def run_sequence_mutation_pipeline(pdb_id_sequence, sequence_mutations): """ Parameters ---------- pdb_id_sequence : tuple (pdb_id, uniprot_id) """ pdb_id, sequence_id = pdb_id_sequence pdb_file = structure_tools.download_pdb_file(pdb_id, conf.CONFIGS["unique_temp_dir"]) sequence_file = elaspic_sequence.download_uniport_sequence(sequence_id, conf.CONFIGS["unique_temp_dir"]) for chain_pos in sequence_mutations[pdb_id_sequence]: for mutation in sequence_mutations[pdb_id_sequence][chain_pos]: mutation_sequence = "{}_{}".format(chain_pos, mutation) lp = standalone_pipeline.StandalonePipeline(pdb_file, sequence_file, mutations=mutation_sequence) lp.run_all_sequences() lp.run_all_models() lp.run_all_mutations() logger.info("Done!\n") logger.info("Pass")
def get_sequence(uniprot_id, input_dir, output_dir, use_remote=True): """Move PDB structure to the local working directory.""" input_file = op.join(input_dir, uniprot_id + ".fasta") output_file = op.join(output_dir, uniprot_id + ".fasta") # If the PDB already exists, do nothing... if op.isfile(output_file): logger.debug("Sequence file {} already exists!".format(output_file)) return output_file # Look for PDB file in the same folder if not op.isfile(input_file): if use_remote: input_file = elaspic_sequence.download_uniport_sequence(uniprot_id, input_dir) else: raise Exception("No PDB input file found!") logger.info("Copying {} to {}...".format(input_file, output_file)) shutil.copy(input_file, output_file) return output_file
def run_sequence_mutation_pipeline(pdb_id_sequence, sequence_mutations): """ Parameters ---------- pdb_id_sequence : tuple (pdb_id, uniprot_id) """ pdb_id, sequence_id = pdb_id_sequence pdb_file = structure_tools.download_pdb_file( pdb_id, conf.CONFIGS["unique_temp_dir"]) sequence_file = elaspic_sequence.download_uniport_sequence( sequence_id, conf.CONFIGS["unique_temp_dir"]) for chain_pos, mutations in sequence_mutations: for mutation in mutations: mutation_sequence = "{}_{}".format(chain_pos, mutation) lp = standalone_pipeline.StandalonePipeline( pdb_file, sequence_file, mutations=mutation_sequence) lp.run_all_sequences() lp.run_all_models() lp.run_all_mutations() logger.info("Pass")
def get_sequence(uniprot_id, input_dir, output_dir, use_remote=True): """Move PDB structure to the local working directory.""" input_file = op.join(input_dir, uniprot_id + ".fasta") output_file = op.join(output_dir, uniprot_id + ".fasta") # If the PDB already exists, do nothing... if op.isfile(output_file): logger.debug("Sequence file {} already exists!".format(output_file)) return output_file # Look for PDB file in the same folder if not op.isfile(input_file): if use_remote: input_file = elaspic_sequence.download_uniport_sequence( uniprot_id, input_dir) else: raise Exception("No PDB input file found!") logger.info("Copying {} to {}...".format(input_file, output_file)) shutil.copy(input_file, output_file) return output_file