viz gives error

[NextGenSeek]

• Spladder version: 3.0.5
• Python version: Python 3.10.13
• Operating System: Mac

Description

After running spladder build and spladder test without errors, I used spladder viz and ran into an error. I tried different viz options, but same error, see below. Could you please help me solving this issue?

What I Did

spladder viz --track coverage file1.bam, file2.bam --outdir direction
spladder viz --track splicegraph gene1 --outdir direction

Traceback (most recent call last): File "/path/to/anaconda3/lib/python3.10/site-packages/scipy/init.py", line 137, in getattr return globals()[name] KeyError: 'array'

During handling of the above exception, another exception occurred: File "/path/to/anaconda3/bin/spladder", line 8, in sys.exit(main()) File "/path/to/anaconda3/lib/python3.10/site-packages/spladder/spladder.py", line 229, in main options.func(options) File "/path/to/anaconda3/lib/python3.10/site-packages/spladder/spladder_viz.py", line 210, in spladder_viz all_gene_names = get_gene_names(options.outdir, options.confidence, options.validate_sg, options.verbose) File "/path/to/anaconda3/lib/python3.10/site-packages/spladder/helpers_viz.py", line 37, in get_gene_names gene_names = sp.array([x.name.split('.')[0] for x in tmp_genes]) File "/path/to/anaconda3/lib/python3.10/site-packages/scipy/init.py", line 139, in getattr raise AttributeError( AttributeError: Module 'scipy' has no attribute 'array'

[akahles]

Thanks for reporting. This was caused by an old scipy dependency. I fixed it in the development branch. Should be available with the next release in the coming days.

[Midreancgle]

Hello I have also encountered the same problem, when will the new version be released to fix this problem?@akahles Expect a quick fix. Thanks!

[ADvorkinGheva]

Hello @akahles, I am using SplAdder 3.1.0 and am still experiencing the same issue - same error messages. Is there a different stable version in which the scipy dependency has been removed? Thank you very much!

[akahles]

Should be addressed now in release 3.1.1