def run(self): self.make_build_profilepy() processo = modeller_caller() processo.run(self.__folder_of_model__() + '/build_profile.py') self.profilePIR = os.path.dirname(self.file_format_pir) + '/build_profilePIR.ali' self.profilePAP = os.path.dirname(self.file_format_pir) + '/build_profilePAP.ali' self.profilePRF = os.path.dirname(self.file_format_pir) + '/build_profile.prf'
def convert_seqali_pir_to_fasta_formar(self, file_name): script = """\ from modeller import * import os os.chdir('""" + self.__folder_of_model__() + """') env = environ() env.io.hetatm = env.io.water = False env.io.atom_files_directory = ['""" + self.__folder_of_model__() + """'] code = '""" + self.strname + """' # estrutura a ser lida# mdl = model(env, file=code, model_segment=('FIRST:A','LAST:A')) aln = alignment(env) aln.append_model(mdl, align_codes=code) aln.write(file='""" + self.__folder_of_model__() + """/template.pir', alignment_format = 'PIR') aln.write(file='""" + self.__folder_of_model__() + """/template.fasta', alignment_format = 'FASTA') aln2 = alignment(env) aln2.append(file='""" + self.__folder_of_model__() + file_name + """', alignment_format = 'PIR') aln2.write(file='""" + self.__folder_of_model__() + """/seq.fasta', alignment_format='FASTA') unalinedfasta = file('""" + self.__folder_of_model__() + """/unaligned.fasta', 'w') templatefasta = file('""" + self.__folder_of_model__() + """/template.fasta', 'r') seqfasta = file('""" + self.__folder_of_model__() + """/seq.fasta', 'r') unalinedlist = templatefasta.readlines() unalinedlist = unalinedlist + seqfasta.readlines() unalinedfasta.writelines("".join(unalinedlist)) unalinedfasta.close() """ arq = file(self.modeldir + 'get_fasta.py', 'w') arq.write(script) arq.close() self.unaligned_seq = self.__folder_of_model__() + '/unaligned.fasta' # self.template_pir = self.__folder_of_model__() + '/template.pir' processo = modeller_caller() processo.run(self.__folder_of_model__() + 'get_fasta.py') self.__get_template_sequence_in_pir_format__()
def __get_template_sequence_in_pir_format__(self): script = """\ from modeller import * import os os.chdir('""" + self.__folder_of_model__() + """') env = environ() env.io.hetatm = env.io.water = True env.io.atom_files_directory = './:../atom_files' code = '""" + self.strname + """' # estrutura a ser lida# mdl = model(env, file=code, model_segment=('FIRST:A','LAST:A')) aln = alignment(env) aln.append_model(mdl, align_codes=code) aln.write(file='""" + self.__folder_of_model__() + """/str.seq', alignment_format = 'PIR') """ arq = file(self.modeldir + 'get_template.py', 'w') arq.write(script) arq.close() # self.unaligned_seq = self.__folder_of_model__() + '/unaligned.fasta' self.template_pir = self.__folder_of_model__() + '/str.seq' processo = modeller_caller() processo.run(self.__folder_of_model__() + 'get_template.py')
def get_model(self): processo = modeller_caller() processo.run(self.myscript)
def model_sequence(self): processo = modeller_caller() processo.run(self.__folder_of_model__() + 'get_model.py')