From 8da8af7e1e36c0ebe3daa92cfcfcab325b651e93 Mon Sep 17 00:00:00 2001 From: Daniel P Brink Date: Thu, 28 Nov 2024 15:56:31 +0100 Subject: [PATCH] Add files for testing NcbiSequenceReportAliasAdapter Experiment synopsis: run dockermake --test, change .assemblies[].refNameAliases.adapter.type from RefNameAliasAdapter to NcbiSequenceReportAliasAdapter, copy of sequence_report.tsv to tests/data/recode_names, run browse script --- tests/config/recode_names/config.json | 85 +++++++++++++++++++ tests/config/recode_names/config.yml | 16 ++++ .../fixtures/recode_names/sequence_report.tsv | 24 ++++++ 3 files changed, 125 insertions(+) create mode 100644 tests/config/recode_names/config.json create mode 100644 tests/config/recode_names/config.yml create mode 100644 tests/fixtures/recode_names/sequence_report.tsv diff --git a/tests/config/recode_names/config.json b/tests/config/recode_names/config.json new file mode 100644 index 00000000..0308a9b7 --- /dev/null +++ b/tests/config/recode_names/config.json @@ -0,0 +1,85 @@ +{ + "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" + } + ] + } + ] + } + ] + } +} diff --git a/tests/config/recode_names/config.yml b/tests/config/recode_names/config.yml new file mode 100644 index 00000000..0c6cbcae --- /dev/null +++ b/tests/config/recode_names/config.yml @@ -0,0 +1,16 @@ +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" \ No newline at end of file diff --git a/tests/fixtures/recode_names/sequence_report.tsv b/tests/fixtures/recode_names/sequence_report.tsv new file mode 100644 index 00000000..fe9a4389 --- /dev/null +++ b/tests/fixtures/recode_names/sequence_report.tsv @@ -0,0 +1,24 @@ +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 \ No newline at end of file