def analyze_construct(self, filenames=None):
self.logger.info("ANALYZING CONSTRUCT STRUCTURES")
# read source files
if not filenames:
filenames = os.listdir(self.construct_data_dir)
for filename in filenames:
if filename[-3:]!='pdb' and filename[-3:]!='ent':
continue
root, ext = os.path.splitext(os.path.basename(filename))
print(filename)
print(root)
filepath = os.sep.join([self.construct_data_dir, filename])
self.logger.info("Working on a file: {}".format(filename))
header = parse_pdb_header(filepath)
parser = SequenceParser(filepath)
json_data = OrderedDict()
json_data["header"] = header
json_data.update(parser.get_fusions())
json_data.update(parser.get_mutations())
json_data.update(parser.get_deletions())
json.dump(json_data, open(os.sep.join([settings.DATA_DIR, "{}_auto.json".format(root)]), 'w'), indent=4, separators=(',', ': '))
def analyze_construct(self, filenames=None):
self.logger.info("ANALYZING CONSTRUCT STRUCTURES")
# read source files
if not filenames:
filenames = os.listdir(self.construct_data_dir)
for filename in filenames:
if filename[-3:] != 'pdb' and filename[-3:] != 'ent':
continue
root, ext = os.path.splitext(os.path.basename(filename))
print(filename)
print(root)
filepath = os.sep.join([self.construct_data_dir, filename])
self.logger.info("Working on a file: {}".format(filename))
header = parse_pdb_header(filepath)
parser = SequenceParser(filepath)
json_data = OrderedDict()
json_data["header"] = header
json_data.update(parser.get_fusions())
json_data.update(parser.get_mutations())
json_data.update(parser.get_deletions())
json.dump(json_data,
open(
os.sep.join(
[settings.DATA_DIR,
"{}_auto.json".format(root)]), 'w'),
indent=4,
separators=(',', ': '))
def post(self, request):
# root, ext = os.path.splitext(request._request.FILES['pdb_file'].name)
pdb_file = StringIO(
request._request.FILES['pdb_file'].file.read().decode(
'UTF-8', "ignore"))
header = parse_pdb_header(pdb_file)
parser = SequenceParser(pdb_file)
json_data = OrderedDict()
json_data["header"] = header
json_data.update(parser.get_fusions())
json_data.update(parser.get_mutations())
json_data.update(parser.get_deletions())
return Response(json_data)
def handle(self, *args, **options):
print("Working on file {}".format(options['pdb_file']))
header = parse_pdb_header(options['pdb_file'])
print(header['compound'])
sp = SequenceParser(options['pdb_file'])
c = list(sp.mapping.keys())[0]
poly = sp.get_chain_peptides(c)
for peptide in poly:
print("Start: {} Stop: {} Len: {}".format(peptide[0].id[1], peptide[-1].id[1], len(peptide)))
sp.map_to_wt_blast(c, peptide, None, int(peptide[0].id[1]))
sp.map_seqres()
sp.save_excel_report("test.xlsx")
#sp.get_report()
def handle(self, *args, **options):
q = QueryPDB()
q.list_xtals(verbose=False)
for record in q.new_structures:
pdb_code = record[0]
wt_id = Protein.objects.get(entry_name=record[1]).id
if not os.path.exists(
os.sep.join([self.pdb_data_dir, "{}.pdb".format(pdb_code)
])):
self.download_pdb(pdb_code)
self.parser = SequenceParser(os.sep.join(
[self.pdb_data_dir, "{}.pdb".format(pdb_code)]),
wt_protein_id=wt_id)
header = parse_pdb_header(
os.sep.join([self.pdb_data_dir, "{}.pdb".format(pdb_code)]))
self.create_yaml(pdb_code, record[1], header)
def handle(self, *args, **options):
q = QueryPDB()
q.list_xtals(verbose=False)
for record in q.new_structures:
pdb_code = record[0]
wt_id = Protein.objects.get(entry_name=record[1]).id
if not os.path.exists(os.sep.join([self.pdb_data_dir, "{}.pdb".format(pdb_code)])):
