Get table of promoter region #34
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Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## main #34 +/- ##
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+ Coverage 93.09% 93.23% +0.14%
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Files 6 6
Lines 333 340 +7
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+ Hits 310 317 +7
Misses 23 23
|
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 | ||
| ) |
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Nice! Would you be up for PR-ing this into bioframe as well? open2c/bioframe#144
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Drafted in open2c/bioframe#152
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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 )