def main():
user_home = find_home_dir()
project_dp = os.path.join(user_home, 'pdb')
uni_dp = os.path.join(project_dp, 'uni_data')
tsv_dp = os.path.join(project_dp, 'tsv_data')
working_dp = os.path.join(project_dp, 'working')
dirs = ProjectFolders(
user_home=user_home,
project_home=project_dp,
uni_data=uni_dp,
tsv_data=tsv_dp,
working=working_dp
)
create_folders(dirs)
fetch_and_write_files(dirs)
initial_filtering(dirs)
fetcher = UniProtFetcher(dirs)
fetcher.fetch_fasta_files()
second_filtering(dirs)
final_filtering(dirs)
uniprot_composite(dirs)
print("Processing finished successfully.")
return None
def test_pdb_seq_tsv_exists_pass(self):
pdb_seq_fp = os.path.join(self.dirs.working, 'pdb_seq.tsv')
with open(pdb_seq_fp, mode='w', encoding='utf-8') as pdb_fh:
pdb_fh.writelines('\n')
self.assertTrue(exists(pdb_seq_fp))
initial_filtering(self.dirs)
self.assertTrue(initial_filtering(self.dirs))
return None
def test_generate_pdb_seq_tsv_pass(self):
expected_pdb_seq_fp = os.path.join(
self.dirs.working,
'pdb_seq.tsv.expected'
)
result_pdb_seq_fp = os.path.join(
self.dirs.working,
'pdb_seq.tsv'
)
initial_filtering(self.dirs)
set_write_permissions(self.temp_dir)
self.assertTrue(exists(result_pdb_seq_fp))
self.assertTrue(
cmp(expected_pdb_seq_fp, result_pdb_seq_fp, shallow=0)
)
return None
