예제 #1
0
파일: tcga_rna.py 프로젝트: arahuja/pytcga
def prefetch_rnaseq_data(disease_code,
                        wait_time=30,
                        cache=True,):

    archive_path = tcga_request(disease=disease_code,
                               level='3',
                               center='7',
                               platformType='RNASeqV2',
                               platform='IlluminaHiSeq_RNASeqV2',
                               wait_time=30)

    return archive_path
예제 #2
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def prefetch_mutation_data(disease_code,
                          wait_time=30,
                          cache=True,):

    archive_path = tcga_request(disease=disease_code,
                               level='2',
                               center='BI',
                               platformType='Somatic Mutations',
                               platform='Automated Mutation Calling',
                               wait_time=wait_time,
                               cache=cache)

    return archive_path
예제 #3
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def prefetch_rnaseq_data(
    disease_code,
    wait_time=30,
    cache=True,
):

    archive_path = tcga_request(disease=disease_code,
                                level='3',
                                center='7',
                                platformType='RNASeqV2',
                                platform='IlluminaHiSeq_RNASeqV2',
                                wait_time=30)

    return archive_path
예제 #4
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def prefetch_mutation_data(disease_code, wait_time=30, cache=True):
    for center in sequencing_centers:
        try:
            archive_path = tcga_request(disease=disease_code,
                                        level='2',
                                        center=center,
                                        platformType='Somatic Mutations',
                                        platform='Automated Mutation Calling',
                                        wait_time=wait_time,
                                        cache=cache)
            break
        except RequestError:
            logging.debug('For {}, center {} has no mutation data.'.format(
                disease_code, center))

    return archive_path
예제 #5
0
def prefetch_mutation_data(disease_code,
                          wait_time=30,
                          cache=True):
    for center in sequencing_centers:
        try:
            archive_path = tcga_request(disease=disease_code,
                                       level='2',
                                       center=center,
                                       platformType='Somatic Mutations',
                                       platform='Automated Mutation Calling',
                                       wait_time=wait_time,
                                       cache=cache)
            break
        except RequestError:
            logging.debug('For {}, center {} has no mutation data.'.format(
                disease_code, center))

    return archive_path