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 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 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=(',', ': '))
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)