use new Isovar API but keep old logic for determining variant effects #186
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
iskandr
changed the title
Closed
julia326
reviewed
Feb 21, 2020
test/test_shell_script.py
Outdated
| @@ -30,7 +30,8 @@ | |||
| "--mhc-predictor", "random", | |||
| "--mhc-alleles", "H2-Kb,H2-Db", | |||
| "--padding-around-mutation", "5", | |||
| "--include-mismatches-after-variant" | |||
| # TODO: figure out what happened to this argument in Isovar | |||
There was a problem hiding this comment.
Found the new name, it's --count-mismatches-after-variant
| "falls below this threshold. (default: %(default)s)")) | ||
|
|
||
| vaccine_peptide_group.add_argument( | ||
| "--num-epitopes-per-vaccine-peptide", |
There was a problem hiding this comment.
I think "per peptide" is too vague given that each epitope is itself a peptide and the longer sequence from which the vaccine peptides are drawn are also peptides.
vaxrank/core_logic.py
Outdated
| @@ -211,26 +160,29 @@ def vaccine_peptides_for_variant( | |||
| At this point, we know the variant has RNA support, as per the | |||
There was a problem hiding this comment.
this comment is no longer true
| return [] | ||
|
|
||
| variant = isovar_result.variant | ||
| long_protein_fragment = MutantProteinFragment.from_isovar_result(isovar_result) |
There was a problem hiding this comment.
why rename this to "long"? is the meaning different from before?
There was a problem hiding this comment.
I wanted to distinguish the 35mer source sequence from the 25mer vaccine peptides below
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
This PR is an attempt to make the smallest possible change while still bringing Vaxrank over to the new Isovar API. To do this I'm leaving some redundant code in Vaxrank for e.g. determine variant effects, which can be removed in a later PR.
Also:
run_vaxrank_from_parsed_args, which simplifies testing--versioninto ArgumentParser instanceImportantly this PR allows use of newer versions of pysam (>0.9), as requested in #179 and by several other people offline
After the next PR I'll start actually re-running PGV patients and comparing reports.