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…ction Prior to this change, we relied on the user supplying an appropriate HGNC symbol for their target as their target name. This is no longer required. Instead, transcript selection follows the following algorithm: 1. Align the target sequence with BLAT. 2. Fetch transcripts which overlap the aligned region (notably, without an HGNC symbol filter). 3. Perform transcript selection within each distinct gene. This will either leave us with (a) one transcript in cases where we have no overlapping genes in a region, or, (2) one transcript per gene when multiple genes overlap an aligned region. These will be our candidate transcripts. 4. If we still have more than one candidate transcript, we compare the similarity of each candidate to the provided target sequence. Select the most similar transcript.
…rence selection to set it
This function queries the Ensembl API with exponential backoff as needed, returning a list of features which overlap the passed region.
…tein-level-alignment
…over-to-protein-level-alignment Auto-failover for Protein Level Alignment
…liance-on-user-supplied-target-metadata Reduce reliance on user supplied target metadata during transcript selection
Computes a new `gene_info` property for all mapped targets. This property is defined by an `hgnc_symbol` and a `selection_method`. The hgnc symbol is the HGNC symbol of the gene to which this target relates. The selection method is the method by which this symbol was selected and may be: - `tx_selection`: via the selected transcript - `alignment_max_covered_bases`: based on the gene 'feature' (via Ensembl) which covered the most bases of the aligned target - `variants_max_covered_bases`: same as `alignment_max_covered_bases`, but based on variant bases rather than aligned bases - `target_metadata`: based on parsing the target metadata the user supplied - `target_category`: no gene info was selected because the target was not protein coding (see #66) Various helpers were added to `dcd_mapping.annotate` which support this calculation. Gene info selection should not cause job failures, and will simply fail to select gene info on failure.
…-for-mapped-targets Output gene name for mapped targets
…ble-cdot-url feat: add CDOT_URL envvar to allow configurable endpoint in seq fetches
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Features
Bug Fixes
c.endogenous mapping targets map to incorrect genomic positions #70 via Fix endogenous genomic mapping #68Maintenance
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