genomelake
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kundajelab
Simple and efficient access to genomic data for deep learning models.
I was using the package on the HG19 fasta file, the collab environment had around 13 gb of ram, but the code consumed all of it and subsequently crashed the...
Is there a way to access the JUND HepG2 data for more than chromosome 22 that is currently available (hopefully for all chromosomes 1-22 and/or X, Y)?
since the pysam dependency cause trouble (when the conda channels as misconfigured) and since chromosome name parsing is very fragile in pysam (https://github.com/kipoi/kipoi/issues/330#issuecomment-420054392), I propose to migrate from `pysam.FastaFile` to...
genomelake lists itself as compatible with python 3.6, and this makes it the only package in basepair's conda environment that prevents me from using python 3.7 and its coroutine goodness....
- closes https://github.com/kundajelab/genomelake/issues/18 - replaced pysam with pyfaidx - removed pybedtools dependency - moved the main package imports into classes (pyBigWig, pyfaidx)
https://www.bioinformatics.org/sms/iupac.html. (N/n and other ambig. symbols must be supported)
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Simple and efficient access to genomic data for deep learning models.