[['1', 'pos', 'ref'], ['1', 'pos', 'germline'], ['1', 'pos', 'somatic'],
['1', 'pos', 'somatic_and_germline'], ['1', 'neg', 'ref'],
['1', 'neg', 'germline'], ['1', 'neg', 'somatic'],
['1', 'neg', 'somatic_and_germline']])
def test_filter_infer_dna_pos(test_id, case, tmpdir, mutation_mode):
tmpdir = str(tmpdir)
test_name = 'test{}{}'.format(test_id, case)
junction_kmer_file_path = os.path.join(
groundtruth_dir, 'build', case, test_name,
'{}_junction_kmer.txt'.format(mutation_mode))
meta_file_path = os.path.join(groundtruth_dir, 'build', case, test_name,
'{}_metadata.tsv.gz'.format(mutation_mode))
output_file_path = os.path.join(tmpdir, 'junction_exact_dna_pos.txt')
genome_path = os.path.join(data_dir, '{}.fa'.format(test_name))
somatic_path = os.path.join(data_dir, '{}.maf'.format(test_name))
germline_path = os.path.join(data_dir, '{}.vcf'.format(test_name))
# infer dna pos output
my_args = [
'filter', '--junction-kmer-tsv-path', junction_kmer_file_path,
'--output-file-path', output_file_path, '--output-dir', tmpdir,
'--meta-file-path', meta_file_path, '--infer-dna-pos'
]
split_mode(my_args)
check_kmer_pos_valid(output_file_path,
genome_file=genome_path,
mutation_mode=mutation_mode,
sample=test_name,
germline_file_path=germline_path,
somatic_file_path=somatic_path)
'--output-dir', out_dir,
'--splice-path',
'{}/{}graph/spladder/genes_graph_conf3.merge_graphs.pickle'.format(
data_dir, case),
'--count-path',
'{}/{}graph/spladder/genes_graph_conf3.merge_graphs.count.hdf5'.format(
data_dir, case),
'--ann-path', '{}/test{}{}.gtf'.format(data_dir, test_id, case),
'--ref-path', '{}/test{}{}.fa'.format(data_dir, test_id, case),
'--germline', '{}/test{}{}.vcf'.format(data_dir, test_id, case),
'--somatic', '{}/test{}{}.maf'.format(data_dir, test_id, case),
'--gtex-junction-path','{}/{}graph/spladder/genes_graph_conf3.test1{}.junction.hdf5'.format(
data_dir, case, case),
'--mutation-mode', mutation_mode,
'--kmer', '4']
ip.split_mode(my_args)
# make_bg mode
for case in case_list:
output_dir = os.path.join(test_file_dir, 'test{}'.format(test_id), 'make_bg',case)
output_file_name = os.path.join(out_dir,'{}_integrated_background_kmer.txt'.format(case))
back_file_dir = os.path.join(test_file_dir,'test{}'.format(test_id),'build',case,'test{}{}'.format(test_id,case))
bg_file_list = [os.path.join(back_file_dir,'{}_back_kmer.txt'.format(mode)) for mode in ['ref','somatic','somatic_and_germline','germline']]
my_args = ['make_bg','--kmer-files']+bg_file_list+['--output-file-path',output_file_name]+['--output-dir',output_dir]
ip.split_mode(my_args)
# diff mode
for case in case_list:
for mutation_mode in mutation_list:
junction_kmer_file_path = os.path.join(test_file_dir, 'test{}'.format(test_id), 'build',
case, 'test{}{}'.format(test_id, case),'{}_junction_kmer.txt'.format(mutation_mode))
data_dir, case), '--count-path',
'{}/{}graph/spladder/genes_graph_conf3.merge_graphs.count.hdf5'.format(
data_dir, case), '--ann-path',
'{}/test{}{}.gtf'.format(data_dir, test_id, case), '--ref-path',
'{}/test{}{}.fa'.format(data_dir, test_id, case), '--germline',
'{}/test{}{}.vcf'.format(data_dir, test_id, case), '--somatic',
'{}/test{}{}.maf'.format(data_dir, test_id,
case), '--gtex-junction-path',
'{}/{}graph/spladder/genes_graph_conf3.test1{}.junction.hdf5'.format(
data_dir, case,
case), '--mutation-mode', mutation_mode, '--kmer', '4'
]
my_args = my_args_build
sample_dir = sample_dir_build
immunopepper.split_mode(my_args)
_assert_files_equal(
os.path.join(sample_dir, '{}_metadata.tsv.gz'.format(mutation_mode)),
os.path.join(out_dir, 'test{}{}'.format(test_id, case),
'{}_metadata.tsv.gz'.format(mutation_mode)))
# peptide
_assert_files_equal(
os.path.join(sample_dir, '{}_peptides.fa'.format(mutation_mode)),
os.path.join(out_dir, 'test{}{}'.format(test_id, case),
'{}_peptides.fa'.format(mutation_mode)))
_assert_files_equal(
os.path.join(sample_dir, '{}_back_peptides.fa'.format(mutation_mode)),
os.path.join(out_dir, 'test{}{}'.format(test_id, case),
'{}_back_peptides.fa'.format(mutation_mode)))
#kmer
_assert_files_equal(