self.download_pdb(pdb_code)
self.parser = SequenceParser(os.sep.join([self.pdb_data_dir, "{}.pdb".format(pdb_code)]), wt_protein_id=wt_id)
header = parse_pdb_header(os.sep.join([self.pdb_data_dir, "{}.pdb".format(pdb_code)]))
self.create_yaml(pdb_code, record[1], header)
def handle(self, *args, **options):
root, ext = os.path.splitext(os.path.basename(options['pdb_file']))
print("Working on file {}".format(options['pdb_file']))
header = parse_pdb_header(options['pdb_file'])
sp = SequenceParser(options['pdb_file'])
print(sp.get_fusions())
print(sp.get_mutations())
print(sp.get_deletions())
json_data = {}
json_data["header"] = header
json_data.update(sp.get_fusions())
json_data.update(sp.get_mutations())
json_data.update(sp.get_deletions())
json.dump(json_data, open(os.sep.join([settings.DATA_DIR, "{}_auto.json".format(root)]), 'w'), indent=4, separators=(',', ': '))
#json.dump(json_data, open("test.json", 'w'), indent=4, separators=(',', ': '))
def handle(self, *args, **options):
root, ext = os.path.splitext(os.path.basename(options['pdb_file']))
print("Working on file {}".format(options['pdb_file']))
header = parse_pdb_header(options['pdb_file'])
sp = SequenceParser(options['pdb_file'])
print(sp.get_fusions())
print(sp.get_mutations())
print(sp.get_deletions())
json_data = {}
json_data["header"] = header
json_data.update(sp.get_fusions())
json_data.update(sp.get_mutations())
json_data.update(sp.get_deletions())
json.dump(
json_data,
open(os.sep.join([settings.DATA_DIR, "{}_auto.json".format(root)]),
'w'),
indent=4,
separators=(',', ': '))
class Command(BaseCommand):
logger = logging.getLogger(__name__)
# source file directory
structure_data_dir = os.sep.join([settings.DATA_DIR, 'structure_data', 'structures'])
structure_build_data_dir = os.sep.join([settings.DATA_DIR, 'structure_data'])
pdb_data_dir = os.sep.join([settings.DATA_DIR, 'structure_data', 'pdbs'])
def handle(self, *args, **options):
q = QueryPDB()
q.list_xtals(verbose=False)
for record in q.new_structures:
pdb_code = record[0]
wt_id = Protein.objects.get(entry_name=record[1]).id
if not os.path.exists(os.sep.join([self.pdb_data_dir, "{}.pdb".format(pdb_code)])):
self.download_pdb(pdb_code)
self.parser = SequenceParser(os.sep.join([self.pdb_data_dir, "{}.pdb".format(pdb_code)]), wt_protein_id=wt_id)
header = parse_pdb_header(os.sep.join([self.pdb_data_dir, "{}.pdb".format(pdb_code)]))
self.create_yaml(pdb_code, record[1], header)
def download_pdb(self, pdb_code):
url = "http://www.rcsb.org/pdb/files/{}.pdb".format(pdb_code)
urllib.request.urlretrieve(url, os.sep.join([self.pdb_data_dir, "{}.pdb".format(pdb_code)]))
def create_yaml(self, pdb_code, prot_name, data):
yaml_pdb_data = {
'pdb' : pdb_code,
'resolution' : data['resolution'],
'publication_date' : data['release_date'][:10],
#PDB header contains full citation
#'pubmed_id' : data['journal_reference'],
}
yaml_struct_annotations = {
'fusion_proteins' : { x : [y[0], y[1]] for x,y in enumerate(self.parser.fusions) }
}
yaml_other_data = {
'construct' : pdb_code.lower(),
'segments' : self.get_segments_data(prot_name),
'segments_in_structure' : self.parser.get_segments(),
}
out_fh = open('{}.yaml'.format(os.sep.join([self.structure_build_data_dir, 'structures', pdb_code])), 'w')
out_fh.write('# PDB data\n\n')
yaml.dump(yaml_pdb_data, out_fh, default_flow_style=False)
out_fh.write('\n# Structure annotations\n\n')
yaml.dump(yaml_struct_annotations, out_fh)
