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)