create_from_cellranger() incompatible w/ Cellranger 3.0

Having installed CellRanger 3.0 (v3.0.1), I tried to generate loom files using create_from_cellranger() (loompy v2.0.16). I got the following:

File "/home/user/virtualenv-15.2.0/pyEnv2/lib/python3.6/site-packages/loompy/loompy.py", line 1025, in create_from_cellranger
    genome = [f for f in os.listdir(matrix_folder) if not f.startswith(".")][0]
FileNotFoundError: [Errno 2] No such file or directory: '/data/user/chromium/samples/10X_069/outs/filtered_gene_bc_matrices'

According to the release notes of CellRanger 3.0, there are some changes in the output file format (quoting some points bellow):

Output File Format Changes

• The file formats of the gene-barcode matrix (now called the feature-barcode matrix) have changed to accomodate Feature Barcoding results.
• The mtx and barcodes.tsv files are now gzipped to save disk space
• The genes.tsv file has been renamed features.tsv.gz, and contains extra columns indicating the feature_type of each gene / feature.

https://support.10xgenomics.com/single-cell-gene-expression/software/release-notes/3-0

[slinnarsson]

I pushed 2.0.17 just now and it should be in pypi shortly.

Note: conda loompy is not updated, so please use pip install -U loompy to update

[pl-ki]

Right, I forgot to push this, will do shortly!