New user "un-boxing" experience

[bwalsh]

Use case: install vrs-python, run vcf_annotation

It would be useful to have a command line oriented "quick start":

• goal: user should be quickly able to do a pip install, download known VCF examples, run vrs-python with remote seqrepo
• setup: documented values for --seqrepo_dp_type --seqrepo_base_url. I was stumped by this until I read through python notebooks to find values.
• data: known vcf files a set of vcf files would be useful. I would up downloading the test fixture to do a sanity check.
  • Question: What is the best population of variants in the known vcf files? Perhaps some that should produce hits in metakb &/or clingen?

It would be useful to have a command line oriented "production ready":

• goal: user should be quickly install local seqrepo and run vrs-python at "scale"
• setup: seqrepo installs to /usr/local/share/seqrepo by default. This may not be possible in environments where user lacks privileges. Perhaps feature --seqrepo_root_dir more prominently in documentation?

Usage:

• Should the seqrepo installation oriented options [seqrepo_dp_type, seqrepo_base_url, seqrepo_root_dir] have environmental variable equivalents? This simplifies downstream scripting.
• --vrs_pickle_out I might be missing something obvious, but I needed to do an eval() in order to use the results.

from pprint import pprint
import pickle
import ast
import requests

# load pickled dict
with open('vrs_objects.pkl', 'rb') as f:
    vrs_objects = pickle.load(f)
    for k, v in vrs_objects.items():
        vrs_objects[k] = ast.literal_eval(v)

# view details        
pprint(vrs_objects)

Application

Once vrs identifiers are calculated, the question is What can I do with them?. It would be useful if there was a known endpoint using the same schema versions. See attached notebook example.

[korikuzma]

Make docs more visible, such as https://github.com/ga4gh/vrs-python/blob/main/docs/extras/vcf_annotator.md

[bwalsh]

notebook:
https://drive.google.com/file/d/1aHH6ii5K6ocseF-qrzMQr9AYPKNzhzfN/view?usp=sharing

[jsstevenson]

Per the last call, @katiestahl and I will be taking a crack at this in the medium-term

[github-actions]

This issue was marked stale due to inactivity.