Python add_reference_resources Beispiele

Beispiel #1

def split(*items):
    """Split samples into all possible genomes for alignment.
    """
    out = []
    for data in [x[0] for x in items]:
        dis_orgs = data["config"]["algorithm"].get("disambiguate")
        if dis_orgs:
            if not data.get("disambiguate", None):
                data["disambiguate"] = {
                    "genome_build": data["genome_build"],
                    "base": True
                }
            out.append([data])
            # handle the instance where a single organism is disambiguated
            if isinstance(dis_orgs, basestring):
                dis_orgs = [dis_orgs]
            for dis_org in dis_orgs:
                dis_data = copy.deepcopy(data)
                dis_data["disambiguate"] = {"genome_build": dis_org}
                dis_data["genome_build"] = dis_org
                dis_data = run_info.add_reference_resources(dis_data)
                out.append([dis_data])
        else:
            out.append([data])
    return out

Beispiel #2

Datei: __init__.py Projekt: curoverse/bcbio-nextgen

def split(*items):
    """Split samples into all possible genomes for alignment.
    """
    out = []
    for data in [x[0] for x in items]:
        dis_orgs = data["config"]["algorithm"].get("disambiguate")
        if dis_orgs:
            data["disambiguate"] = {"genome_build": data["genome_build"],
                                    "base": True}
            out.append([data])
            for dis_org in dis_orgs:
                dis_data = copy.deepcopy(data)
                dis_data["disambiguate"] = {"genome_build": dis_org}
                dis_data["genome_build"] = dis_org
                dis_data = run_info.add_reference_resources(dis_data)
                out.append([dis_data])
        else:
            out.append([data])
    return out

Beispiel #3

def split(items):
    """Split samples into all possible genomes for alignment.
    """
    out = []
    for data in [x[0] for x in items]:
        dis_orgs = data["config"]["algorithm"].get("disambiguate")
        if dis_orgs:
            data["disambiguate"] = {
                "genome_build": data["genome_build"],
                "base": True
            }
            out.append([data])
            for dis_org in dis_orgs:
                dis_data = copy.deepcopy(data)
                dis_data["disambiguate"] = {"genome_build": dis_org}
                dis_data["genome_build"] = dis_org
                dis_data = run_info.add_reference_resources(dis_data)
                out.append([dis_data])
        else:
            out.append([data])
    return out

Beispiel #4

Datei: __init__.py Projekt: Cyberbio-Lab/bcbio-nextgen

def split(*items):
    """Split samples into all possible genomes for alignment.
    """
    out = []
    for data in [x[0] for x in items]:
        dis_orgs = data["config"]["algorithm"].get("disambiguate")
        if dis_orgs:
            if not data.get("disambiguate", None):
                data["disambiguate"] = {"genome_build": data["genome_build"],
                                        "base": True}
            out.append([data])
            # handle the instance where a single organism is disambiguated
            if isinstance(dis_orgs, basestring):
                dis_orgs = [dis_orgs]
            for dis_org in dis_orgs:
                dis_data = copy.deepcopy(data)
                dis_data["disambiguate"] = {"genome_build": dis_org}
                dis_data["genome_build"] = dis_org
                dis_data = run_info.add_reference_resources(dis_data)
                out.append([dis_data])
        else:
            out.append([data])
    return out

Beispiel #5

Datei: test_ericscript.py Projekt: limbus-medtec/bcbio-nextgen-1

 def config_without_disambiguate(self):
     config = self._get_base_config()
     config["genome_build"] = "hg19"
     config.update(self._get_filepaths())
     config = run_info.add_reference_resources(config)
     return config

Beispiel #6

Datei: test_ericscript.py Projekt: biocyberman/bcbio-nextgen

 def config_without_disambiguate(self):
     config = self._get_base_config()
     config["genome_build"] = "hg19"
     config.update(self._get_filepaths())
     config = run_info.add_reference_resources(config)
     return config