out_fh.write('\n# Structure annotations\n\n')
yaml.dump(yaml_other_data, out_fh)
out_fh.close()
yaml_construct = {
'name' : pdb_code.lower(),
'protein' : prot_name,
}
construct_fh = open('auto_{}.yaml'.format(os.sep.join([self.structure_build_data_dir, 'constructs', pdb_code])), 'w')
yaml.dump(yaml_construct, construct_fh, indent=4)
construct_fh.close()
def get_segments_data(self, prot_entry_name):
output = {}
segments = ProteinSegment.objects.all()
for segment in segments:
resi = list(Residue.objects.filter(protein_segment = segment,
protein_conformation__protein__entry_name = prot_entry_name).order_by('sequence_number'))
try:
if resi:
output[segment.slug] = [resi[0].sequence_number, resi[-1].sequence_number]
except Exception as e:
output[segment.slug] = ['-,-']
return output
class Command(BaseCommand):
logger = logging.getLogger(__name__)
# source file directory
structure_data_dir = os.sep.join(
[settings.DATA_DIR, 'structure_data', 'structures'])
structure_build_data_dir = os.sep.join(
[settings.DATA_DIR, 'structure_data'])
pdb_data_dir = os.sep.join([settings.DATA_DIR, 'structure_data', 'pdbs'])
def handle(self, *args, **options):
q = QueryPDB()
q.list_xtals(verbose=False)
for record in q.new_structures:
pdb_code = record[0]
wt_id = Protein.objects.get(entry_name=record[1]).id
if not os.path.exists(
os.sep.join([self.pdb_data_dir, "{}.pdb".format(pdb_code)
])):
self.download_pdb(pdb_code)
self.parser = SequenceParser(os.sep.join(
[self.pdb_data_dir, "{}.pdb".format(pdb_code)]),
wt_protein_id=wt_id)
header = parse_pdb_header(
os.sep.join([self.pdb_data_dir, "{}.pdb".format(pdb_code)]))
self.create_yaml(pdb_code, record[1], header)
def download_pdb(self, pdb_code):
url = "https://www.rcsb.org/pdb/files/{}.pdb".format(pdb_code)
urllib.request.urlretrieve(
url, os.sep.join([self.pdb_data_dir, "{}.pdb".format(pdb_code)]))
def create_yaml(self, pdb_code, prot_name, data):
yaml_pdb_data = {
'pdb': pdb_code,
'resolution': data['resolution'],
'publication_date': data['release_date'][:10],
#PDB header contains full citation
#'pubmed_id' : data['journal_reference'],
}
yaml_struct_annotations = {
'fusion_proteins':
{x: [y[0], y[1]]
for x, y in enumerate(self.parser.fusions)}
}
yaml_other_data = {
'construct': pdb_code.lower(),
'segments': self.get_segments_data(prot_name),
'segments_in_structure': self.parser.get_segments(),
}
out_fh = open(
'{}.yaml'.format(
os.sep.join(
[self.structure_build_data_dir, 'structures', pdb_code])),
'w')
out_fh.write('# PDB data\n\n')
yaml.dump(yaml_pdb_data, out_fh, default_flow_style=False)
out_fh.write('\n# Structure annotations\n\n')
yaml.dump(yaml_struct_annotations, out_fh)
out_fh.write('\n# Structure annotations\n\n')
yaml.dump(yaml_other_data, out_fh)
out_fh.close()
yaml_construct = {
'name': pdb_code.lower(),
'protein': prot_name,
}
construct_fh = open(
'auto_{}.yaml'.format(
os.sep.join(
[self.structure_build_data_dir, 'constructs', pdb_code])),
'w')
yaml.dump(yaml_construct, construct_fh, indent=4)
construct_fh.close()
def get_segments_data(self, prot_entry_name):
output = {}
segments = ProteinSegment.objects.all()
for segment in segments:
resi = list(
Residue.objects.filter(
protein_segment=segment,
protein_conformation__protein__entry_name=prot_entry_name).
order_by('sequence_number'))
try:
if resi:
output[segment.slug] = [
resi[0].sequence_number, resi[-1].sequence_number
]
except Exception as e:
output[segment.slug] = ['-,-']
return output
