def return_igv(genome):
return (html.Div(
[dashbio.Igv(
id='default-igv',
genome=genome,
minimumBases=100,
)]))
def return_igv(genome, bases):
return (html.Div([
dash_bio.Igv(
id=_COMPONENT_ID,
genome=genome,
reference=None,
minimumBases=bases,
)
]))
def test_dbigv002_ASM985889v3_tracks(dash_duo):
app = dash.Dash(__name__)
try:
requests.get('https://www.google.com/').status_code
data_path = 'https://s3.amazonaws.com/igv.org.genomes/'
except requests.exceptions.ConnectionError:
print("Running test with local datasets")
data_path = app.get_asset_url('')
app.layout = html.Div(
simple_app_layout(
dash_bio.Igv(
id=_COMPONENT_ID,
reference={
"id":
"ASM985889v3",
"name":
"Sars-CoV-2 (ASM985889v3)",
"fastaURL":
data_path +
"covid_ASM985889v3/GCF_009858895.2_ASM985889v3_genomic.fna",
"indexURL":
data_path +
"covid_ASM985889v3/GCF_009858895.2_ASM985889v3_genomic.fna.fai",
"order":
1000000,
"tracks": [{
"name": "Annotations",
"url": data_path +
"covid_ASM985889v3/GCF_009858895.2_ASM985889v3_genomic.gff.gz",
"displayMode": "EXPANDED",
"nameField": "gene",
"height": 150
}]
},
tracks=
[{ # normally, tracks listed here would not duplicate those already present above
"name": "Genes",
"type": "annotation",
"url": data_path +
"covid_ASM985889v3/GCF_009858895.2_ASM985889v3_genomic.gff.gz",
"displayMode": "EXPANDED"
}],
minimumBases=100,
style=igvStyle), ))
dash_duo.start_server(app)
# Check that the genome loaded
dash_duo.wait_for_text_to_equal('.igv-current-genome', 'ASM985889v3')
# Check that track(s) loaded
tracks = dash_duo.find_elements('.igv-track-label')
assert tracks[0].text == 'Annotations'
assert tracks[1].text == 'Genes'
def test_ASM985889v3_tracks(dash_duo):
app = dash.Dash(__name__)
app.layout = html.Div(simple_app_layout(
dash_bio.Igv(
id=_COMPONENT_ID,
reference={
"id": "ASM985889v3",
"name": "Sars-CoV-2 (ASM985889v3)",
"fastaURL": "https://s3.amazonaws.com/igv.org.genomes/covid_ASM985889v3/GCF_009858895.2_ASM985889v3_genomic.fna",
"indexURL": "https://s3.amazonaws.com/igv.org.genomes/covid_ASM985889v3/GCF_009858895.2_ASM985889v3_genomic.fna.fai",
"order": 1000000,
"tracks": [
{
"name": "Annotations",
"url": "https://s3.amazonaws.com/igv.org.genomes/covid_ASM985889v3/GCF_009858895.2_ASM985889v3_genomic.gff.gz",
"displayMode": "EXPANDED",
"nameField": "gene",
"height": 150
}
]
},
tracks=[{ # normally, tracks listed here would not duplicate those already present above
"name": "Genes",
"type": "annotation",
"url": "https://s3.amazonaws.com/igv.org.genomes/covid_ASM985889v3/GCF_009858895.2_ASM985889v3_genomic.gff.gz",
"displayMode": "EXPANDED"
}],
minimumBases=100,
style=igvStyle
),
))
dash_duo.start_server(app)
# Check that the genome loaded
dash_duo.wait_for_text_to_equal('#igv-current_genome', 'ASM985889v3')
# Check that track(s) loaded
tracks = dash_duo.find_elements('.igv-track-label')
assert tracks[0].text == 'Annotations'
assert tracks[1].text == 'Genes'
def test_dbigv003_sacCer3(dash_duo):
app = dash.Dash(__name__)
try:
requests.get('https://www.google.com/').status_code
data_path = 'https://s3.dualstack.us-east-1.amazonaws.com/igv.org.genomes/'
except requests.exceptions.ConnectionError:
print("Running test with local datasets")
data_path = app.get_asset_url('')
app.layout = html.Div(
simple_app_layout(
dash_bio.Igv(id=_COMPONENT_ID,
reference={
"id":
"sacCer3",
"name":
"S. cerevisiae (sacCer3)",
"fastaURL":
data_path + "sacCer3/sacCer3.fa",
"indexURL":
data_path + "sacCer3/sacCer3.fa.fai",
"tracks": [{
"name": "Ensembl Genes",
"type": "annotation",
"format": "ensgene",
"displayMode": "EXPANDED",
"url": data_path + "sacCer3/ensGene.txt.gz",
"indexed": False,
"supportsWholeGenome": False
}]
},
minimumBases=100,
style=igvStyle), ))
dash_duo.start_server(app)
# Check that the genome loaded
dash_duo.wait_for_text_to_equal('.igv-current-genome', 'sacCer3')
# Check that track(s) loaded
tracks = dash_duo.find_elements('.igv-track-label')
assert len(tracks) == 1
assert tracks[0].text == 'Ensembl Genes'
def test_sacCer3(dash_duo):
app = dash.Dash(__name__)
app.layout = html.Div(simple_app_layout(
dash_bio.Igv(
id=_COMPONENT_ID,
reference={
"id": "sacCer3",
"name": "S. cerevisiae (sacCer3)",
"fastaURL": "https://s3.dualstack.us-east-1.amazonaws.com/igv.org.genomes/sacCer3/sacCer3.fa",
"indexURL": "https://s3.dualstack.us-east-1.amazonaws.com/igv.org.genomes/sacCer3/sacCer3.fa.fai",
"tracks": [
{
"name": "Ensembl Genes",
"type": "annotation",
"format": "ensgene",
"displayMode": "EXPANDED",
"url": "https://s3.dualstack.us-east-1.amazonaws.com/igv.org.genomes/sacCer3/ensGene.txt.gz",
"indexed": False,
"supportsWholeGenome": False
}
]
},
minimumBases=100,
style=igvStyle
),
))
dash_duo.start_server(app)
# Check that the genome loaded
dash_duo.wait_for_text_to_equal('#igv-current_genome', 'sacCer3')
# Check that track(s) loaded
tracks = dash_duo.find_elements('.igv-track-label')
assert len(tracks) == 1
assert tracks[0].text == 'Ensembl Genes'