nucleome_browser_chr.py

import re
from omero.gateway import BlitzGateway, MapAnnotationWrapper, LongAnnotationWrapper

conn = BlitzGateway("user", "pass", port=4064, host="localhost")
conn.connect()

# Some example chromosome regions we want to annotate Images with...
regions = [
    "hg19:chr19:15200000-15560000",
    "hg19:chr19:14680000-15200000",
    "hg19:chr19:13840000-14680000",
    "hg19:chr19:13320000-13840000",
    "hg19:chr19:12760000-13320000",
    "hg19:chr19:11720000-12760000",
    "hg19:chr19:9920000-11720000",
    "hg19:chr19:8680000-9920000",
    "hg19:chr19:7400000-8680000",
    "hg38:chr18:41032946-41237107",
    "hg38:chr17:71701970-71881251",
    "hg38:chr18:48801892-48998008",
    "hg38:chr6:31726513-31941166",
    "hg38:chr17:81838938-82011412",
    "hg38:chr7:100470711-100665335",
    "hg38:chr2:24775316-24986873",
    "hg38:chr18:48801892-48998008",
    "hg38:chr18:36192874-36397035",
]

dataset = conn.getObject("Dataset", 52)

for region, image in zip(regions, dataset.listChildren()):

    g = re.search(r'chr(\d+):(\d+)-(\d+)', region)
    data = {
        'chr': int(g.group(1)),
        'start': int(g.group(2)),
        'end': int(g.group(3))
    }

    # Add map annotation
    namespace = "chromosome.region.4dn"
    key_value_data = [
        ["regions", region],
        ['chromosome', str(data['chr'])],
        ['start', str(data['start'])],
        ['end', str(data['end'])]
    ]
    map_ann = MapAnnotationWrapper(conn)
    map_ann.setNs(namespace)
    map_ann.setValue(key_value_data)
    map_ann.save()
    image.linkAnnotation(map_ann)

    # Long annotation...
    for name, value in data.items():
        a = LongAnnotationWrapper(conn)
        a.setNs("chromosome.region.%s" % name)
        a.setValue(value)
        image.linkAnnotation(a)

conn.close()

# Then config MAPR to search for these

# omero config append omero.web.mapr.config '{"menu": "4dn", "config":{"default":["regions"], "all":["regions"], "ns":["chromosome.region.4dn"], "label":"4DN Regions"}}'
# omero config append omero.web.ui.top_links '["4DN Regions", {"viewname": "maprindex_4dn"}, {"title": "Find 4DN Regions"}]'