Metabolic reconstruction #1413
Merged
Metabolic reconstruction #1413
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
…ithout unique key in first column of table
…ver possible to avoid confusion later
|
Amazing work, @ivagljiva. I see a lot of very good programming practices in here. thank you for that and I can't wait for people to start playing with this new anvi'o toy! I will send some relatively minor comments for things I saw as I went through the code in a second for your consideration. |
meren
reviewed
Apr 22, 2020
|
Wow, @meren, thank you for reviewing so thoroughly and quickly! I'll get to work on fixing these things :) |
…eset, and check for writability of dir
…ecified directory with --reset
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Outdated suggestions cannot be applied.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.
Dear @meren, @ekiefl, @watsonar, @semiller10 (and anyone else who is interested),
The purpose of this pull request is primarily to merge the metabolic estimation code that I have so far, but also includes a couple of other related improvements to the codebase. I would be grateful if you could review it and provide some feedback.
The major changes you will find here are:
anvi-run-pfamsandanvi-run-hmmshmmsearchrather thanhmmscan. For pfams,hmmsearchis now the defaulthmmpressis run during pfams setup rather than unpacking the profiles into a temporary directory before doing the HMM searchThank you very much!