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!pip install jbrowse-jupyter
Collecting jbrowse-jupyter
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Downloading Flask_Compress-1.10.1-py3-none-any.whl (7.9 kB)
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Downloading ansi2html-1.7.0-py3-none-any.whl (15 kB)
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Downloading retrying-1.3.3.tar.gz (10 kB)
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Collecting pluggy<2.0,>=0.12
Downloading pluggy-1.0.0-py2.py3-none-any.whl (13 kB)
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Collecting brotli
Downloading Brotli-1.0.9-cp37-cp37m-manylinux1_x86_64.whl (357 kB)
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Building wheels for collected packages: dash-core-components, dash-html-components, dash-table, retrying
Building wheel for dash-core-components (setup.py) ... done
Created wheel for dash-core-components: filename=dash_core_components-2.0.0-py3-none-any.whl size=3822 sha256=8265edfa47273dc954f7f3c20f0d52ba56c0592fe07bcc6f74f9e006a8a8d155
Stored in directory: /root/.cache/pip/wheels/00/f9/c7/1a6437d794ed753ea9bc9079e761d4fc803a1f1f5d3697b9ec
Building wheel for dash-html-components (setup.py) ... done
Created wheel for dash-html-components: filename=dash_html_components-2.0.0-py3-none-any.whl size=4090 sha256=0d1db5cfa4ba42752f156d6f1a562fa75e3fb6a50e8bb90c40dce635cba6790b
Stored in directory: /root/.cache/pip/wheels/ec/6b/81/05aceabd8b27f724e2c96784016287cc1bfbc349ebfda451de
Building wheel for dash-table (setup.py) ... done
Created wheel for dash-table: filename=dash_table-5.0.0-py3-none-any.whl size=3912 sha256=c6c041525c7205a215a7b4f551fbd91f80e519c205d3a56bbfaac90315e97c82
Stored in directory: /root/.cache/pip/wheels/85/5d/4e/7c276b57992951dbe770bf5caad6448d0539c510663aefd2e2
Building wheel for retrying (setup.py) ... done
Created wheel for retrying: filename=retrying-1.3.3-py3-none-any.whl size=11447 sha256=72c0f939f5572af84c8f05ce4d9c5bbb5e18b0cedfd314deb74ac303eec458b7
Stored in directory: /root/.cache/pip/wheels/f9/8d/8d/f6af3f7f9eea3553bc2fe6d53e4b287dad18b06a861ac56ddf
Successfully built dash-core-components dash-html-components dash-table retrying
Installing collected packages: brotli, importlib-metadata, flask-compress, dash-table, dash-html-components, dash-core-components, retrying, pyflakes, pycodestyle, pluggy, mccabe, dash, ansi2html, pytest, jupyter-dash, flake8, dash-jbrowse, jbrowse-jupyter
Attempting uninstall: importlib-metadata
Found existing installation: importlib-metadata 4.11.0
Uninstalling importlib-metadata-4.11.0:
Successfully uninstalled importlib-metadata-4.11.0
Attempting uninstall: pluggy
Found existing installation: pluggy 0.7.1
Uninstalling pluggy-0.7.1:
Successfully uninstalled pluggy-0.7.1
Attempting uninstall: pytest
Found existing installation: pytest 3.6.4
Uninstalling pytest-3.6.4:
Successfully uninstalled pytest-3.6.4
ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
markdown 3.3.6 requires importlib-metadata>=4.4; python_version < "3.10", but you have importlib-metadata 4.2.0 which is incompatible.
datascience 0.10.6 requires folium==0.2.1, but you have folium 0.8.3 which is incompatible.
Successfully installed ansi2html-1.7.0 brotli-1.0.9 dash-2.0.0 dash-core-components-2.0.0 dash-html-components-2.0.0 dash-jbrowse-1.0.1 dash-table-5.0.0 flake8-4.0.1 flask-compress-1.10.1 importlib-metadata-4.2.0 jbrowse-jupyter-1.2.1 jupyter-dash-0.4.1 mccabe-0.6.1 pluggy-1.0.0 pycodestyle-2.8.0 pyflakes-2.4.0 pytest-7.0.1 retrying-1.3.3
In [ ]:
from dash import html, Dash, dcc
from dash.dependencies import Input, Output
from jupyter_dash import JupyterDash
from jbrowse_jupyter import create, create_component
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app = JupyterDash(__name__)
server = app.server
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# locations of interest and name
# sources:
# https://jbrowse.org/demos/cancer-demo-2020/#embed
# https://genome.cshlp.org/content/early/2018/06/28/gr.231100.117.abstract
locations = [
{"value": "NC_000014.8:50234871..50253103", "label": "KLHDC2"
