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_known_obsolete_pass(self):
"""Test zero length HTTP 200 UniProt download."""
uni_id = 'Q8NI70'
fetcher = UniProtFetcher(self.dirs)
fetcher._download_uniprot(uni_id)
self.assertTrue(uni_id in fetcher.obs)
return None
def test_404_assigned_as_obsolete(self):
"""HTTP 404 errors should be assigned as obsolete, not missing."""
uni_id = 'P123451'
fetcher = UniProtFetcher(self.dirs)
fetcher._download_uniprot(uni_id)
self.assertTrue(uni_id in fetcher.obs)
return None
def test_download_uniprot_pass(self):
self._generate_dir_names()
expected = '>sp|P12345|AATM_RABIT Aspartate aminotransferase, mitochondrial OS=Oryctolagus cuniculus GN=GOT2 PE=1 SV=2\nMALLHSARVLSGVASAFHPGLAAAASARASSWWAHVEMGPPDPILGVTEAYKRDTNSKKM\nNLGVGAYRDDNGKPYVLPSVRKAEAQIAAKGLDKEYLPIGGLAEFCRASAELALGENSEV\nVKSGRFVTVQTISGTGALRIGASFLQRFFKFSRDVFLPKPSWGNHTPIFRDAGMQLQSYR\nYYDPKTCGFDFTGALEDISKIPEQSVLLLHACAHNPTGVDPRPEQWKEIATVVKKRNLFA\nFFDMAYQGFASGDGDKDAWAVRHFIEQGINVCLCQSYAKNMGLYGERVGAFTVICKDADE\nAKRVESQLKILIRPMYSNPPIHGARIASTILTSPDLRKQWLQEVKGMADRIIGMRTQLVS\nNLKKEGSTHSWQHITDQIGMFCFTGLKPEQVERLTKEFSIYMTKDGRISVAGVTSGNVGY\nLAHAIHQVTK\n'
uni_id = 'P12345'
fetcher = UniProtFetcher(self.dirs)
result = fetcher._download_uniprot(uni_id)
self.assertEqual(expected, result)
return None
def test_download_uniprot_with_obsolete_pass(self):
self._write_initial_tsv()
self._write_initial_uni()
fetcher = UniProtFetcher(self.dirs)
fetcher.fetch_fasta_files()
with open(self.tsv_test_fp, 'r', encoding='utf-8') as result_fh:
result = result_fh.read()
self.assertEqual(result, TsvData.pdb_seq_tsv_valid)
return None
