Conversation
- no installation script - parallelized - lid on memory - modularized, easier to make changes - definitions file - file-format control - logging
- made agnostic towards tree with more leafs than those present in the current dataset - added new column: EC - renamed columns: - OG_type -> OG_AT - OG_NODE_COV > OG_NP
- improved column names - added `nodes.summary` file - checked correctness
- small speedup (~0.2s per iteration faster) through `np.select()` instead of `pd.apply()` logic
- better default for `-M`
- speedup of OG_type_TG1 - added median back in
- removed df_orthogroups as arg (it pulls it from input folder)
- changed default format to parquet - changed default filenames - interpro-specific changes
- convenience getter functions for dfs - added filter arg to parquet loading
- better function calls - more loading from disk than keeping in memory - interpro works - entropy works - curve data
- improved color handling
- changed order of columns in annotation_df
validated entropy
Reduced memory reqs
- added preprocess module - added detection of orphan elements in FASTA/OGs - added tally plot - changed plotting - isolated tree part
- repeats - plotting volcano
Improved interpro
![sourcery-ai[bot]](https://avatars.githubusercontent.com/in/48477?s=60&v=4){kind=small}
There was a problem hiding this comment.
Sorry @DRL, your pull request is larger than the review limit of 150000 diff characters
This file contains hidden or 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
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
No description provided.