Draft code to standardize frame of motifs#486
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…tion motif if needed
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Adding auto generated to reference descriptions and removing from gene descriptions Editing descriptions to say explicitly say auto generated from gene Fix formatting fix formatting Editing script to derive canonical motifs from schema fixing adding canonical_motifs to function call
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This looks good! I'm going to hold off on merging and do it with the lit review. |
| chr4 3076660 3076696 CCG 3 HD_HTT_flank | ||
| chr4 39350099 39350103 AAGGG 5 CANVAS_RFC1 | ||
| chr4 41747989 41748049 GCN 3 CCHS_PHOX2B | ||
| chr4 41747989 41748049 NGC 3 CCHS_PHOX2B |
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Why isn't this one GCN? It's on the preferred motifs list.
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I don't know. I think GCN is especially relevant because this one is protein coding.
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Okay I think I understand what is happening. NGC is the reverse complement of GCN. We changed the code to make the gene orientation the canonical one, and GCN is the canonical orientation for this motif. Because of this, the reference orientation is now found using the reverse complement script (as this one is - strand), and the reverse complement is NGC. Since this .bed file is updated using the reference orientation, it switched to NGC.
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So I don't think it is necessarily a bug but it might be a problem that stems from making the gene orientation overwrite the ref direction
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You're right, and I actually think this is correct behavior. The N should be in the first position when the gene is on the negative strand.
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Your changes look right, but some of the downstream files don't look right to me. I might need to investigate a little further before merging in case there's a bug. |
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Description
Summarize the changes
Fixes: # Link to any relevant issues and/or discussions
Major Changes
Minor Changes
-Minor formatting changes in "check_loci"
Checklist
CITATION.cff, format X.Y.Z. If any major changes, increment Y. If only minor changes, increment Z. If the breaking change (rare), increment X.