},
{"value": "NC_000017.10:76670129..76778424", "label": "CYTH1"},
{"value": "NC_000020.10:34213953..34252822", "label": "CPNE1"},
{"value": "NC_000017.10:38060848..38074903", "label": "GSDMB"},
{"value": "8:116962736..117337297", "label": "LINC00536"},
{"value": "8:121547996..121824286", "label": "SNTB1"},
{"value": "8:117654369..117768062", "label": "EIF3H"},
{"value": "NC_000020.10:47240790..47444536", "label": "PREX1"},
{"value": "8:125500735..125551329", "label": "TATDN1"},
{"value": "8:128,806,779..129,113,499", "label": "PVT1"}
]
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# track data, track name, track id
tracks = [
("https://s3.amazonaws.com/jbrowse.org/genomes/hg19/skbr3/reads_lr_skbr3.fa_ngmlr-0.2.3_mapped.splitters.bam", "SKBR3 pacbio (NGMLR) splitters only","ngmlr_splitters"),
("https://s3.amazonaws.com/jbrowse.org/genomes/hg19/skbr3/reads_lr_skbr3.fa_ngmlr-0.2.3_mapped.splitters.cram", "SKBR3 pacbio (NGMLR) splitters only (CRAM)","ngmlr_splitters_cram"),
("https://s3.amazonaws.com/jbrowse.org/genomes/hg19/skbr3/reads_lr_skbr3.fa_ngmlr-0.2.3_mapped.down.bam", "SKBR3 pacbio (NGMLR) 0.3 downsample","ngmlr_downsample"),
("https://s3.amazonaws.com/jbrowse.org/genomes/hg19/skbr3/reads_lr_skbr3.fa_ngmlr-0.2.3_mapped.down.cram", "SKBR3 pacbio (NGMLR) 0.3 downsample (CRAM)","reads_lr_skbr3.fa_ngmlr-0.2.3_mapped.down"),
("https://s3.amazonaws.com/jbrowse.org/genomes/hg19/reads_lr_skbr3.fa_ngmlr-0.2.3_mapped.bam.regions.bw", "SKBR3 pacbio coverage (NGMLR)","ngmlr_cov"),
("https://s3.amazonaws.com/jbrowse.org/genomes/hg19/reads_lr_skbr3.fa_ngmlr-0.2.3_mapped.bam.sniffles1kb_auto_l8_s5_noalt.vcf.gz", "SKBR3 pacbio (sniffles VCF)","breast_cancer_sniffles_hg19"),
("https://s3.amazonaws.com/jbrowse.org/genomes/hg19/skbr3/SKBR3_550bp_pcrFREE_S1_L001_AND_L002_R1_001.101bp.bwamem.ill.mapped.sort.bam", "SKBR3 illumina bwamem (BAM)","SKBR3 illumina bwamem (BAM)-id"),
("https://s3.amazonaws.com/jbrowse.org/genomes/hg19/skbr3/SKBR3_550bp_pcrFREE_S1_L001_AND_L002_R1_001.101bp.bwamem.ill.mapped.sort.cram", "SKBR3 illumina bwamem (CRAM)","SKBR3 illumina bwamem (CRAM)-id"),
("https://s3.amazonaws.com/jbrowse.org/genomes/hg19/reads_lr_skbr3.fa_ngmlr-0.2.3_mapped.bam", "SKBR3 pacbio (NGMLR)","ngmlr"),
("https://s3.amazonaws.com/jbrowse.org/genomes/hg19/GRCh37_latest_genomic.sort.gff.gz", "NCBI RefSeq (GFF3Tabix)","ncbi_gff_hg19")
]
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conf_lgv = create("LGV", genome="hg19")
conf_cgv = create("CGV", genome="hg19")
for track in tracks:
data = track[0]
track_name = track[1]
track_id = track[2]
conf_lgv.add_track(data, name=track_name, track_id=track_id)
# adding a text search adapter for LGV
ix = "https://jbrowse.org/genomes/hg19/trix/hg19.ix"
ixx = "https://jbrowse.org/genomes/hg19/trix/hg19.ixx"
meta = "https://jbrowse.org/genomes/hg19/trix/meta.json"
conf_lgv.add_text_search_adapter(ix, ixx, meta)
conf_lgv.set_default_session(['ncbi_gff_hg19'], False)
conf_cgv.add_track("https://s3.amazonaws.com/jbrowse.org/genomes/hg19/reads_lr_skbr3.fa_ngmlr-0.2.3_mapped.bam.sniffles1kb_auto_l8_s5_noalt.vcf.gz",name="SKBR3 pacbio (sniffles VCF)", track_id="breast_cancer_sniffles_hg19")
conf_cgv.set_default_session(["breast_cancer_sniffles_hg19"], False)
component_test = create_component(conf_cgv.get_config(), id="cgv-test", dash_comp="CGV")
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# Return the component with a specific location.
@app.callback(
Output("LGV-component", "children"),
Input("location-to-view", "value")
)
def return_jbrowse(location):
conf_lgv.set_location(location)
return create_component(conf_lgv.get_config(), id="lgv-test", dash_comp="LGV")
In [ ]:
app.layout = html.Div(
[
html.P(" SKBR3 Genes involved in fusions "),
dcc.Dropdown(
id="location-to-view", options=locations, value="1:229354402..229354403", placeholder="Select a gene to view."
),
html.Hr(),
dcc.Loading(id="LGV-component"),
html.P("Circular Genome View with SKBR3 pacbio (sniffles VCF) track"),
component_test
]
)
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app.run_server(mode="inline", height=1000, use_reloader=False, debug=True, port=3031)