Get table of promoter region #34
Draft
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
Codecov Report
Additional details and impacted files@@ Coverage Diff @@
## main #34 +/- ##
==========================================
+ Coverage 88.40% 88.96% +0.55%
==========================================
Files 6 6
Lines 138 145 +7
==========================================
+ Hits 122 129 +7
Misses 16 16
|
ivirshup
reviewed
May 2, 2023
Comment on lines
+167
to
+177
| tx_ss = np.where( | ||
| tx_table["seq_strand"] == 1, | ||
| tx_table["gene_seq_start"], | ||
| tx_table["gene_seq_end"], | ||
| ) | ||
| tx_table["promoter_seq_start"] = np.where( | ||
| tx_table["seq_strand"] == 1, tx_ss - upstream, tx_ss - downstream | ||
| ) | ||
| tx_table["promoter_seq_end"] = np.where( | ||
| tx_table["seq_strand"] == 1, tx_ss + downstream, tx_ss + upstream | ||
| ) |
There was a problem hiding this comment.
Nice! Would you be up for PR-ing this into bioframe as well? open2c/bioframe#144
There was a problem hiding this comment.
Drafted in open2c/bioframe#152
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Outdated suggestions cannot be applied.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.
Closes #4
Implemented strand-aware selection of region around TSS.
Example usage:
TO DO
seq_nameandseq_strandfor each gene (i.e. relies on merging Initial columns functions #22 )