Louis BECQUEY / RNANet

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Louis BECQUEY
ce2cba25 1 parent 7196427d

more resolution-specific statistics

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Showing 2 changed files with 21 additions and 19 deletions
#!/usr/bin/python3.8
import Bio
import Bio.PDB as pdb
import concurrent.futures
import getopt
import gzip
......@@ -25,7 +26,8 @@ from multiprocessing import Pool, Manager
from time import sleep
from tqdm import tqdm
from setproctitle import setproctitle
from Bio import AlignIO, SeqIO
from Bio.Align import AlignInfo
def trace_unhandled_exceptions(func):
@wraps(func)
......@@ -112,7 +114,7 @@ class SelectivePortionSelector(object):
return 1
class BufferingSummaryInfo(Bio.Align.AlignInfo.SummaryInfo):
class BufferingSummaryInfo(AlignInfo.SummaryInfo):
def get_pssm(self, family, index):
"""Create a position specific score matrix object for the alignment.
......@@ -139,7 +141,7 @@ class BufferingSummaryInfo(Bio.Align.AlignInfo.SummaryInfo):
score_dict[this_residue] = 1.0
pssm_info.append(('*', score_dict))
return Bio.Align.AlignInfo.PSSM(pssm_info)
return AlignInfo.PSSM(pssm_info)
class Chain:
......@@ -198,11 +200,11 @@ class Chain:
with warnings.catch_warnings():
# Ignore the PDB problems. This mostly warns that some chain is discontinuous.
warnings.simplefilter('ignore', Bio.PDB.PDBExceptions.PDBConstructionWarning)
warnings.simplefilter('ignore', Bio.PDB.PDBExceptions.BiopythonWarning)
warnings.simplefilter('ignore', pdb.PDBExceptions.PDBConstructionWarning)
warnings.simplefilter('ignore', pdb.PDBExceptions.BiopythonWarning)
# Load the whole mmCIF into a Biopython structure object:
mmcif_parser = Bio.PDB.MMCIFParser()
mmcif_parser = pdb.MMCIFParser()
try:
s = mmcif_parser.get_structure(self.pdb_id, path_to_3D_data + "RNAcifs/"+self.pdb_id+".cif")
except ValueError as e:
......@@ -223,7 +225,7 @@ class Chain:
sel = SelectivePortionSelector(model_idx, self.pdb_chain_id, valid_set, khetatm)
# Save that selection on the mmCIF object s to file
ioobj = Bio.PDB.mmcifio.MMCIFIO()
ioobj = pdb.MMCIFIO()
ioobj.set_structure(s)
ioobj.save(self.file, sel)
......@@ -1115,7 +1117,7 @@ class Pipeline:
print(f"nohup bash -c 'time {fileDir}/RNAnet.py --3d-folder ~/Data/RNA/3D/ --seq-folder ~/Data/RNA/sequences -s' &")
sys.exit()
elif opt == '--version':
print("RNANet 1.1 beta")
print("RNANet 1.2, parallelized, Dockerized")
sys.exit()
elif opt == "-r" or opt == "--resolution":
assert float(arg) > 0.0 and float(arg) <= 20.0
......@@ -1445,7 +1447,7 @@ class Pipeline:
# Update the database
data = []
for r in results:
align = Bio.AlignIO.read(path_to_seq_data + "realigned/" + r[0] + "++.afa", "fasta")
align = AlignIO.read(path_to_seq_data + "realigned/" + r[0] + "++.afa", "fasta")
nb_3d_chains = len([1 for r in align if '[' in r.id])
if r[0] in SSU_set: # SSU v138 is used
nb_homologs = 2225272 # source: https://www.arb-silva.de/documentation/release-138/
......@@ -1535,9 +1537,9 @@ class Pipeline:
# Run statistics
if self.RUN_STATS:
# Remove previous precomputed data
subprocess.run(["rm", "-f", runDir + "/data/wadley_kernel_eta.npz",
