Пример #1
0
    def handle(self, *args, **options):

        project_id = args[0]
        project = Project.objects.get(project_id=project_id)

        file_map = {}
        for path in os.listdir(args[1]):
            sample = path.replace(".bam.csv", "")
            sample = sample.replace(".", "")
            sample = sample.replace("-", "")
            file_map[sample] = os.path.abspath(os.path.join(args[1], path))

        for indiv in project.get_individuals():
            sample = indiv.indiv_id.replace("-", "")
            if sample in file_map:
                indiv.exome_depth_file = file_map[sample]
                indiv.save()
                get_cnv_store().add_sample(str(indiv.pk), open(indiv.exome_depth_file))
Пример #2
0
    def handle(self, *args, **options):

        project_id = args[0]
        project = Project.objects.get(project_id=project_id)

        file_map = {}
        for path in os.listdir(args[1]):
            sample = path.replace('.bam.csv', '')
            sample = sample.replace('.', '')
            sample = sample.replace('-', '')
            file_map[sample] = os.path.abspath(os.path.join(args[1], path))

        for indiv in project.get_individuals():
            sample = indiv.indiv_id.replace('-', '')
            if sample in file_map:
                indiv.exome_depth_file = file_map[sample]
                indiv.save()
                get_cnv_store().add_sample(str(indiv.pk),
                                           open(indiv.exome_depth_file))
Пример #3
0
def clean_project(project_id):
    """
    Clear data for this project from all the xbrowse resources:
     - datastore
     - coverage store
     - cnv store
    Does not remove any of the project's data links - so no data is lost, but everything must be rebuilt
    """
    project = Project.objects.get(project_id=project_id)
    individuals = project.get_individuals()

    # datastore
    get_mall(project_id).variant_store.delete_project(project_id)

    # coverage store
    for individual in individuals:
        get_coverage_store().remove_sample(individual.get_coverage_store_id())

    # cnv store
    for individual in individuals:
        get_cnv_store().remove_sample(individual.get_coverage_store_id())
Пример #4
0
def clean_project(project_id):
    """
    Clear data for this project from all the xbrowse resources:
     - datastore
     - coverage store
     - cnv store
    Does not remove any of the project's data links - so no data is lost, but everything must be rebuilt
    """
    project = Project.objects.get(project_id=project_id)
    individuals = project.get_individuals()

    # datastore
    get_mall(project_id).variant_store.delete_project(project_id)

    # coverage store
    for individual in individuals:
        get_coverage_store().remove_sample(individual.get_coverage_store_id())

    # cnv store
    for individual in individuals:
        get_cnv_store().remove_sample(individual.get_coverage_store_id())
Пример #5
0
def get_gene_diangostic_info(family, gene_id, variant_filter=None):

    diagnostic_info = GeneDiagnosticInfo(gene_id)

    diagnostic_info._gene_phenotype_summary = get_gene_phenotype_summary(
        get_reference(), gene_id)
    diagnostic_info._gene_sequencing_summary = get_gene_sequencing_summary(
        get_coverage_store(), family, gene_id)
    diagnostic_info._variants = get_diagnostic_search_variants_in_family(
        get_mall(family.project).variant_store, family, gene_id,
        variant_filter)
    diagnostic_info._cnvs = get_diagnostic_search_cnvs_in_family(
        get_cnv_store(),
        family,
        gene_id,
    )

    return diagnostic_info
Пример #6
0
def get_gene_diangostic_info(family, gene_id, variant_filter=None):

    diagnostic_info = GeneDiagnosticInfo(gene_id)

    diagnostic_info._gene_phenotype_summary = get_gene_phenotype_summary(get_reference(), gene_id)
    diagnostic_info._gene_sequencing_summary = get_gene_sequencing_summary(get_coverage_store(), family, gene_id)
    diagnostic_info._variants = get_diagnostic_search_variants_in_family(
        get_mall(family.project).variant_store,
        family,
        gene_id,
        variant_filter
    )
    diagnostic_info._cnvs = get_diagnostic_search_cnvs_in_family(
        get_cnv_store(),
        family,
        gene_id,
    )

    return diagnostic_info