Tavi Nathanson
Tavi Nathanson
Hello! I store all my files in S3 buckets, and run a sync with S3 before and after every Snakemake job. S3 does not support preserving the original last modified...
I often see errors like: ``` opam@7641e4cbcf64:/coclo$ ./disco.sh add-new-nfs tavi-cloud-nfs-16 2000 /nfs-pool-16 mount.nfs: access denied by server while mounting tavi-cloud-nfs-16:/nfs-pool ``` I then need to manually mount, add the server...
We use the caching functions a lot, but don't expose any simple primitives to make caching cleaner and less repetitive.
Thanks for the suggestion, @rohanpai!
Which means that, if the `StopIteration` was due to a real issue vs. just a truly empty VCF, that error will be hidden after the empty `VariantCollection` is cached. See...
We haven't necessarily wanted to incorporate multiple samples into one `Cohort` object, as that complicates every part of the library. For example: * Which samples does `missense_snv_count` count? * How...
Currently, if `on` is specified as a `cohort` in e.g. `plot_benefit`, a `kwargs are not supported when collecting multiple functions` is raised; however, if `on` just has a single key/value...
Making a `Cohort` with appropriate `Patient` and `Sample` objects can be a bit of a pain. It's a necessary pain when reading in data from multiple sources, as we often...
While using Epidisco to generate e.g. neoantigen calls is non-ideal for integration with Cohorts, where we want to have all the intermediate files available in the Cohorts cache, perhaps we...
From @julia326: ``` /home/julia/envs/smoking3/lib/python3.4/site-packages/cohorts/cohort.py in () 41 import varcode 42 from varcode import EffectCollection, VariantCollection ---> 43 from mhctools import NetMHCcons, EpitopeCollection 44 from topiary import predict_epitopes_from_variants, epitopes_to_dataframe 45 from...