Difference between revisions of "Genome Browser json"
From BioUML platform
Anna Ryabova (Talk | contribs) |
Anna Ryabova (Talk | contribs) |
||
| Line 2: | Line 2: | ||
<br> | <br> | ||
All fields available for setup are described by comments below. Note, that to use this json obect as an example, all comments should be romoved.<br> | All fields available for setup are described by comments below. Note, that to use this json obect as an example, all comments should be romoved.<br> | ||
| − | + | <pre> | |
| − | //Path to genome in BioUML server repository | + | { |
| − | "sequencePath":"databases/EnsemblHuman100/Sequences/chromosomes GRCh38", | + | //Path to genome in BioUML server repository |
| − | //[optional] Track with chromosome to be displayed on top, set "" to hide this track | + | "sequencePath":"databases/EnsemblHuman100/Sequences/chromosomes GRCh38", |
| − | "chromosomeTrack": "databases/EnsemblHuman100/Tracks/Karyotype", | + | //[optional] Track with chromosome to be displayed on top, set "" to hide this track |
| − | //[optional] Chromosome to be opened first | + | "chromosomeTrack": "databases/EnsemblHuman100/Tracks/Karyotype", |
| − | "chromosome":"1", | + | //[optional] Chromosome to be opened first |
| − | //[optional] Start position | + | "chromosome":"1", |
| − | "from":1234, | + | //[optional] Start position |
| − | //[optional] End position | + | "from":1234, |
| − | "to": 5678, | + | //[optional] End position |
| − | // Tracks available for display, | + | "to": 5678, |
| − | // Each track is set as "Label":"Path to track in BioUML server repository" | + | // Tracks available for display, |
| − | // BigBed tracks can be shown by http/https links | + | // Each track is set as "Label":"Path to track in BioUML server repository" |
| − | "tracks":{ | + | // BigBed tracks can be shown by http/https links |
| − | "GC content":"databases/EnsemblHuman100/Tracks/GC content", | + | "tracks":{ |
| − | "Genes":"databases/EnsemblHuman100/Tracks/Genes", | + | "GC content":"databases/EnsemblHuman100/Tracks/GC content", |
| − | "Extended genes":"databases/EnsemblHuman100/Tracks/ExtendedGeneTrack", | + | "Genes":"databases/EnsemblHuman100/Tracks/Genes", |
| − | "Transcripts":"databases/EnsemblHuman100/Tracks/Transcripts" | + | "Extended genes":"databases/EnsemblHuman100/Tracks/ExtendedGeneTrack", |
| − | }, | + | "Transcripts":"databases/EnsemblHuman100/Tracks/Transcripts" |
| − | //Some specific track properties, set {} if no specific properties required | + | }, |
| − | "trackProperties":{ | + | //Some specific track properties, set {} if no specific properties required |
| − | "BBTrack_1":{"chr_name_mapping":"hg38_ucsc_to_ensembl"} | + | "trackProperties":{ |
| − | }, | + | "BBTrack_1":{"chr_name_mapping":"hg38_ucsc_to_ensembl"} |
| − | //[optional] Tracks visible when browser is opened, by labels in 'tracks' field | + | }, |
| − | //if not set, first two tracks will be shown | + | //[optional] Tracks visible when browser is opened, by labels in 'tracks' field |
| − | "initialTracks": ["Genes", "Transcripts"] | + | //if not set, first two tracks will be shown |
| + | "initialTracks": ["Genes", "Transcripts"] | ||
} | } | ||
| + | </pre> | ||
Revision as of 20:02, 3 February 2022
The BioUML Genome browser iframe and be adjusted with settings in json format.
All fields available for setup are described by comments below. Note, that to use this json obect as an example, all comments should be romoved.
{
//Path to genome in BioUML server repository
"sequencePath":"databases/EnsemblHuman100/Sequences/chromosomes GRCh38",
//[optional] Track with chromosome to be displayed on top, set "" to hide this track
"chromosomeTrack": "databases/EnsemblHuman100/Tracks/Karyotype",
//[optional] Chromosome to be opened first
"chromosome":"1",
//[optional] Start position
"from":1234,
//[optional] End position
"to": 5678,
// Tracks available for display,
// Each track is set as "Label":"Path to track in BioUML server repository"
// BigBed tracks can be shown by http/https links
"tracks":{
"GC content":"databases/EnsemblHuman100/Tracks/GC content",
"Genes":"databases/EnsemblHuman100/Tracks/Genes",
"Extended genes":"databases/EnsemblHuman100/Tracks/ExtendedGeneTrack",
"Transcripts":"databases/EnsemblHuman100/Tracks/Transcripts"
},
//Some specific track properties, set {} if no specific properties required
"trackProperties":{
"BBTrack_1":{"chr_name_mapping":"hg38_ucsc_to_ensembl"}
},
//[optional] Tracks visible when browser is opened, by labels in 'tracks' field
//if not set, first two tracks will be shown
"initialTracks": ["Genes", "Transcripts"]
}
