def get_pdb_template(
self,
sequence,
):
"""
Retrieve a template structure from PDB from a BLAST search
Parameters
----------
sequence: str
A string of the protein sequence
Returns
-------
hits: dict
A dictionary generated from ProDy with PDB hits.
"""
from prody import blastPDB
import tempfile
import pickle
blast_record = blastPDB(sequence)
hits = blast_record.getHits()
# TODO need to address when BLAST search times out
# TODO add option based on sequency similarity cut off
return hits
def prody_blast(opt):
"""Blast search PDB based on command line arguments."""
import prody
LOGGER = prody.LOGGER
seq = opt.seq
title = None
if os.path.isfile(seq):
title, seq = readFirstSequenceFasta(seq)
LOGGER.info("First sequence ({0:s}) is parsed from {1:s}."
.format(title, repr(seq)))
if not seq.isalpha() or not seq.isupper():
opt.subparser.error("{0:s} is not a valid sequence or a file"
.format(repr(seq)))
folder, identity, coverage = opt.folder, opt.identity, opt.coverage
if not 0 < identity < 100:
opt.subparser.error('identity must be between 0 and 100')
if not 0 < coverage < 100:
opt.subparser.error('overlap must be between 0 and 100')
blast_results = prody.blastPDB(seq)
hits = blast_results.getHits(percent_identity=identity,
percent_coverage=coverage)
#sort hits by decreasing percent identity
hits2 = []
for pdb in hits:
hits2.append( (-hits[pdb]['percent_identity'], pdb) )
hits2.sort()
for identity, pdb in hits2:
chain = hits[pdb]['chain_id']
percent_identity = hits[pdb]['percent_identity']
title = hits[pdb]['title']
print(pdb + ' ' + chain + ' ' + ('%5.1f%%' % (percent_identity)) +
' ' + title)
# download hits if --folder is given
if opt.folder:
LOGGER.info('Downloading hits to ' + opt.folder)
pdblist = [ pdb for identity, pdb in hits2 ]
pdblist2 = prody.fetchPDB(pdblist, opt.folder,
compressed=opt.gzip, copy=True)
def get_PDBs(pdbdir):
skip_blast = False
for pdb_file in os.listdir(pdbdir):
if pdb_file.endswith('.pdb'):
print "\n***Now BLASTing %s***" % pdb_file
actual_pdb_file = pdb_file
output_dir = os.path.join('/kortemmelab/home/james.lucas/Mutant_PDBs', pdb_file[:-4])
try:
os.makedirs(output_dir)
except:
print 'File directory %s already exists!!!' % pdb_file[:-4]
skip_blast = True
if skip_blast == False:
pdb_chains = re.split(r'_', pdb_file)[1][:-4]
pdb_id = re.split(r'_', pdb_file)[0]
hv = prody.parsePDB(os.path.join(pdbdir, pdb_file)).getHierView()
blast_dict = generate_mut_seq(pdbdir, hv)
hit_list = []
for sequence in blast_dict:
set_dict = {}
temp_set = set()
blast_me = prody.blastPDB(blast_dict[sequence], timeout = 600)
hits_dict = blast_me.getHits(percent_identity=95)
for hit in hits_dict:
temp_set.add(hit)
hit_list.append(temp_set)
common_set = hit_list[0]
for entry in hit_list[1:]:
common_set.intersection_update(entry)
for hit in common_set:
rcsb.download_pdb(hit, output_dir)
alignments(actual_pdb_file, common_set, pdbdir)
else:
print 'Blast skipped!'
def prody_blast(sequence, **kwargs):
"""Blast search PDB and download hits.
:arg sequence: sequence or file in fasta format
:arg identity: percent sequence identity for blast search, default is 90.0
:type identity: float
:arg overlap: percent sequence overlap between sequences, default is 90.0
:type overlap: float
:arg outdir: download uncompressed PDB files to given directory
:type outdir: str
:arg gzip: write compressed PDB file
*Blast Parameters*
:arg filename: a *filename* to save the results in XML format
:type filename: str
:arg hitlist_size: search parameters, default is 250
:type hitlist_size: int
:arg expect: search parameters, default is 1e-10
:type expect: float
:arg sleep: how long to wait to reconnect for results, default is 2
sleep time is doubled when results are not ready.
:type sleep: int
:arg timeout: when to give up waiting for results. default is 30
:type timeout: int"""
import prody
LOGGER = prody.LOGGER
title = None
if os.path.isfile(sequence):
title, sequence = readFirstSequenceFasta(sequence)
LOGGER.info("First sequence ({0}) is parsed from {1}."
