rename sample ids #4
Open
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
wasade
reviewed
Oct 12, 2016
| qiime_mapping_header = line | ||
| continue | ||
| # use filename as key | ||
| key = line[3] |
There was a problem hiding this comment.
This seems a bit fragile. What about using pandas to parse the table and pull out the column of interest?
import pandas as pd
table = pd.read_csv(qiime_mapping_file_fp, sep='\t', dtype=object)
table.set_index('#SampleID', inplace=True)...that will trigger changes in the below code but I think the result will be better
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Outdated suggestions cannot be applied.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.
Script renames sample IDs in mapping file and BIOM table.