def test_end_to_end_merge(test_id, case, tmpdir):
data_dir = os.path.join(os.path.dirname(__file__), 'testcase_{}'.format(test_id), 'data')
result_dir = os.path.join(os.path.dirname(__file__), 'testcase_{}'.format(test_id), 'results_merged_{}'.format(case))
out_dir = str(tmpdir)
my_args = ['spladder',
'build',
'-a', os.path.join(data_dir, 'annotation_{}.gtf'.format(case)),
'-o', out_dir,
'-b', ','.join([os.path.join(data_dir, 'align', '{}_{}.bam'.format(case, i+1)) for i in range(5)]),
'--merge-strat', 'merge_graphs',
'--extract-as',
'-n', '15',
'--output-conf-icgc',
'--output-txt',
'--output-txt-conf',
'--output-gff3',
'--output-struc',
'--output-struc-conf',
'--output-bed',
'--output-conf-bed',
'--output-conf-tcga',
'--set-mm-tag', 'NM',
'-v']
spladder.main(my_args)
### check that files are identical
_check_files_spladder(result_dir, out_dir, prefix='merge_graphs')
def test_end_to_end_testing_cram(test_id, tmpdir):
data_dir = os.path.join(os.path.dirname(__file__),
'testcase_{}'.format(test_id), 'data')
result_dir = os.path.join(os.path.dirname(__file__),
'testcase_{}'.format(test_id),
'results_merged_cram')
out_dir = str(tmpdir)
my_args = [
'spladder', 'build', '-a',
os.path.join(data_dir, 'testcase_{}_spladder.gtf'.format(test_id)),
'-o', out_dir, '-b', ','.join([
os.path.join(
data_dir, 'align',
'testcase_{}_1_sample{}.cram'.format(test_id, idx + 1))
for idx in range(20)
]), '--cram-reference',
os.path.join(data_dir, 'genome.fa'), '--event-types',
'exon_skip,intron_retention,alt_3prime,alt_5prime,mutex_exons,mult_exon_skip',
'--merge-strat', 'merge_graphs', '--extract-ase', '--readlen', '50',
'--output-conf-icgc', '--output-txt', '--output-txt-conf',
'--output-gff3', '--output-struc', '--output-struc-conf',
'--output-bed', '--output-conf-bed', '--output-conf-tcga',
'--output-conf-icgc', '-v'
]
spladder.main(my_args)
### check that event files are identical
_check_files_spladder(result_dir, out_dir, prefix='merge_graphs')
bamsA = os.path.join(out_dir, 'cramlistA.txt')
bamsB = os.path.join(out_dir, 'cramlistB.txt')
with open(bamsA, 'w') as fh:
fh.write('\n'.join([
os.path.join(
data_dir, 'align', 'testcase_{}_1_sample{}.cram'.format(
test_id, idx + 1)) for idx in range(10)
]) + '\n')
with open(bamsB, 'w') as fh:
fh.write('\n'.join([
os.path.join(
data_dir, 'align', 'testcase_{}_1_sample{}.cram'.format(
test_id, idx + 11)) for idx in range(10)
]) + '\n')
my_args = [
'spladder', 'test', '-o', out_dir, '-v', '--diagnose-plots', '-f',
'ps', '--readlen', '50', '--merge-strat', 'merge_graphs',
'--event-types', 'exon_skip', '-a', bamsA, '-b', bamsB
]
spladder.main(my_args)
### check that files are identical
_check_files_testing(os.path.join(result_dir, 'testing'),
os.path.join(out_dir, 'testing'),
suffixes=['*.tsv'])
def test_end_to_end_testing(test_id, tmpdir):
data_dir = os.path.join(os.path.dirname(__file__), 'testcase_{}'.format(test_id), 'data')
result_dir = os.path.join(os.path.dirname(__file__), 'testcase_{}'.format(test_id), 'results_merged')
out_dir = str(tmpdir)
my_args = ['spladder',
'build',
'-a', os.path.join(data_dir, 'testcase_{}_spladder.gtf'.format(test_id)),
