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Wrapper to read fast5, slow5, blow5 and pod5 files.
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rnajena/read5
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- Read5 is a python wrapper to read fast5, slow5/blow5 and pod5 files using the same overloaded functions from different APIs.
- Read5_ont is a python wrapper to read fast5 and pod5 files using the same overloaded functions from different APIs.
pip install read5
Pod5 is now available viaconda (19.07.2023).
conda create -n read5 -c jannessp read5conda activate read5
Click here to see a full documentation about the classes and function.
my_file can be a fast5, slow5, blow5 or pod5 file. The wrapper detects the file format depending on the file extension.
fromread5importread# or from read5.Reader import readr5=read(my_file)# file with one of these extensions: .fast5, .slow5, .blow5, .pod5forreadidinr5:signal=r5.getSignal(readid)# returns raw integer values stored in the filepA_signal=r5.getpASignal(readid)# returns pA signalnorm_signal=r5.getZNormSignal(readid)# returns normalized read signal: norm_signal = (signal - median(signal)) / mad(signal)polyAstdSignal=r5.getPolyAStandardizedSignal(readid,polyAstart,polyAend)# returns polyA standardized read signal# default polyAMean : float = 108.901413, polyAStdev : float = 2.676522, this can be changed using the parameterschannel=r5.getChannelNumber(readid)sampleid=r5.getSampleID(readid)runid=r5.getRunID(readid)# ...readid_list=r5.getReads()
If you want to use the file readers you can import the corresponding class like this:
fromread5.Fast5ReaderimportFast5Reader# contains the Fast5 Reader classfromread5.Slow5ReaderimportSlow5Reader# contains the Slow5 Reader class - !not available in read5_ont!fromread5.Pod5ReaderimportPod5Reader# contains the Pod5 Reader class
fromread5.AbstractFileReaderimportAbstractFileReader
fromread5.ExceptionsimportUnknownFileFormatException,UnknownNormalizationMode
- UnknownFileFormatException: is raised, when the file extension does not match one of ['.fast5', '.slow5', '.blow5', '.pod5'] (or ['.fast5', '.pod5'] inread5_ont)
- UnknownNormalizationMode: is raised, when an unknown mode is provided for the signal normalization function
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Wrapper to read fast5, slow5, blow5 and pod5 files.
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