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EB-140: Investigate if alias files can be used to recode more meaningful scaffold names #74

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EB-140: Investigate if alias files can be used to recode more meaningful scaffold names #74

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85 changes: 85 additions & 0 deletions tests/config/recode_names/config.json
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{
"assemblies": [
{
"name": "Linum_tenue_thrum_v1",
"refNameAliases": {
"adapter": {
"type": "NcbiSequenceReportAliasAdapter",
"location": {
"uri": "sequence_report.tsv"
}
}
},
"displayName": "L. tenue genome assembly GCA_946122785.1"
}
],
"defaultSession": {
"id": "lten_default_session",
"name": "Linum tenue",
"widgets": {
"hierarchicalTrackSelector": {
"id": "hierarchicalTrackSelector",
"type": "HierarchicalTrackSelectorWidget",
"view": "lten_default_session_view",
"faceted": {
"showSparse": false,
"showFilters": true,
"showOptions": false,
"panelWidth": 400
}
}
},
"activeWidgets": {
"hierarchicalTrackSelector": "hierarchicalTrackSelector"
},
"views": [
{
"id": "lten_default_session_view",
"minimized": false,
"type": "LinearGenomeView",
"trackLabels": "offset",
"offsetPx": 0,
"bpPerPx": 100,
"displayedRegions": [
{
"refName": "LG1",
"start": 0,
"end": 72476498,
"reversed": false,
"assemblyName": "Linum_tenue_thrum_v1"
}
],
"tracks": [
{
"id": "lten_default_protein_coding_genes",
"type": "FeatureTrack",
"configuration": "ltenue_v1_genes.gff",
"minimized": false,
"displays": [
{
"id": "lten_default_protein_coding_genes_display",
"type": "LinearBasicDisplay",
"heightPreConfig": 180,
"configuration": "ltenue_v1_genes.gff-LinearBasicDisplay"
}
]
},
{
"id": "lten_default_repeats",
"type": "FeatureTrack",
"configuration": "L_tenue_v1_rep.bed",
"minimized": false,
"displays": [
{
"id": "lten_default_repeats_display",
"type": "LinearBasicDisplay",
"heightPreConfig": 200,
"configuration": "L_tenue_v1_rep.bed-LinearBasicDisplay"
}
]
}
]
}
]
}
}
16 changes: 16 additions & 0 deletions tests/config/recode_names/config.yml
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organism: "Linum tenue"
assembly:
name: Linum_tenue_thrum_v1
displayName: "L. tenue genome assembly GCA_946122785.1"
accession: GCA_946122785.1
# The following url points to the original ENA upload of the assembly. It will require an alias file to be able to load the protein coding genes track
url: "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/946/122/785/GCA_946122785.1_Linum_tenue_thrum_v1/GCA_946122785.1_Linum_tenue_thrum_v1_genomic.fna.gz"
# Temp storage for alias file.
aliases: "sequence_report.tsv"
tracks:
- name: "Protein-coding genes"
url: "https://figshare.scilifelab.se/ndownloader/files/45076090"
fileName: "ltenue_v1_genes.gff.zip"
- name: "Repeats"
url: "https://figshare.scilifelab.se/ndownloader/files/48879751"
fileName: "L_tenue_v1_rep.bed.gz"
24 changes: 24 additions & 0 deletions tests/fixtures/recode_names/sequence_report.tsv
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Assembly Accession Assembly Unplaced Count Assembly-unit accession Chromosome name GC Count GC Percent GenBank seq accession Molecule type Ordering RefSeq seq accession Role Seq length UCSC style name Unlocalized Count
GCA_946122785.1 Primary Assembly CAMGYJ010000002.1 Chromosome ABCDE assembled-molecule 123556469 LG1
GCA_946122785.1 Primary Assembly CAMGYJ010000004.1 Chromosome ABCDE assembled-molecule LG2
GCA_946122785.1 Primary Assembly CAMGYJ010000005.1 Chromosome ABCDE assembled-molecule LG3
GCA_946122785.1 Primary Assembly CAMGYJ010000006.1 Chromosome ABCDE assembled-molecule LG4
GCA_946122785.1 Primary Assembly CAMGYJ010000007.1 Chromosome ABCDE assembled-molecule LG5
GCA_946122785.1 Primary Assembly CAMGYJ010000008.1 Chromosome ABCDE assembled-molecule LG6
GCA_946122785.1 Primary Assembly CAMGYJ010000009.1 Chromosome ABCDE assembled-molecule LG7
GCA_946122785.1 Primary Assembly CAMGYJ010000010.1 Chromosome ABCDE assembled-molecule LG8
GCA_946122785.1 Primary Assembly CAMGYJ010000011.1 Chromosome ABCDE assembled-molecule LG9
GCA_946122785.1 Primary Assembly CAMGYJ010000003.1 Chromosome ABCDE assembled-molecule LG10
GCA_946122785.1 Primary Assembly CAMGYJ010000001.1 Chromosome ABCDE assembled-molecule CHL
GCA_946122785.1 Primary Assembly CAMGYJ010000012.1 Chromosome ABCDE assembled-molecule MIT1
GCA_946122785.1 Primary Assembly CAMGYJ010000013.1 Chromosome ABCDE assembled-molecule MIT10
GCA_946122785.1 Primary Assembly CAMGYJ010000014.1 Chromosome ABCDE assembled-molecule MIT11
GCA_946122785.1 Primary Assembly CAMGYJ010000015.1 Chromosome ABCDE assembled-molecule MIT12
GCA_946122785.1 Primary Assembly CAMGYJ010000016.1 Chromosome ABCDE assembled-molecule MIT2
GCA_946122785.1 Primary Assembly CAMGYJ010000017.1 Chromosome ABCDE assembled-molecule MIT3
GCA_946122785.1 Primary Assembly CAMGYJ010000018.1 Chromosome ABCDE assembled-molecule MIT4
GCA_946122785.1 Primary Assembly CAMGYJ010000019.1 Chromosome ABCDE assembled-molecule MIT5
GCA_946122785.1 Primary Assembly CAMGYJ010000020.1 Chromosome ABCDE assembled-molecule MIT6
GCA_946122785.1 Primary Assembly CAMGYJ010000021.1 Chromosome ABCDE assembled-molecule MIT7
GCA_946122785.1 Primary Assembly CAMGYJ010000022.1 Chromosome ABCDE assembled-molecule MIT8
GCA_946122785.1 Primary Assembly CAMGYJ010000023.1 Chromosome ABCDE assembled-molecule MIT9