Difference between revisions of "Genome Browser json"
Anna Ryabova (Talk | contribs) |
Anna Ryabova (Talk | contribs) |
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| − | The BioUML [[Genome Browser iframe]] | + | The BioUML [[Genome Browser iframe]] can be adjusted with settings in json format. |
<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> | ||
| − | < | + | |
| − | + | {<br> | |
| − | + | <span style="color:#4a736f">//Path to genome in BioUML server repository</span><br> | |
| − | + | "sequencePath":"databases/EnsemblHuman100/Sequences/chromosomes GRCh38",<br> | |
| − | + | <span style="color:#4a736f">//[optional] Track with chromosome to be displayed on top, set "" to hide this track</span><br> | |
| − | + | "chromosomeTrack": "databases/EnsemblHuman100/Tracks/Karyotype",<br> | |
| − | + | <span style="color:#4a736f">//[optional] Chromosome to be opened first</span><br> | |
| − | + | "chromosome":"1",<br> | |
| − | + | <span style="color:#4a736f">//[optional] Start position</span><br> | |
| − | + | "from":1234,<br> | |
| − | + | <span style="color:#4a736f">//[optional] End position</span><br> | |
| − | + | "to": 5678,<br> | |
| − | + | <span style="color:#4a736f">// Tracks available for display,</span><br> | |
| − | + | <span style="color:#4a736f">// Each track is set as "Label":"Path to track in BioUML server repository"</span><br> | |
| − | + | <span style="color:#4a736f">// BigBed tracks can be shown by http/https links</span><br> | |
| − | + | "tracks":{<br> | |
| − | + | "GC content":"databases/EnsemblHuman100/Tracks/GC content",<br> | |
| − | + | "Genes":"databases/EnsemblHuman100/Tracks/Genes",<br> | |
| − | + | "Extended genes":"databases/EnsemblHuman100/Tracks/ExtendedGeneTrack",<br> | |
| − | + | "Transcripts":"databases/EnsemblHuman100/Tracks/Transcripts"<br> | |
| − | + | },<br> | |
| − | + | <span style="color:#4a736f">//Some specific track properties, set {} if no specific properties required</span><br> | |
| − | + | "trackProperties":{<br> | |
| − | + | "BBTrack_1":{"chr_name_mapping":"hg38_ucsc_to_ensembl"}<br> | |
| − | + | },<br> | |
| − | + | <span style="color:#4a736f">//[optional] Tracks visible when browser is opened, by labels in 'tracks' field</span><br> | |
| − | + | <span style="color:#4a736f">//if not set, first two tracks will be shown</span><br> | |
| − | + | "initialTracks": ["Genes", "Transcripts"]<br> | |
} | } | ||
| − | |||
Latest revision as of 09:05, 4 February 2022
The BioUML Genome Browser iframe can 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"]
}