'-o', out_dir,
'-b', ','.join([os.path.join(data_dir, 'align', 'testcase_{}_1_sample{}.bam'.format(test_id, idx+1)) for idx in range(20)]),
'--event-types', 'exon_skip,intron_retention,alt_3prime,alt_5prime,mutex_exons,mult_exon_skip',
'--merge-strat', 'merge_graphs',
'--extract-ase',
'--readlen', '50',
'--output-conf-icgc',
'--output-txt',
'--output-txt-conf',
'--output-gff3',
'--output-struc',
'--output-struc-conf',
'--output-bed',
'--output-conf-bed',
'--output-conf-tcga',
'--output-conf-icgc',
'-v']
spladder.main(my_args)
### check that event files are identical
_check_files_spladder(result_dir, out_dir, prefix='merge_graphs')
bamsA = os.path.join(out_dir, 'bamlistA.txt')
bamsB = os.path.join(out_dir, 'bamlistB.txt')
with open(bamsA, 'w') as fh:
fh.write('\n'.join([os.path.join(data_dir, 'align', 'testcase_{}_1_sample{}.bam'.format(test_id, idx+1)) for idx in range(10)]) + '\n')
with open(bamsB, 'w') as fh:
fh.write('\n'.join([os.path.join(data_dir, 'align', 'testcase_{}_1_sample{}.bam'.format(test_id, idx+11)) for idx in range(10)]) + '\n')
my_args = ['spladder',
'test',
'-o', out_dir,
'-v',
'--diagnose-plots',
'-f', 'ps',
'--readlen', '50',
'--merge-strat', 'merge_graphs',
'--event-types', 'exon_skip',
'-a', bamsA,
'-b', bamsB]
spladder.main(my_args)
### check that files are identical
_check_files_testing(os.path.join(result_dir, 'testing'), os.path.join(out_dir, 'testing'), suffixes=['*.tsv'])
def test_end_to_end_single(test_id, case, tmpdir):
data_dir = os.path.join(os.path.dirname(__file__), 'testcase_{}'.format(test_id), 'data')
result_dir = os.path.join(os.path.dirname(__file__), 'testcase_{}'.format(test_id), 'results_single_{}'.format(case))
out_dir = str(tmpdir)
my_args = ['spladder',
'build',
'-a', os.path.join(data_dir, 'annotation_{}.gtf'.format(case)),
'-o', out_dir,
'-b', os.path.join(data_dir, 'align', '{}_1.bam'.format(case)),
'--merge-strat', 'single',
'--extract-ase',
'-n', '15',
'--output-conf-icgc',
'-v']
spladder.main(my_args)
my_args = ['spladder',
'build',
'-a', os.path.join(data_dir, 'annotation_{}.gtf'.format(case)),
'-o', out_dir,
'-b', os.path.join(data_dir, 'align', '{}_1.bam'.format(case)),
'--merge-strat', 'single',
'--extract-ase',
'-n', '15',
'--output-conf-icgc',
'--sparse-bam',
'-v']
spladder.main(my_args)
### check that files are identical
_check_files_spladder(result_dir, out_dir, prefix='{}_1'.format(case))
'--merge-strat', 'merge_graphs',
'--extract-as',
'-n', '15',
'--output-conf-icgc',
'--output-txt',
'--output-txt-conf',
'--output-gff3',
'--output-struc',
'--output-struc-conf',
'--output-bed',
'--output-conf-bed',
'--output-conf-tcga',
'--set-mm-tag', 'NM',
'-v']
spladder.main(my_args)
### check that files are identical
_check_files_spladder(result_dir, out_dir, prefix='merge_graphs')
#### test visualization
#my_args = ['spladder',
# 'viz',
# '-o', out_dir,
# '-b', ':'.join([','.join([os.path.join(data_dir, 'align', '{}_{}.bam'.format(case, i+1)) for i in range(3)]),
# ','.join([os.path.join(data_dir, 'align', '{}_{}.bam'.format(case, i+4)) for i in range(2)])]),
# '-L', 'group1,group2',
# '-f', 'ps',
# '-v']
#spladder.main(my_args)