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
