From 683fca2d165757cbf9291f2d521618bba9b06f1c Mon Sep 17 00:00:00 2001 From: Jeremy Arbesfeld Date: Thu, 3 Oct 2024 13:56:39 -0400 Subject: [PATCH 1/4] Use 1-indexing for exon numbers in convert coordinates --- .../components/Utilities/GetCoordinates/GetCoordinates.tsx | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/client/src/components/Utilities/GetCoordinates/GetCoordinates.tsx b/client/src/components/Utilities/GetCoordinates/GetCoordinates.tsx index a7cfe57..e93dc84 100644 --- a/client/src/components/Utilities/GetCoordinates/GetCoordinates.tsx +++ b/client/src/components/Utilities/GetCoordinates/GetCoordinates.tsx @@ -254,13 +254,13 @@ 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) From 31e6add95ee773b84ea8a69bae3c9ce6d78ecbae Mon Sep 17 00:00:00 2001 From: Jeremy Arbesfeld Date: Fri, 4 Oct 2024 14:22:28 -0400 Subject: [PATCH 2/4] Fix styling --- .../GetCoordinates/GetCoordinates.tsx | 55 +++++++++++++------ server/src/curfu/routers/utilities.py | 4 +- 2 files changed, 40 insertions(+), 19 deletions(-) diff --git a/client/src/components/Utilities/GetCoordinates/GetCoordinates.tsx b/client/src/components/Utilities/GetCoordinates/GetCoordinates.tsx index e93dc84..1b6ab81 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(() => ({ @@ -356,19 +357,39 @@ const GetCoordinates: React.FC = () => { {genomicCoordinateInfo} - setStart(event.target.value)} - helperText={start ? startText : ""} - /> - setEnd(event.target.value)} - /> + + The starting genomic position of the transcript segment. + Inter-residue. + + } + > + setStart(event.target.value)} + helperText={start ? startText : ""} + /> + + + The ending genomic position of the transcript segment. + Inter-residue + + } + > + 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 From 1a61f862d9f4858c4607825a658fdf6e7d003c13 Mon Sep 17 00:00:00 2001 From: Jeremy Arbesfeld Date: Mon, 7 Oct 2024 08:50:15 -0400 Subject: [PATCH 3/4] Fix inter-residue --- .../src/components/Utilities/GetCoordinates/GetCoordinates.tsx | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/client/src/components/Utilities/GetCoordinates/GetCoordinates.tsx b/client/src/components/Utilities/GetCoordinates/GetCoordinates.tsx index 1b6ab81..55575fe 100644 --- a/client/src/components/Utilities/GetCoordinates/GetCoordinates.tsx +++ b/client/src/components/Utilities/GetCoordinates/GetCoordinates.tsx @@ -379,7 +379,7 @@ const GetCoordinates: React.FC = () => { title={ The ending genomic position of the transcript segment. - Inter-residue + Inter-residue. } > From 2636d05c3af5dfa0c3f10c71482b7f701efdb138 Mon Sep 17 00:00:00 2001 From: Jeremy Arbesfeld Date: Mon, 7 Oct 2024 09:09:02 -0400 Subject: [PATCH 4/4] format fix --- .../Utilities/GetCoordinates/GetCoordinates.tsx | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/client/src/components/Utilities/GetCoordinates/GetCoordinates.tsx b/client/src/components/Utilities/GetCoordinates/GetCoordinates.tsx index 55575fe..f9edd56 100644 --- a/client/src/components/Utilities/GetCoordinates/GetCoordinates.tsx +++ b/client/src/components/Utilities/GetCoordinates/GetCoordinates.tsx @@ -361,8 +361,8 @@ const GetCoordinates: React.FC = () => { placement="bottom" title={ - The starting genomic position of the transcript segment. - Inter-residue. + The starting genomic position (inter-residue) of the + transcript segment. } > @@ -378,8 +378,8 @@ const GetCoordinates: React.FC = () => { placement="bottom" title={ - The ending genomic position of the transcript segment. - Inter-residue. + The ending genomic position (inter-residue) of the + transcript segment. } >