def test_examples(self):
with TempDirectory() as output_dir:
def out_path(filename):
return os.path.join(output_dir.path, filename)
def in_path(filename):
return os.path.join(INPUT_DIR, filename)
input_bam = "sample1-original.bam"
output_deduped_bam = "sample1-deduped.bam"
output_deduped_bai = output_deduped_bam + ".bai"
output_annotated_bam = "sample1-annotated.bam"
output_annotated_bai = output_annotated_bam + ".bai"
input_bam_path = in_path(input_bam)
expect_deduped_bam_path = in_path(output_deduped_bam)
expect_deduped_bai_path = in_path(output_deduped_bai)
expect_annotated_bam_path = in_path(output_annotated_bam)
expect_annotated_bai_path = in_path(output_annotated_bai)
output_deduped_bam_path = out_path(output_deduped_bam)
output_deduped_bai_path = out_path(output_deduped_bai)
output_annotated_bam_path = out_path(output_annotated_bam)
output_annotated_bai_path = out_path(output_annotated_bai)
connor.main(["program_name",
input_bam_path,
output_deduped_bam_path,
"--annotated_output_bam",
output_annotated_bam_path,
"--verbose",
"--simplify_pg_header",
"--force"])
def compare_files(expected_path, output_path):
expected_name = os.path.basename(expected_path)
output_name = os.path.basename(output_path)
if not os.path.isfile(output_path):
result = 'output file {} not found'.format(output_name)
elif not os.path.isfile(expected_path):
result = 'expected file {} not found'.format(expected_name)
elif not filecmp.cmp(expected_path, output_path, shallow=False):
msg = '{} does not match expected'
result = msg.format(output_path)
else:
result = 'OK'
return expected_name, result
comparisons = [(expect_deduped_bam_path,
output_deduped_bam_path),
(expect_deduped_bai_path,
output_deduped_bai_path),
(expect_annotated_bam_path,
output_annotated_bam_path),
(expect_annotated_bai_path,
output_annotated_bai_path)]
diff_files = dict([compare_files(expected, output) for expected, output in comparisons])
files_match = set(diff_files.values()) == set(["OK"])
self.assertTrue(files_match, diff_files)
#!/usr/bin/env python
"""Convenience wrapper for running connor directly from source tree."""
from connor.connor import main
import sys
if __name__ == '__main__':
# import cProfile
# cProfile.run('main()')
main(sys.argv)