Python read_hla_file Examples

Example #1

File: test_load_tcga_data.py Project: hammerlab/immuno

def test_load_tcga_paad():
    maf_filename = 'data/PAAD.maf'
    hla_filename = 'data/PAAD.hla'
    alleles = read_hla_file(hla_filename)
    transcripts_df, vcf_df, variant_report = load_file(maf_filename)
    assert len(vcf_df) > 0
    assert len(transcripts_df) > 0

Example #2

def test_load_tcga_paad():
    maf_filename = 'data/PAAD.maf'
    hla_filename = 'data/PAAD.hla'
    alleles = read_hla_file(hla_filename)
    transcripts_df, vcf_df, variant_report = load_file(maf_filename)
    assert len(vcf_df) > 0
    assert len(transcripts_df) > 0

Example #3

def test_read_hla():
    # contains two C identical C alleles
    hla_filename = 'data/SKCM.hla'
    alleles = read_hla_file(hla_filename)
    print alleles
    assert alleles == [
        'HLA-A*01:01', 'HLA-A*03:01', 'HLA-B*08:01', 'HLA-B*07:02',
        'HLA-C*07:02', 'HLA-C*07:02'
    ]

Example #4

File: test_read_hla_alleles.py Project: hammerlab/immuno

def test_read_hla():
    # contains two C identical C alleles
    hla_filename = 'data/SKCM.hla'
    alleles = read_hla_file(hla_filename)
    print alleles
    assert alleles == [
        'HLA-A*01:01',
        'HLA-A*03:01',
        'HLA-B*08:01',
        'HLA-B*07:02',
        'HLA-C*07:02',
	'HLA-C*07:02'
   ]