WASP: allele-specific pipeline for unbiased read mapping and molecular QTL discovery
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VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated #103
starting chromosome chr22
reading SNPs from file '/wynton/home/reiter/gloeb/WASP/examples/example_data/genotypes/snp_tab.h5'
/wynton/home/reiter/gloeb/miniconda3/envs/wasp/lib/python3.8/site-packages/tables/leaf.py:544: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify 'dtype=object' when creating the ndarray
key = numpy.array(key)
reducing 247303 SNPs on chromosome chr22 to 98622 positions that are polymorphic in sample of 10 individuals
processing reads
My understanding is that this won't cause a problem with current version of numpy but will for future versions?
Using numpy 1.19.4.
Running example_mapping_workflow.sh
get following warning:
My understanding is that this won't cause a problem with current version of numpy but will for future versions? Using numpy 1.19.4.