temporary directory of the respective OS will be used.
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data
¶ numpy.ndarray or numpy.memmap – One-dimensional array containing the data
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tmpNumpyFileName
¶ str – Name of temporary numpy memory-mapped file
Parameters: - filename (str) – Input text file
- shape (int) – Size of array required to built
- binsize (int) – Size of bins expected in input file. If
binsize = None
, binsize will be determined from the files, however, it is good to give expected binsize to check whether expected binsize match with binsize present in input text file. - title (str) – Title of the input data
- workDir (str) – Directory where temporary files will be generated. If
None
, default temporary directory of the respective OS will be used.
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_generateTempNumpyFile
()¶ Generate temporary numpy memory-mapped file
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_getBinSize
()¶ Determine binsize from input file
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_removeTempNumpyFile
()¶ Remove temporary numpy memory-mapped file
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readData
()¶ Read data from input file
Read data from input file and store in
TextFileHandler.data
as one-dimensional array
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