Find the ensembl_transcript_id and codon postions for one variant
getTranscriptIdsForOneCodonVariant(
variant,
transcriptRegions,
checkRegion,
start,
end
)one row of variants table
transcripts structure table from ensembl
check if a transcript within a region stopCodon or startCodon
column name of the start region of checkRegion in transcripts structure table
column name of the end region of checkRegion in transcripts structure table
A data table containing two columns: ensembl_transcript_id (id of transcripts for each variant which its mutation Pos is within those transcripts checkRegion.) codon_positions (positions of each nucleotides in the codon)
For each variant, get all transcripts and extract their checkRegion's coordinates. For each transcript, check if the mutation Pos is within the region, if so, add that transcript's ensembl_transcript_id. If the mutation Pos is within multiple transcripts checkRegions, the transcripts ids are concatenate into one string with ";".