investigating alignment errors

Former-commit-id: a95cfdfe
Showing 1 changed file with 23 additions and 7 deletions
......@@ -2593,20 +2593,32 @@ def use_infernal(rfam_acc, alignopts):
new_ali_path = path_to_seq_data + f"realigned/{rfam_acc}_new.stk"
# Align the new sequences
with open(new_ali_path, 'w') as o:
with open(path_to_seq_data + f"realigned/{rfam_acc}_new.log", 'w') as o:
p1 = subprocess.run(["cmalign", "--ifile", path_to_seq_data + f"realigned/{rfam_acc}.ins",
"--sfile", path_to_seq_data + f"realigned/{rfam_acc}.tsv",
"-o", path_to_seq_data + f"realigned/{rfam_acc}++.stk",
"-o", path_to_seq_data + f"realigned/{rfam_acc}_new.stk",
path_to_seq_data + f"realigned/{rfam_acc}.cm",
path_to_seq_data + f"realigned/{rfam_acc}_new.fa"],
stdout=o, stderr=subprocess.PIPE)
if "--mxsize" in p1.stderr.decode("utf-8"):
# not enough available RAM to allocate the DP matrix
warn(f"Not enough RAM to allocate cmalign DP matrix for family {rfam_acc}. Use --sina or --cmalign-opts.", error=True)
notify("Aligned new sequences together")
# Detect doublons and remove them
existing_stk = AlignIO.read(existing_ali_path, "stockholm")
existing_stk = AlignIO.read(existing_ali_path, "stockholm")
except ValueError:
# Not a stockholm file
warn(f"Existing alignment is not a Stockholm file !", error=True)
existing_ids = [r.id for r in existing_stk]
del existing_stk
new_stk = AlignIO.read(new_ali_path, "stockholm")
new_stk = AlignIO.read(new_ali_path, "stockholm")
except ValueError:
# Not a stockholm file
warn(f"New alignment {new_ali_path} is not a Stockholm file !", error=True)
new_ids = [r.id for r in new_stk]
del new_stk
doublons = [i for i in existing_ids if i in new_ids]
......@@ -2622,10 +2634,14 @@ def use_infernal(rfam_acc, alignopts):
os.remove(path_to_seq_data + "realigned/toremove.txt")
# And we merge the two alignments
p2 = subprocess.run(["esl-alimerge", "-o", path_to_seq_data + f"realigned/{rfam_acc}_merged.stk",
"--rna", existing_ali_path, new_ali_path],
p2 = subprocess.run(["cmalign", "--merge" "-o", path_to_seq_data + f"realigned/{rfam_acc}_merged.stk",
"--rna", path_to_seq_data + f"realigned/{rfam_acc}.cm", existing_ali_path, new_ali_path],
stdout=subprocess.DEVNULL, stderr=subprocess.PIPE)
stderr = p1.stderr.decode('utf-8') + p2.stderr.decode('utf-8')
alignErrors = p1.stderr.decode('utf-8')
mergeErrors = p2.stderr.decode('utf-8')
alignErrors = "Alignment: "+ alignErrors if len(alignErrors) else ""
mergeErrors = "Alignment: "+ mergeErrors if len(mergeErrors) else ""
stderr = alignErrors + mergeErrors
subprocess.run(["mv", path_to_seq_data + f"realigned/{rfam_acc}_merged.stk", existing_ali_path])
notify("Merged alignments into one")