Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

adding help text for seq details. #1203

Merged
merged 2 commits into from
Sep 27, 2023
Merged

adding help text for seq details. #1203

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
b0efd5c
adding help text for seq details. UNTESTED!
scottcain Sep 27, 2023
520e4b4
fixed formatting/syntax
scottcain Sep 27, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
44 changes: 44 additions & 0 deletions apps/main-app/src/components/sequencePanel/sequencePanelSectionHelp.js
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,44 @@
import React from 'react';

const SequencePanelSectionHelp = () => (
<div>
<p>
The set of genome features contributed by each MOD is used by this
section to obtain the sequence of the gene and a list of transcripts.
When a transcript is selected, Sequence Details will highlight it
according to the scheme selected in the “Mode” menu. The options are:
</p>
<ul>
<li>gene - The genomic sequence from start to end with portions that
are UTR and coding highlighted</li>
<li>CDS - The coding sequence of the mRNA that is the result of in
silico splicing</li>
<li>cDNA - The CDS with UTRs added</li>
<li>protein - The amino acid sequence that results from the CDS in
silico transcription</li>
<li>genomic - The stretch of sequence from start to end with no
special highlighting</li>
<li>genomic +500bp up and down stream - The stretch of sequence from
start to end with 500 base pairs of padding on both ends</li>
<li>gene with collapsed introns - same as gene, but the introns are
compressed to 10 base pairs at the splice junction and the remainder
replaced with ellipses</li>
<li>gene with 500bp up and down stream - same as “gene” but with 500bp
of up and down stream sequence added</li>
<li>gene with 500bp up and down stream and collapsed introns - same as
“gene with collapsed introns” but with up and downstream padding
added</li>
</ul>
<p>
After selecting the mode, you can copy either the “plain text” of the
sequence (that is, without any color highlighting) or copy the
highlighted text with the provided buttons. The plain text option is
provided for copying into web forms (such as BLAST) and text editors that
don’t allow formatting. The copy with highlights button will allow you to
paste into a “rich” text editor that will preserve the highlighting from
the web page.
</p>
</div>
);

export default SequencePanelSectionHelp;
6 changes: 5 additions & 1 deletion apps/main-app/src/containers/genePage/index.js
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -45,6 +45,7 @@ import GeneSymbol from '../../components/GeneSymbol';
import PhenotypeCrossRefs from './PhenotypeCrossRefs';
import SpeciesName from '../../components/SpeciesName';
import SequenceFeatureViewerSectionHelp from '../../components/sequenceFeatureViewer/sequenceFeatureViewerSectionHelp';
import SequencePanelSectionHelp from '../../components/sequencePanel/sequencePanelSectionHelp';
import TransgenicAlleleSectionHelp from '../../components/transgenicAlleles/transgenicAllelesSectionHelp';
import DiseaseSectionHelp from '../../components/disease/diseaseSectionHelp';

Expand Down Expand Up @@ -212,7 +213,10 @@ const GenePage = ({geneId}) => {
/>
</Subsection>

<Subsection title={SEQUENCE_DETAILS}>
<Subsection
help={<SequencePanelSectionHelp />}
title={SEQUENCE_DETAILS}
>
<SequencePanel
refseq={genomeLocation.chromosome}
start={genomeLocation.start}
Expand Down