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Better 10x read errors #444

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merged 5 commits into from Jan 26, 2019

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ivirshup commented Jan 23, 2019

An addendum to #442, now if you try to read a 10x file and pass a genome it doesn't have, the error tells you which file it was and the genomes it does have:

In [1]: import scanpy as sc 
   ...: sc.read_10x_h5("scanpy/tests/_data/10x_data/1.2.0/filtered_gene_bc_matrices_h5.h5", "not a genome")                                                                          
---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)

...

ValueError: Could not find genome 'not a genome' in 'scanpy/tests/_data/10x_data/1.2.0/filtered_gene_bc_matrices_h5.h5'. Available genomes are: ['hg19_chr21']

Previous behavior:

In [1]: import scanpy as sc 
   ...: sc.read_10x_h5("scanpy/tests/_data/10x_data/1.2.0/filtered_gene_bc_matrices_h5.h5", "not a genome")                                                                          
---------------------------------------------------------------------------
NoSuchNodeError                           Traceback (most recent call last)

...

Exception: Genome not a genome does not exist in this file.

ivirshup and others added some commits Jan 23, 2019

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falexwolf commented Jan 26, 2019

Great!

@falexwolf falexwolf merged commit a29bd92 into theislab:master Jan 26, 2019

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