ADD: detect donor indicators pipeline #109
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
Oddant1
reviewed
Nov 5, 2024
| import pandas as pd | ||
| from qiime2 import Metadata | ||
|
|
||
| # TODO: Change Import path. |
There was a problem hiding this comment.
Yes,
I would love to hear your opinion but the imports are going to change once this massive pr gets merged(#101 ) but I didnt want to base this pr off that pr, so I left a todo
| from q2_fmt._peds import _check_for_time_column, _check_reference_column | ||
|
|
||
|
|
||
| def detect_donor_indicators(ctx, table, reference_column, time_column, |
There was a problem hiding this comment.
There should probably be tests that call this pipeline
q2_fmt/_ancombc.py
Outdated
Comment on lines
46
to
47
| """Checks if column is in the metdata | ||
| Checks that column is in the metdata and creates helpful error messages. |
There was a problem hiding this comment.
This doesn't seem to be an accurate description of what this does.
|
@cherman2 most of these are trivial only like 1 or 2 are real |
Co-authored-by: Anthony Simard <[email protected]>
Co-authored-by: Anthony Simard <[email protected]>
Co-authored-by: Anthony Simard <[email protected]>
Co-authored-by: Anthony Simard <[email protected]>
|
Hi @Oddant1, |
ebolyen
reviewed
Nov 7, 2024
Co-authored-by: Evan Bolyen <[email protected]>
|
I think this is ready to merge @Oddant1, Would you merge for me? |
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Outdated suggestions cannot be applied.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.
Adds a pipeline for filtering feature-table down to baseline and donors, and running ancombc to detect important donor features.