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# For its use in colab notebook
!pip install jbrowse-jupyter

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# For its use in colab notebook
!pip install pandas
!pip install --force-reinstall MarkupSafe==2.0.1

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import pandas as pd
from jbrowse_jupyter import launch, create

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hg38 = create('LGV', genome='hg38')

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data = {'refName':['10', '10', '10', '10'],
        'start':[100, 150, 200, 250],
        'end':[175, 225, 275, 325],
        'name':['feature1', 'feature2', 'feature3', 'feature4']}

df = pd.DataFrame(data)
print(df)
hg38.add_df_track(df, 'track_name', track_id="df_track_id", overwrite=True)

  refName  start  end      name
0      10    100  175  feature1
1      10    150  225  feature2
2      10    200  275  feature3
3      10    250  325  feature4

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hg38.set_location("10:100..350")
hg38.set_default_session(['df_track_id'], False)
new_conf = hg38.get_config()
launch(new_conf, port=3013)

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tracks = [
    ("https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/ncbi_refseq/GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.sorted.gff.gz", "gff-demo"),
    ("https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/skbr3/SKBR3_Feb17_GRCh38.sorted.bam", "bam-demo"),
    ("https://hgdownload.cse.ucsc.edu/goldenpath/hg38/phyloP100way/hg38.phyloP100way.bw", "bigwig-demo"),
    ("https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar.vcf.gz", "vcf-demo"),
    ("https://jbrowse.org/genomes/GRCh38/repeats.bb", "bigbed")
]
for track in tracks:
    data = track[0]
    track_id = track[1]
    hg38.add_track(data, track_id=track_id)

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# set theme
hg38.set_theme("#311b92", "#0097a7", "#f57c00", "#d50000")
hg38.set_default_session(['gff-demo', 'bigbed'],False)
hg38.set_location("1:110654228..110936130")
new_conf2 = hg38.get_config()
launch(new_conf2, id="test-2",height=800, dash_comp="LGV", port=8000)

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