in silico deletion script: hound_isd_bed #43
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added 2 commits
September 25, 2024 13:57
davek44
reviewed
Oct 1, 2024
| scores_h5.create_dataset("seqs", dtype="bool", shape=(num_seqs, options.mut_len, 4)) | ||
| for snp_stat in options.snp_stats: | ||
| scores_h5.create_dataset( | ||
| snp_stat, dtype="float16", shape=(num_seqs, options.mut_len, 4, num_targets) |
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Shouldn't the 3rd axis disappear? In ISM, it represents the alternative nucleotides, but they don't exist here.
| ref_preds_stitch, alt_preds, options.snp_stats, None | ||
| ) | ||
| for snp_stat in options.snp_stats: | ||
| scores_h5[snp_stat][si, mi - mut_start, 0] = ism_scores[snp_stat] |
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By dropping the 3rd axis, you can remove the "0]" here.
| ref_preds.append(ref_preds_shift) | ||
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| # for mutation positions | ||
| for mi in range(mut_start, mut_end): |
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If the deletion size is >1, I think you'd want to advance your index by the size. Otherwise, your deleting overlapping k-mers, and I can't think of a scenario where you'd prefer that over the single nt deletions.
| ) | ||
| parser.add_option( | ||
| "-s", | ||
| dest="del_len", |
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"del_size" maybe so -s matches the first letter?
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Description of your changes
Added new script hound_isd_bed.py analogous to the hound_ism_bed.py. The ISD script performs in silico deletions instead of in silico mutations.
Stitching is performed on reference to avoid doubling of the deleted sequence portion in the left and right shifts in alternative.
New arguments: "-s", dest="del_len" (Deletion size for ISD [Default: 1])
Type of change
(If applicable) How has this been tested?
Tested on the MPRA-deletion dataset (M Kircher, Nat Comm 2019) -- F9, HBG1 and LDLR gene promoters