def __init__(self, view, ds_h):
AttrH.__init__(self,
"OP_dtrees",
title="Presence in decision trees",
tooltip="Decision trees positive on variant")
self.mDS = ds_h
self.setAspect(view)
def __init__(self, view):
AttrH.__init__(self,
"BEACONS",
title="Beacons",
tooltip="Search what other organizations have "
"observed the same variant")
self.setAspect(view)
def __init__(self, view, ds_h):
AttrH.__init__(self,
"OP_filters",
title="Presence in filters",
tooltip="Filters positive on variant")
self.mDS = ds_h
self.setAspect(view)
def __init__(self, view, ds_h):
AttrH.__init__(self,
"OP_has_variant",
title="Has variant",
tooltip="Samples having variant")
self.mDS = ds_h
self.mFamilyInfo = self.mDS.getFamilyInfo()
self.setAspect(view)
class IGV_AttrH(AttrH):
def __init__(self, app, view_gen, case, samples, reference):
bam_base = app.getOption("http-bam-base")
AttrH.__init__(self,
"IGV",
kind="hidden" if bam_base is None else None)
self.mBase = "hg38" if reference and "38" in reference else "hg19"
self.setAspect(view_gen)
if bam_base is None:
self.mPreUrl = None
return
# we are not sure what is the key to samples, so have to repackage
samples = {info["id"]: info["name"] for info in samples.values()}
samples_ids = sorted(samples)
samples_names = [samples[id] for id in samples_ids]
file_urls = ','.join([
"%s/%s/%s.%s.bam" % (bam_base, case, sample_id, self.mBase)
for sample_id in samples_ids
])
class IGV_AttrH(AttrH):
def __init__(self, app, view_gen, case, samples, reference):
bam_base = app.getOption("http-bam-base")
AttrH.__init__(self,
"IGV",
kind="hidden" if bam_base is None else None)
self.mBase = "hg38" if reference and "38" in reference else "hg19"
self.setAspect(view_gen)
if bam_base is None:
self.mPreUrl = None
return
# we are not sure what is the key to samples, so have to repackage
samples = {info["id"]: info["name"] for info in samples.values()}
samples_ids = sorted(samples.keys())
samples_names = ",".join([samples[id] for id in samples_ids])
file_urls = ','.join([
f"{bam_base}/{case}/{sample_id}.{self.mBase}.bam"
for sample_id in samples_ids
])
self.mPreUrl = (
f"http://localhost:60151/load?file={file_urls}"
f"&genome={self.mBase}&merge=false&name={samples_names}")
def __init__(self, view):
AttrH.__init__(self,
"UNIPROT_ACC",
title="Uniprot",
tooltip="View on Uniprot site")
self.setAspect(view)
def __init__(self, view, name, title, tooltip):
AttrH.__init__(self, name, title=title, tooltip=tooltip)
self.setAspect(view)
def __init__(self, view):
AttrH.__init__(self, "MEDGEN", title="MedGen", tooltip="Search MedGen")
self.setAspect(view)
def __init__(self, view):
AttrH.__init__(self,
"GREV",
title="GeneReviews®",
tooltip="Search GeneReviews®")
self.setAspect(view)
def __init__(self, view):
AttrH.__init__(self, "OMIM")
self.setAspect(view)
def __init__(self, view):
AttrH.__init__(self,
"GTEx",
title="View on GTEx",
tooltip="View this gene on GTEx portal")
self.setAspect(view)
def __init__(self, view):
AttrH.__init__(self,
"REFERENCES",
title="Found in PubMed",
tooltip="PubMed Abstracts")
self.setAspect(view)
def __init__(self, view):
AttrH.__init__(self,
"HGMD_PMIDs",
title="HGMD PMIDs",
tooltip="PubMed Abstracts (from HGMD)")
self.setAspect(view)
def __init__(self, view, key, is_simple):
AttrH.__init__(self, key.upper(), title=key.title())
self.setAspect(view)
self.key = key
self.simple = is_simple
def __init__(self, view_gen):
AttrH.__init__(self, "UCSC")
self.setAspect(view_gen)
def __init__(self, view):
AttrH.__init__(self,
"GENE_CARDS",
title="GeneCards",
tooltip="Read GeneCards")
self.setAspect(view)
