diff --git a/client/src/components/Utilities/GetCoordinates/GetCoordinates.tsx b/client/src/components/Utilities/GetCoordinates/GetCoordinates.tsx index a7cfe57..f9edd56 100644 --- a/client/src/components/Utilities/GetCoordinates/GetCoordinates.tsx +++ b/client/src/components/Utilities/GetCoordinates/GetCoordinates.tsx @@ -30,6 +30,7 @@ import { HelpPopover } from "../../main/shared/HelpPopover/HelpPopover"; import ChromosomeField from "../../main/shared/ChromosomeField/ChromosomeField"; import TranscriptField from "../../main/shared/TranscriptField/TranscriptField"; import LoadingMessage from "../../main/shared/LoadingMessage/LoadingMessage"; +import HelpTooltip from "../../main/shared/HelpTooltip/HelpTooltip"; const GetCoordinates: React.FC = () => { const useStyles = makeStyles(() => ({ @@ -254,13 +255,13 @@ const GetCoordinates: React.FC = () => { {genomicEnd != null ? renderRow("Genomic end", genomicEnd) : null} {renderRow("Transcript", results.tx_ac)} {txSegStart?.exon_ord != null - ? renderRow("Exon start", txSegStart.exon_ord) + ? renderRow("Exon start", txSegStart.exon_ord + 1) : null} {txSegStart?.offset != null ? renderRow("Exon start offset", txSegStart.offset) : null} {txSegEnd?.exon_ord != null - ? renderRow("Exon end", txSegEnd.exon_ord) + ? renderRow("Exon end", txSegEnd.exon_ord + 1) : null} {txSegEnd?.offset != null ? renderRow("Exon end offset", txSegEnd.offset) @@ -356,19 +357,39 @@ const GetCoordinates: React.FC = () => { {genomicCoordinateInfo} - setStart(event.target.value)} - helperText={start ? startText : ""} - /> - setEnd(event.target.value)} - /> + + The starting genomic position (inter-residue) of the + transcript segment. + + } + > + setStart(event.target.value)} + helperText={start ? startText : ""} + /> + + + The ending genomic position (inter-residue) of the + transcript segment. + + } + > + setEnd(event.target.value)} + /> + ); @@ -379,8 +400,8 @@ const GetCoordinates: React.FC = () => { setExonStart(event.target.value)} error={exonStart === "" && exonStartText !== ""} @@ -397,8 +418,8 @@ const GetCoordinates: React.FC = () => { setExonEnd(event.target.value)} error={exonEnd !== "" && exonEndText !== ""} diff --git a/server/src/curfu/routers/utilities.py b/server/src/curfu/routers/utilities.py index ef8fdfa..1120e74 100644 --- a/server/src/curfu/routers/utilities.py +++ b/server/src/curfu/routers/utilities.py @@ -71,8 +71,8 @@ async def get_genome_coords( FUSOR and UTA-associated tools. :param gene: gene symbol/ID on which exons lie :param transcript: transcript accession ID - :param exon_start: starting exon number - :param exon_end: ending exon number + :param exon_start: starting exon number. 1-indexed + :param exon_end: ending exon number. 1-indexed :param exon_start_offset: base offset count from starting exon :param exon_end_offset: base offset count from end exon :return: CoordsUtilsResponse containing relevant data or warnings if unsuccesful