IMP: additional aligned sequence transformers #248
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
thermokarst
added
the
stat:blocking-other
thermokarst
suggested changes
Jun 16, 2020
There was a problem hiding this comment.
Discussed out of band with @gregcaporaso - unit tests will be added to exercise these new transformations.
Comment on lines
375
to
378
| with ff.open() as f: | ||
| for id_, seq in data.iteritems(): | ||
| sequence = skbio.DNA(seq, metadata={'id': id_}) | ||
| skbio.io.write(sequence, format='fasta', into=f) |
There was a problem hiding this comment.
This block shows up more than once in this file - might be a good candidate for a util function.
|
Do we need an |
Discussed out of band with @thermokarst - we do already have that in this plugin. |
thermokarst
removed
the
stat:blocking-other
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Outdated suggestions cannot be applied.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 adds transformers needed for qiime2/q2-feature-table#232 and qiime2/q2-alignment#70