Adds support for clinical annotations #89
Merged
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
Rohan-cod
force-pushed
the
clinical-annotations
branch
3 times, most recently
from
6ad9643 to
e182dcc
Compare
Rohan-cod
force-pushed
the
clinical-annotations
branch
7 times, most recently
from
e440e30 to
2ea2a3f
Compare
Rohan-cod
force-pushed
the
clinical-annotations
branch
2 times, most recently
from
c21a49c to
3eb7166
Compare
The following changes were made in this commit: * Updated the code to add support for clinical annotations. * Added the corresponding integration test.
Rohan-cod
force-pushed
the
clinical-annotations
branch
from
3eb7166 to
329e34c
Compare
srgothi92
approved these changes
Aug 24, 2021
rhdolin
approved these changes
Aug 24, 2021
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Outdated suggestions cannot be applied.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.
Description
Updated the code to add support for
clinical annotations. As part of this, a new parameter(annotation_filename) was added to get the file that contains the annotations, a new data structure(diagnostic_implication) was added for the clinical significance and phenotype components, and three more variant components, namely transcript reference sequence, DNA change, and Amino Acid change were added.Added the corresponding
integration test.Fixes #88
How Has This Been Tested?
The code has been tested by running all the unit tests using the command
python -m unittestand validated the PEP 8 formatting usingpycodestyle.