runDir + "/data/wadley_kernel_eta_prime.npz",
runDir + "/data/pair_counts.csv"])
subprocess.run(["rm", "-f", runDir + f"/data/wadley_kernel_eta_{self.CRYSTAL_RES}.npz",
runDir + f"/data/wadley_kernel_eta_prime_{self.CRYSTAL_RES}.npz",
runDir + f"/data/pair_counts_{self.CRYSTAL_RES}.csv"])
for f in self.fam_list:
subprocess.run(["rm", "-f", runDir + f"/data/{f}.npy",
runDir + f"/data/{f}_pairs.csv",
......@@ -2124,7 +2126,7 @@ def work_mmcif(pdb_id):
# if not, read the CIF header and register the structure
if not len(r):
# Load the MMCIF file with Biopython
mmCif_info = Bio.PDB.MMCIF2Dict.MMCIF2Dict(final_filepath)
mmCif_info = pdb.MMCIF2Dict.MMCIF2Dict(final_filepath)
# Get info about that structure
try:
......@@ -2218,7 +2220,7 @@ def work_prepare_sequences(dl, rfam_acc, chains):
if rfam_acc in LSU_set | SSU_set: # rRNA
if os.path.isfile(path_to_seq_data + f"realigned/{rfam_acc}++.afa"):
# Detect doublons and remove them
existing_afa = Bio.AlignIO.read(path_to_seq_data + f"realigned/{rfam_acc}++.afa", "fasta")
existing_afa = AlignIO.read(path_to_seq_data + f"realigned/{rfam_acc}++.afa", "fasta")
existing_ids = [r.id for r in existing_afa]
del existing_afa
new_ids = [str(c) for c in chains]
......@@ -2227,7 +2229,7 @@ def work_prepare_sequences(dl, rfam_acc, chains):
if len(doublons):
warn(f"Removing {len(doublons)} doublons from existing {rfam_acc}++.fa and using their newest version")
fasta = path_to_seq_data + f"realigned/{rfam_acc}++.fa"
seqfile = Bio.SeqIO.parse(fasta, "fasta")
seqfile = SeqIO.parse(fasta, "fasta")
# remove it and rewrite it with its own content filtered
os.remove(fasta)
with open(fasta, 'w') as f:
......@@ -2268,7 +2270,7 @@ def work_prepare_sequences(dl, rfam_acc, chains):
with open(path_to_seq_data + f"realigned/{rfam_acc}++.fa", "w") as plusplus:
ids = set()
# Remove doublons from the Rfam hits
for r in Bio.SeqIO.parse(path_to_seq_data + f"realigned/{rfam_acc}.fa", "fasta"):
for r in SeqIO.parse(path_to_seq_data + f"realigned/{rfam_acc}.fa", "fasta"):
if r.id not in ids:
ids.add(r.id)
plusplus.write('> '+r.description+'\n'+str(r.seq)+'\n')
......@@ -2343,10 +2345,10 @@ def work_realign(rfam_acc):
notify("Aligned new sequences together")
# Detect doublons and remove them
existing_stk = Bio.AlignIO.read(existing_ali_path, "stockholm")
existing_stk = AlignIO.read(existing_ali_path, "stockholm")
existing_ids = [r.id for r in existing_stk]
del existing_stk
new_stk = Bio.AlignIO.read(new_ali_path, "stockholm")
new_stk = AlignIO.read(new_ali_path, "stockholm")
new_ids = [r.id for r in new_stk]
del new_stk
doublons = [i for i in existing_ids if i in new_ids]
......@@ -2447,7 +2449,7 @@ def work_pssm(f, fill_gaps):
# Open the alignment
try:
align = Bio.AlignIO.read(path_to_seq_data + f"realigned/{f}++.afa", "fasta")
align = AlignIO.read(path_to_seq_data + f"realigned/{f}++.afa", "fasta")
except:
warn(f"{f}'s alignment is wrong. Recompute it and retry.", error=True)
with open(runDir + "/errors.txt", "a") as errf:
......
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