def pbassign_cli():
"""
PBassign command line.
"""
options, pdb_name_lst = user_inputs()
if options.p:
if pdb_name_lst:
print("{} PDB file(s) to process".format(len(pdb_name_lst)))
else:
print("Nothing to do. Good bye.")
return
# PB assignement of PDB structures
chains = pbx.chains_from_files(pdb_name_lst)
else:
# PB assignement of a Gromacs trajectory
chains = pbx.chains_from_trajectory(options.x, options.g)
all_comments = []
all_sequences = []
for comment, chain in chains:
dihedrals = chain.get_phi_psi_angles()
sequence = pbx.assign(dihedrals)
all_comments.append(comment)
all_sequences.append(sequence)
fasta_name = options.o + ".PB.fasta"
with open(fasta_name, "w") as outfile:
pbx.io.write_fasta(outfile, all_sequences, all_comments)
print("wrote {0}".format(fasta_name))
def test_loader_PDB(self):
"""
Test for API loader function on PDBs
"""
filename = os.path.join(here, "test_data/2LFU.pdb")
comment, chain = list(pbx.chains_from_files([filename]))[0]
ref_comment = "{0} | model 1 | chain A".format(filename)
ref_chain = "Chain A / model 1: 2372 atoms"
assert ref_comment == comment
assert ref_chain == format(chain)
def test_loader_PDB(self):
"""
Test for API loader function on PDBs
"""
filename = os.path.join(here, "test_data/2LFU.pdb")
comment, chain = list(pbx.chains_from_files([filename]))[0]
ref_comment = "{0} | model 1 | chain A".format(filename)
ref_chain = "Chain A / model 1: 2372 atoms"
self.assertEqual(ref_comment, comment)
self.assertEqual(ref_chain, format(chain))
def pbassign_cli():
"""
PBassign command line.
"""
options, pdb_name_lst = user_inputs()
if options.p:
if pdb_name_lst:
print("{} PDB file(s) to process".format(len(pdb_name_lst)))
else:
print('Nothing to do. Good bye.')
return
# PB assignement of PDB structures
chains = pbx.chains_from_files(pdb_name_lst)
else:
# PB assignement of a Gromacs trajectory
chains = pbx.chains_from_trajectory(options.x, options.g)
all_comments = []
all_sequences = []
for comment, chain in chains:
try:
dihedrals = chain.get_phi_psi_angles()
sequence = pbx.assign(dihedrals)
all_comments.append(comment)
all_sequences.append(sequence)
except FloatingPointError:
print(
"The computation of angles produced NaN. This typically means there are issues"
" with some residues coordinates. Check your input file ({0})".
format(comment),
file=sys.stderr)
if all_comments:
fasta_name = options.o + ".PB.fasta"
with open(fasta_name, 'w') as outfile:
pbx.io.write_fasta(outfile, all_sequences, all_comments)
print("wrote {0}".format(fasta_name))
else:
print("No output file was written")
def liste_sequence(path_sequences):
'''
Parse le dossier contenant les fichiers pdb a analyses.
Assigne a chaque PDB une sequence de blocs proteique.
Retourne une liste de sequences de blocs proteique (sequences) ainsi
que la liste des PDB (liste_PDB) presents dans le repertoire
(path_sequences).
'''
sequences = []
liste_PDB = []
liste_chain = []
for element in os.listdir(path_sequences):
if element.endswith('.pdb'):
liste_PDB.append(element)
for chain_name, chain in pbx.chains_from_files(
[path_sequences + "/" + element]):
liste_chain.append(chain_name)
# Calcule angle phi et psi
dihedrials = chain.get_phi_psi_angles()
# assignation des blocks proteique
pb_seq = pbx.assign(dihedrials)
sequences.append(pb_seq)
return sequences, liste_PDB, liste_chain
def cli(args=None):
"""Entry point for seq_to_first_iso's CLI.
Parameters
----------
args : list of str, optional
CLI arguments, args are used for testing (default is None for CLI).
Returns
-------
None
Writes a csv file and possibly a gml file.
Raises
------
SystemExit
If no sequences were found on the file.
Notes
-----
Main function of the script, for use with CLI.
"""
if not args:
args = sys.argv[1:]
options, pdb_name_lst = user_inputs()
if options.pdb:
if pdb_name_lst:
print("{} PDB file(s) to process".format(len(pdb_name_lst)))
else:
print('Nothing to do. Good bye.')
return
# PB assignement of PDB structures
chains = pbx.chains_from_files(pdb_name_lst)
else:
# PB assignement of a Gromacs trajectory
chains = pbx.chains_from_trajectory(options.x, options.g)
all_comments = []
all_sequences = []
for comment, chain in chains:
try:
dihedrals = chain.get_phi_psi_angles()
sequence = pbx.assign(dihedrals)
all_comments.append(comment)
all_sequences.append(sequence)
except FloatingPointError:
log.error("The computation of angles produced NaN. "
"This typically means there are issues with "
"some residues coordinates. "
f"Check your input file ({comment})")
log.info(f"There are {len(all_sequences)} sequences of length "
f"{len(all_sequences[0])}")
log.info("Calculating the Mutual Information matrix ...")
MI_matrix = mutual_information_matrix(all_sequences)
# Write to a file
log.info(f"Writing the matrix as {options.output} ...")
df = pd.DataFrame(MI_matrix)
df.to_csv(options.output)
# Add option in CLI, centrality
# Creating a network.
if options.network:
log.info("Creating a network ...")
PB_graph = interaction_graph(MI_matrix)
log.info(f"Writing the network as {options.network} ...")
# Write the graph to GML format.
nx.write_gml(PB_graph, path=options.network)
