add command line option for oncokb annotation

[rjcorb]

Purpose/implementation Section

Update 09-lollipop analysis module so that OncoKB access token is provided in command line when running analysis module.

What scientific question is your analysis addressing?

NA

What was your approach?

• Divided the analysis module into three scripts:

  1. 01-create-maf-subset.Rmd subsets MAF for oncokb annotation2.
  2. 02-run-oncokb-annotation.sh runs MafAnnotator.py from oncokb_annotator GitHub repo3.
  3. 03-create-lollipop.Rmd generates lollipop plots 4.

• Set variable ONCOKB to be defined with Oncokb access token when running run_lollipop.sh shell script.

• Created README file with instructions on defining access token variable when running module.

What GitHub issue does your pull request address?

Ticket #59

Directions for reviewers. Tell potential reviewers what kind of feedback you are soliciting.

Which areas should receive a particularly close look?

• confirm that module runs with personal Oncokb access token
• confirm changes in plot atria-lollipop-comp.tiff is as expected

Is there anything that you want to discuss further?

No

Is the analysis in a mature enough form that the resulting figure(s) and/or table(s) are ready for review?

Results

What types of results are included (e.g., table, figure)?

MAF subset tables: hgat-goi.maf.tsv snv-dgd-goi.maf.tsv

OncoKB annotation results: dgd_maf-goi-oncokb.tsv snv-consensus-plus-hotspots-hgat-oncokb.maf.tsv

Lollipop plots: atrx-lollipop-all.pdf atrx-lollipop-alt-neg.tiff atrx-lollipop-alt-pos.tiff atrx-lollipop-comp.tiff atrx-lollipop-oncogenic.pdf atrx-lollipop-vus.pdf

What is your summary of the results?

The atria-lollipop-comp.tiff plot now includes one additional sample in the ALT- group (N=47 vs N=46 previously).

Documentation Checklist

• [X] This analysis module has a README and it is up to date.
• [X] The analytical code is documented and contains comments.

[jharenza]

Script 01 runs fine for me, but I am getting an error with script 2:

Traceback (most recent call last):
  File "/home/oncokb-annotator/MafAnnotator.py", line 7, in <module>
    from AnnotatorCore import setsampleidsfileterfile
  File "/home/oncokb-annotator/AnnotatorCore.py", line 5, in <module>
    import requests
ModuleNotFoundError: No module named 'requests'

My token is still valid, so I am not sure if I don't fully have the oncokb annotator fully installed in the docker image somehow. Assuming this worked fine for you in docker?

[rjcorb]

I just checked and there are two dependencies not installed in the docker image. I believe I installed them while in the docker container, hence why it isn't reproducible currently.

[jharenza]

Perfect, thanks - will update the dockerfile in a separate PR - I just looked over there and missed the "common" ones when checking!