Track lost samples from rarefaction #351
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
…com/squirrelo/qiita into track-lost-samples-from-rarefaction
…ples-from-rarefaction
…ples-from-rarefaction
…od that was erased at some point in context.py
| table = load_table(filepath) | ||
| # remove the samples from the sets as they are found in the table | ||
| for sample in table.ids(): | ||
| proc_data_id = table.metadata(sample)['Proccessed_id'] |
There was a problem hiding this comment.
will this vary within a table?
There was a problem hiding this comment.
No but this was the "easiest" to have it ready.
There was a problem hiding this comment.
excellent, that suggests a really easy solution:
proc_data_id = table.metadata()[0]['Processed_id']
ids = set(table.ids())
all_samples[proc_data_id] = all_samples[proc_data_id] - ids
|
This seems good but travis isn't passing. I think there is a more efficient way to do the subsetting which is worth exploring particularly if |
|
Thanks @wasade for the suggestion. The change has been made and the tests |
|
Can someone else review? |
josenavas
added a commit
that referenced
this pull request
Oct 10, 2014
…tion Track lost samples from rarefaction
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Outdated suggestions cannot be applied.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 should replace #329. Note that if you have an ipython cluster running you need to terminate and then reload after doing a pull.