def queryPolyPhen2(filename,
dump=True,
prefix='pph2',
fasta_file=None,
fix_isoforms=False,
ignore_errors=False,
**kwargs):
# original PolyPhen-2 curl command (see:
# http://genetics.bwh.harvard.edu/pph2/dokuwiki/faq ):
#
# curl -F _ggi_project=PPHWeb2 -F _ggi_origin=query \
# -F _ggi_target_pipeline=1 -F MODELNAME=HumDiv \
# -F UCSCDB=hg19 -F SNPFUNC=m -F [email protected] \
# -F _ggi_batch_file=@example_batch.txt \
# -D - http://genetics.bwh.harvard.edu/cgi-bin/ggi/ggi2.cgi
assert type(dump) is bool
assert type(prefix) is str
LOGGER.info('Submitting query to PolyPhen-2...')
num_lines = sum(1 for line in open(filename, 'rb') if line[0] != '#')
input_file = open(filename, 'rb')
# submit query
address = 'http://genetics.bwh.harvard.edu/cgi-bin/ggi/ggi2.cgi'
files = {
'_ggi_project': (None, 'PPHWeb2'),
'_ggi_origin': (None, 'query'),
'_ggi_target_pipeline': (None, '1'),
'_ggi_batch_file': ('query.txt', input_file),
'MODELNAME': (None, kwargs.get('MODELNAME', 'HumDiv')),
'UCSCDB': (None, kwargs.get('UCSCDB', 'hg19')),
'SNPFUNC': (None, kwargs.get('SNPFUNC', 'm'))
}
if fasta_file is not None:
# upload custom sequences
custom_fasta = open(fasta_file, 'rb')
files['uploaded_sequences_1'] = ('sequences.fa', custom_fasta)
response = requests.post(address, files=files)
# parse job ID from response page
jobID = response.cookies['polyphenweb2']
# results and semaphore files
results_dir = f'http://genetics.bwh.harvard.edu/ggi/pph2/{jobID}/1/'
files = {
'started': results_dir + 'started.txt',
'completed': results_dir + 'completed.txt',
'short': results_dir + 'pph2-short.txt',
'full': results_dir + 'pph2-full.txt',
'log': results_dir + 'pph2-log.txt',
'snps': results_dir + 'pph2-snps.txt'
}
# keep checking if the job has started/completed and,
# when done, fetch output files
output = {}
exts = ['started', 'completed', 'short', 'full', 'log', 'snps']
for k in exts:
# delay = timeout + backoff_factor*[2^(total_retries - 1)]
if k == 'started':
LOGGER.timeit('_started')
r = _requests_retry_session(retries=16).get(files[k])
LOGGER.report('Query to PolyPhen-2 started in %.1fs.', '_started')
LOGGER.info('PolyPhen-2 is running...')
elif k == 'completed':
LOGGER.timeit('_queryPP2')
r = _requests_retry_session(retries=200,
timeout=log(num_lines) / 2).get(
files[k])
LOGGER.report('Query to PolyPhen-2 completed in %.1fs.',
'_queryPP2')
else:
r = _requests_retry_session(retries=12).get(files[k])
output[k] = r.text
# print to file, if requested
if dump:
with open(prefix + '-' + k + '.txt', 'w', 1) as f:
print(r.text, file=f)
# check for conflicts between Uniprot sequences and isoforms used
# by Polyhen-2 (which are sometimes outdated)
Uniprot_accs = _check_log_errors(output['log'])
if Uniprot_accs:
if fix_isoforms:
LOGGER.info('PolyPhen-2 may have picked the wrong isoforms.')
LOGGER.info('Resubmitting query with correct isoforms --- '
'it may take up to a few hours to complete...')
# print file with freshly downloaded Uniprot sequences
fasta_fname, new_accs = _print_fasta_file(Uniprot_accs)
# replace accession numbers in list of SAVs
tmp_fname = filename + '.tmp'
_replace_strings_in_file(filename, tmp_fname, new_accs)
# resubmit query by manually uploading fasta sequences
output = queryPolyPhen2(tmp_fname,
dump=dump,
prefix=prefix,
fasta_file=fasta_fname,
fix_isoforms=False,
**kwargs)
os.remove(tmp_fname)
# restore original accession numbers in output
orig_accs = dict([[v, k] for k, v in new_accs.items()])
for k in exts:
output[k] = _replace_strings_in_text(output[k], orig_accs)
if dump:
outfile = f'pph2-{k}.txt'
_replace_strings_in_file(outfile, outfile, orig_accs)
elif not ignore_errors:
LOGGER.warn('Please check PolyPhen-2 log file')
else:
LOGGER.error('Please check PolyPhen-2 log file')
return output
def alignCustomPDB(self, PDB, chain='all', title=None, recover=False):
"""Aligns the Uniprot sequence with the sequence from the given PDB.
"""
assert isinstance(PDB, (str, pd.Atomic)), \
'PDB must be a PDBID or an Atomic instance (e.g. AtomGroup).'
assert isinstance(chain, str) or all(
isinstance(s, str) for s in chain), \
"'chain' must be a string or a list of strings."
assert isinstance(title, str) or title is None
# parse/import pdb and assign title
if isinstance(PDB, str):
try:
pdb = pd.parsePDB(PDB, subset='calpha')
except Exception as e:
msg = ('Unable to import PDB: PDB ID might be invalid or '
f'PDB file might be corrupted. Error message: {e}')
LOGGER.error(msg)
if title is None:
title = os.path.basename(PDB.strip())
title = title.replace(' ', '_')
else:
pdb = PDB.ca
if title is None:
title = PDB.getTitle()
# check if a record is already present
rec = [d for d in self.customPDBmappings if d['PDB'] == title]
if recover and len(rec) > 1:
raise RuntimeError('Multiple records found with same ID.')
elif recover and len(rec) == 1:
customPDBrecord = rec[0]
else:
# create record for custom PDB
customPDBrecord = {
'PDB': title,
'chain_res': {},
'chain_seq': {},
'warnings': []
}
self.customPDBmappings.append(customPDBrecord)
# check given chain list
all_chains = set(pdb.getChids())
if chain == 'all' or chain == '@':
chains_to_align = list(all_chains)
elif type(chain) is list:
chains_to_align = chain
else:
chains_to_align = [
chain,
]
invalid_chIDs = [c for c in chains_to_align if c not in all_chains]
if invalid_chIDs != []:
raise ValueError('Invalid chain: {}.'.format(invalid_chIDs))
# store resids and sequence of selected chains
for c in chains_to_align:
if c in customPDBrecord['chain_res']:
continue
customPDBrecord['chain_res'][c] = pdb[c].getResnums()
customPDBrecord['chain_seq'][c] = pdb[c].getSequence()
# align selected chains with BioPython module pairwise2
self._calcCustomAlignments(title, chains_to_align)
return customPDBrecord