.format(title, repr(sequence)))
if not sequence.isalpha() or not sequence.isupper():
raise ValueError("{0} is not a valid sequence or a file"
.format(repr(sequence)))
outdir = kwargs.get('outdir')
identity, overlap = kwargs.get('identity', 90), kwargs.get('overlap', 90)
if not 0 < identity < 100:
raise ValueError('identity must be between 0 and 100')
if not 0 < overlap < 100:
raise ValueError('overlap must be between 0 and 100')
filename = kwargs.get('filename', None)
hitlist_size = kwargs.get('hitlist_size', 250)
expect = kwargs.get('expect', 1e-10)
sleep, timeout = kwargs.get('sleep', 2), kwargs.get('timeout', 30)
blast_results = prody.blastPDB(sequence,filename=filename,
hitlist_size=hitlist_size, expect=expect,
sleep=sleep, timeout=timeout)
if blast_results is None:
raise IOError('blast search timed out, please try again')
hits = blast_results.getHits(percent_identity=identity,
percent_overlap=overlap)
#sort hits by decreasing percent identity
hits2 = []
for pdb in hits:
hits2.append( (-hits[pdb]['percent_identity'], pdb) )
hits2.sort()
stdout = kwargs.get('stdout', False)
if not stdout:
finalHits = []
else:
from sys import stdout
for identity, pdb in hits2:
chain = hits[pdb]['chain_id']
percent_identity = hits[pdb]['percent_identity']
title = hits[pdb]['title']
if stdout:
stdout.write(pdb + ' ' + chain + ' ' +
('%5.1f%%' % (percent_identity)) + ' ' + title)
else:
finalHits.append((pdb, chain, ('%5.1f%%' % (percent_identity)),
title))
# download hits if --output-dir is given
if outdir:
LOGGER.info('Downloading hits to ' + outdir)
pdblist = [ pdb for identity, pdb in hits2 ]
pdblist2 = prody.fetchPDB(pdblist, outdir,
compressed=kwargs.get('gzip'), copy=True)
if not stdout:
return finalHits
def prody_blast(sequence, **kwargs):
"""Blast search PDB and download hits.
:arg sequence: sequence or file in fasta format
:arg identity: percent sequence identity for blast search, default is 90.0
:type identity: float
:arg overlap: percent sequence overlap between sequences, default is 90.0
:type overlap: float
:arg outdir: download uncompressed PDB files to given directory
:type outdir: str
:arg gzip: write compressed PDB file
*Blast Parameters*
:arg filename: a *filename* to save the results in XML format
:type filename: str
:arg hitlist_size: search parameters, default is 250
:type hitlist_size: int
:arg expect: search parameters, default is 1e-10
:type expect: float
:arg sleep: how long to wait to reconnect for results, default is 2
sleep time is doubled when results are not ready.
:type sleep: int
:arg timeout: when to give up waiting for results. default is 30
:type timeout: int"""
import prody
LOGGER = prody.LOGGER
title = None
if os.path.isfile(sequence):
title, sequence = readFirstSequenceFasta(sequence)
LOGGER.info("First sequence ({0}) is parsed from {1}.".format(
title, repr(sequence)))
if not sequence.isalpha() or not sequence.isupper():
raise ValueError("{0} is not a valid sequence or a file".format(
repr(sequence)))
outdir = kwargs.get('outdir')
identity, overlap = kwargs.get('identity', 90), kwargs.get('overlap', 90)
if not 0 < identity < 100:
raise ValueError('identity must be between 0 and 100')
if not 0 < overlap < 100:
raise ValueError('overlap must be between 0 and 100')
filename = kwargs.get('filename', None)
hitlist_size = kwargs.get('hitlist_size', 250)
expect = kwargs.get('expect', 1e-10)
sleep, timeout = kwargs.get('sleep', 2), kwargs.get('timeout', 30)
blast_results = prody.blastPDB(sequence,
filename=filename,
hitlist_size=hitlist_size,
expect=expect,
sleep=sleep,
timeout=timeout)
if not blast_results.isSuccess:
raise IOError('blast search timed out, please try again')
hits = blast_results.getHits(percent_identity=identity,
percent_overlap=overlap)
#sort hits by decreasing percent identity
hits2 = []
for pdb in hits:
hits2.append((-hits[pdb]['percent_identity'], pdb))
hits2.sort()
stdout = kwargs.get('stdout', False)
if not stdout:
finalHits = []
else:
from sys import stdout
for identity, pdb in hits2:
chain = hits[pdb]['chain_id']
percent_identity = hits[pdb]['percent_identity']
title = hits[pdb]['title']
if stdout:
stdout.write(pdb + ' ' + chain + ' ' +
('%5.1f%%' % (percent_identity)) + ' ' + title)
else:
finalHits.append(
(pdb, chain, ('%5.1f%%' % (percent_identity)), title))
# download hits if --outdir is given
if outdir:
LOGGER.info('Downloading hits to ' + outdir)
pdblist = [pdb for identity, pdb in hits2]
pdblist2 = prody.fetchPDB(pdblist,
outdir,
compressed=kwargs.get('gzip'),
copy=True)
if not stdout:
return finalHits
