def _process(self):
tmoFile = File(self._pdbtmfile,'w', True)
for xmlfile in Path.list_files(os.path.join(self._local,'pdbtm/database/'), '*.xml'):
xmldata = TM(pdb = os.path.splitext(os.path.split(xmlfile)[1])[0].upper())
skip_chains = set()
read = False
fdxml = open(xmlfile)
for line in fdxml:
if line.startswith(' <TMRES>'): xmldata.tmres = line
elif line.startswith(' <TMTYPE'): xmldata.tmtype = line
elif line.startswith(' <PDBKWRES'): xmldata.kwres = line
elif line.startswith(' <SIDEDEFINITION'):
m = re.search('Side1="(\S+)"', line)
xmldata.side = m.group(1)
elif line.startswith(' <APPLY_TO_CHAIN'):
m = re.search('NEW_CHAINID=\"(\S{1})\"', line)
if m: skip_chains.add(m.group(1))
elif line.startswith(' <CHAIN '):
m = re.search('CHAINID=\"(\S{1})\" NUM_TM=\"(\d{1})\" TYPE=\"(\S+)\"', line)
if m:
chain, num, tmtype = m.group(1), m.group(2), m.group(3)
if not chain in skip_chains:
cdata = tuple([chain, num, tmtype])
xmldata.set_chain(cdata)
read = True
elif line.startswith(' <REGION ') and read:
m = re.search('pdb_beg=\"(\-*\d+\w*)\"[\s\S]+pdb_end=\"(\-*\d+\w*)\"\s+type=\"(\w{1})\"', line)
ini, end, tmtype = m.group(1), m.group(2), m.group(3)
xmldata.set_chain(cdata, tuple([ini, end, tmtype]))
elif line.startswith(' </CHAIN>'): read = False
fdxml.close()
if len(xmldata.chains) > 0:
tmoFile.write(str(xmldata)+"\n")
tmoFile.close()
def format2file(self, filename, extension='pdb', center=False):
if extension not in ('pdb', 'js'):
raise AttributeError('Not accepted extension')
structure = File('.'.join([filename, extension]), 'w')
if extension == 'pdb': structure.write(self.pdb_format(center=center))
elif extension == 'js': structure.write(self.js_format(center=center))
structure.close()
def _process(self):
enzymes = self._parse_enzclass() + self._parse_enzymedat()
enzymes.sort()
enzFile = File(self._enzfile, 'w', True)
for e in enzymes:
enzFile.write(repr(e) + "\n")
enzFile.close()
def _process(self):
targets = self._process_targets()
drugs = self._process_drugs(targets)
drugFile = File(self._drugfile, 'w', True)
for d in drugs:
drugFile.write(repr(d) + "\n")
drugFile.close()
def get_FASTA_IDX_by_names_to_file(self, names, outfile):
fastafile = Fasta(self.PDBseq)
selectedfasta = fastafile.retrieve(copy.deepcopy(names))
output_fasta = File(outfile, 'w')
for sequence in selectedfasta:
output_fasta.write(sequence.format('FASTA') + "\n")
output_fasta.close()
idxfile = self.PDBseq + '.idx'
output_idx = File(outfile + '.idx', 'w')
input_idx = File(idxfile, 'r')
for line in input_idx.descriptor:
info = line.split()
pdbname = info[0][1:]
if pdbname in names:
output_idx.write(line)
input_idx.close()
output_idx.close()
def _process(self):
go_dic = {}
parseFile = File(os.path.join(self.local, self._gfile), 'r')
go = None
for line in parseFile.descriptor:
line = re.sub('\'', '\\\'', line)
if line.startswith('[Term]'):
if go is not None:
go_dic[go.id] = go
if line.startswith('id:'):
go = GOterm(id=line.split()[1].strip())
continue
if line.startswith('name:'):
go.name = " ".join(line.split()[1:]).strip()
continue
if line.startswith('namespace:'):
go.namespace = line.split()[1].strip()
continue
if line.startswith('alt_id:'):
go.alt_id.append(line.split()[1].strip())
continue
if line.startswith('is_obsolete:'):
go.obsolete = True
continue
if line.startswith('is_a:'):
go.parents.add(line.split()[1].strip())
continue
if line.startswith('relationship:'):
go.relations.append(
(line.split()[1].strip(), line.split()[2].strip()))
continue
if line.startswith('[Typedef]'):
go_dic[go.id] = go
break
parseFile.close()
for go in go_dic:
go_dic[go].parents = self._search_parents(go_dic, go)
goFile = File(self._gofile, 'w', True)
for go in go_dic:
go_dic[go].parents.add(go)
goFile.write(str(go_dic[go]) + "\n")
goFile.close()
def _process(self):
inh = {}
nodefile = File(file_name=self._nodes, action='r')
for line in nodefile.descriptor:
line = re.sub('\'', '\\\'', line)
line_data = line.split('|')
inh[line_data[0].strip()] = TaxID(line_data[0].strip())
inh[line_data[0].strip()].parent = line_data[1].strip()
inh[line_data[0].strip()].rank = line_data[2].strip()
nodefile.close()
namefile = File(file_name=self._names, action='r')
for line in namefile.descriptor:
line = re.sub('\'', '\\\'', line)
line_data = line.split('|')
if line_data[3].strip() == 'scientific name':
inh[line_data[0].strip()].name = line_data[1].strip()
namefile.close()
delefile = File(file_name=self._delet, action='r')
for line in delefile.descriptor:
data = line.split('|')
inh[data[0].strip()] = TaxID(data[0].strip())
inh[data[0].strip()].old = True
delefile.close()
mrgefile = File(file_name=self._merged, action='r')
for line in mrgefile.descriptor:
data = line.split('|')
inh[data[0].strip()] = TaxID(data[0].strip())
inh[data[0].strip()].old = True
inh[data[0].strip()].new = data[1].strip()
mrgefile.close()
taxFile = File(self._taxid, 'w', True)
for taxid in inh:
taxFile.write(str(inh[taxid]) + "\n")
taxFile.close()
def _parse_uniprot_file(self, source, destination, fasta, code):
sourceFile = File(source, 'r')
destinFile = File(destination, 'w', True)
fastaFile = File(fasta, 'w', True)
protein = None
for line in sourceFile.descriptor:
if line.startswith('ID'):
protein = Uniprot(line.split()[1].strip(), code)
if line.startswith('AC'):
protein.accession = line.split()[1:]
if line.startswith('OX'):
protein.taxid = line.split()[1]
if line.startswith('OH'):
protein.hosts = line.split()[1]
if line.startswith('DR'):
protein.databases = line.split()[1:3]
if line.startswith(' '):
protein.sequence = line.strip().replace(' ', '')
if line.startswith('//'):
destinFile.write(str(protein) + "\n")
fastaFile.write(repr(protein) + "\n")
sourceFile.close()
destinFile.close()
