Change add_dna_sequences to use get_seq
#1867
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Codecov ReportBase: 90.42% // Head: 90.42% // No change to project coverage 👍
Additional details and impacted files@@ Coverage Diff @@
## main #1867 +/- ##
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Coverage 90.42% 90.42%
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Files 141 141
Lines 11058 11058
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Hits 9999 9999
Misses 1059 1059
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martinkim0
commented
Jan 25, 2023
| @@ -357,7 +357,6 @@ def _concat_anndata(multi_anndata, other): | |||
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| def _dna_to_code(nt: str) -> int: | |||
| nt = nt.upper() | |||
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not necessary as sequences are uppercased in add_dna_sequences
added 2 commits
January 25, 2023 14:48
martinkim0
commented
Jan 25, 2023
Comment on lines
+446
to
448
| block_mid = (chrom_df[start_var_key] + chrom_df[end_var_key]) // 2 | ||
| block_starts = block_mid - (seq_len // 2) | ||
| block_ends = block_starts + seq_len |
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adamgayoso
approved these changes
Jan 26, 2023
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add_dna_sequencefails in some datasets such as the Buenrostro 2018 used in scBasset batch correction. See notebook: https://colab.research.google.com/drive/1cTkQqQGmbTAV7jtFiV5bK7sr7nD0g3rJ?usp=sharing. New code outputs the same dna sequence for the initial tutorial.