@pnrobinson the PR has code to support drawing the variant plots, as required by #112
Please check out the Visualizers notebook for an example usage.
The PR adds several useful items:
implements genophenocorr.preprocessing.VVTranscriptCoordinateService - the class calls VV REST API to fetch the coordinates for a tx ID, e.g. NM_002834.5 #63
implements contains_pos on a Region so that we can check if a region contains a 1-based position, such as a nucleotide or an aminoacid
exposes classes that use variant validator API from genophenocorr.preprocessing package.
adds convenience methods on TranscriptCoordinates:
get 5' and 3' UTRs
get coding regions
get number of coding bases (excluding stop codon)
get number of aminoacid codons (excluding stop codon)
See an example usage in the Gather the data for visualization | Transcript coordinates section of the Visualizers notebook.
ielis
commented
6 months ago
@pnrobinson the PR has code to support drawing the variant plots, as required by #112
Please check out the Visualizers notebook for an example usage.
The PR adds several useful items:
genophenocorr.preprocessing.VVTranscriptCoordinateService- the class calls VV REST API to fetch the coordinates for a tx ID, e.g.NM_002834.5#63contains_poson aRegionso that we can check if a region contains a 1-based position, such as a nucleotide or an aminoacidgenophenocorr.preprocessingpackage.TranscriptCoordinates:Fixes #63, #112