def instantiate_test(self, alignment, record):
"""
Create a test instance, populate the attributes, and append it to the test list
:param alignment:
:param record
"""
test = Test()
pdb_id = ParseAlignment.get_alignment_pdb_id(alignment)
chain_id = ParseAlignment.get_alignment_pdb_chain(alignment)
# set the pdb_id
test.set_pdb_id(pdb_id)
# determine coverage & identity
coverage, identity = ParseAlignment.coverage_and_identity(alignment, record)
# set the test sequence
test.set_sequence(pdb_id, chain_id)
# set the coverage & identity values
test.set_coverage(coverage)
test.set_identity(identity)
# get the experimental method
test.set_expt_method()
# parse the pdb and pull out the resolution
test.set_resolution()
# parse the pdb and pull ligand information
test.set_ligands()
self.test_list.append(test)
def run_blast(self, pdb_db):
"""
Run BLASTP
:return:
"""
# this will only work for the simplest monomer case....add functionality for oligomer
for key in self.sequences.keys():
# write a fasta file
fasta_file = key + '.fasta' # want this to be pdb_id.chain_id.fasta add error checking
SeqIO.write(self.sequences[key], fasta_file, "fasta")
#FastaIO.write_fasta(fasta_file, self.sequences[key])
# run blastp
cline = NcbiblastpCommandline(cmd='blastp', query=fasta_file, db=pdb_db, evalue=0.001, outfmt=5)
std_out, std_err = cline()
# parse the output
blast_records = NCBIXML.parse(StringIO(std_out))
record = next(blast_records)
# iterate over the test alignments
# 1) verify the D3R criteria are satisfied
# 2) create a test object & add it to the test_list
for alignment in record.alignments:
# check D3R criteria for each test alignment
if not ParseAlignment.filter_blast_result(alignment, record):
continue
else:
# extract pdb_id and a list of pdb_ids already assigned
pdb_id = ParseAlignment.get_alignment_pdb_id(alignment)
if not self.test_list:
self.instantiate_test(alignment,record)
else:
assigned = [x.get_pdb_id() for x in self.test_list]
# if the test object exists then append the sequence
if pdb_id in assigned:
chain_id = ParseAlignment.get_alignment_pdb_chain(alignment)
index = assigned.index(pdb_id)
self.test_list[index].set_sequence(pdb_id, chain_id)
# if it doesn't exist, instantiate the object and add it to the list
else:
self.instantiate_test(alignment,record)
os.remove(fasta_file)
