Louis BECQUEY / RNANet

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Louis BECQUEY
0621fb8c 1 parent 3ba3c7d7

Alignment options used in alignment updates

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Showing 5 changed files with 8 additions and 107 deletions
......@@ -2692,7 +2692,10 @@ def use_infernal(rfam_acc, alignopts):
# Align the new sequences
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",
cmd = ["cmalign"]
if alignopts is not None:
cmd += alignopts
p1 = subprocess.run(cmd + ["--ifile", path_to_seq_data + f"realigned/{rfam_acc}.ins",
"--sfile", path_to_seq_data + f"realigned/{rfam_acc}.tsv",
"-o", new_ali_path,
path_to_seq_data + f"realigned/{rfam_acc}.cm",
......@@ -2705,6 +2708,7 @@ def use_infernal(rfam_acc, alignopts):
warn(f"Not enough RAM to allocate cmalign DP matrix for family {rfam_acc}. Use --sina or --cmalign-opts.", error=True)
else:
warn(align_errors, error=True)
return
notify("Aligned new sequences together")
# Detect doublons and remove them
......@@ -2721,6 +2725,7 @@ def use_infernal(rfam_acc, alignopts):
except ValueError:
# Not a stockholm file
warn(f"New alignment {new_ali_path} is not a Stockholm file !", error=True)
return
new_ids = [r.id for r in new_stk]
del new_stk
doublons = [i for i in existing_ids if i in new_ids]
......
......@@ -16,7 +16,7 @@
# Method 1 : Installation using Docker
* Step 1 : Download the [Docker container](https://entrepot.ibisc.univ-evry.fr/d/1aff90a9ef214a19b848/files/?p=/rnanet_v1.5b_docker.tar&dl=1). Open a terminal and move to the appropriate directory.
* Step 1 : Download the [Docker container](https://entrepot.ibisc.univ-evry.fr/d/1aff90a9ef214a19b848/files/?p=/rnanet_v1.6b_docker.tar&dl=1). Open a terminal and move to the appropriate directory.
* Step 2 : Extract the archive to a Docker image named *rnanet* in your local installation
```
$ docker load -i rnanet_v1.5b_docker.tar
......
6ydp_1_AA_1176-2737
6ydw_1_AA_1176-2737
7d1a_1_A_805-902
7d0g_1_A_805-913
7d0f_1_A_817-913
1vy7_1_AY_1-73
1vy7_1_CY_1-73
4w2h_1_CY_1-73
7o7z_1_AH_144-220
4c9d_1_D_29-1
4c9d_1_C_29-1
7aih_1_1_2984-3610
7aih_1_1_2400-2963
7ane_1_2_2489-3115
7ane_1_2_1904-2468
5g2x_1_A_595-692
7aor_1_2_2589-3210
7aor_1_2_2020-2579
7a5p_1_2_259-449
7aor_1_A_2589-3210
7aor_1_A_2020-2579
7am2_1_1_2491-3117
7am2_1_1_1904-2470
7ane_1_1_2489-3115
7ane_1_1_1904-2468
6uz7_1_8_2140-2825
6ydp_1_AA_1176-2737
Could not find nucleotides of chain AA in annotation 6ydp.json. Either there is a problem with 6ydp mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
6ydw_1_AA_1176-2737
Could not find nucleotides of chain AA in annotation 6ydw.json. Either there is a problem with 6ydw mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
7d1a_1_A_805-902
Could not find nucleotides of chain A in annotation 7d1a.json. Either there is a problem with 7d1a mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
7d0g_1_A_805-913
Could not find nucleotides of chain A in annotation 7d0g.json. Either there is a problem with 7d0g mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
7d0f_1_A_817-913
Could not find nucleotides of chain A in annotation 7d0f.json. Either there is a problem with 7d0f mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
1vy7_1_AY_1-73
Sequence is too short. (< 5 resolved nts)
1vy7_1_CY_1-73
Sequence is too short. (< 5 resolved nts)
4w2h_1_CY_1-73
Sequence is too short. (< 5 resolved nts)
7o7z_1_AH_144-220
Could not find nucleotides of chain AH in annotation 7o7z.json. Either there is a problem with 7o7z mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
4c9d_1_D_29-1
Mapping is reversed, this case is not supported (yet).
4c9d_1_C_29-1
Mapping is reversed, this case is not supported (yet).
7aih_1_1_2984-3610
Could not find nucleotides of chain 1 in annotation 7aih.json. Either there is a problem with 7aih mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
7aih_1_1_2400-2963
Could not find nucleotides of chain 1 in annotation 7aih.json. Either there is a problem with 7aih mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
7ane_1_2_2489-3115
Could not find nucleotides of chain 2 in annotation 7ane.json. Either there is a problem with 7ane mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
7ane_1_2_1904-2468
Could not find nucleotides of chain 2 in annotation 7ane.json. Either there is a problem with 7ane mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
5g2x_1_A_595-692
Sequence is too short. (< 5 resolved nts)
7aor_1_2_2589-3210
Could not find nucleotides of chain 2 in annotation 7aor.json. Either there is a problem with 7aor mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
7aor_1_2_2020-2579
Could not find nucleotides of chain 2 in annotation 7aor.json. Either there is a problem with 7aor mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
7a5p_1_2_259-449
Could not find nucleotides of chain 2 in annotation 7a5p.json. Either there is a problem with 7a5p mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
7aor_1_A_2589-3210
Could not find nucleotides of chain A in annotation 7aor.json. Either there is a problem with 7aor mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
7aor_1_A_2020-2579
Could not find nucleotides of chain A in annotation 7aor.json. Either there is a problem with 7aor mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
7am2_1_1_2491-3117
Could not find nucleotides of chain 1 in annotation 7am2.json. Either there is a problem with 7am2 mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
7am2_1_1_1904-2470
Could not find nucleotides of chain 1 in annotation 7am2.json. Either there is a problem with 7am2 mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
7ane_1_1_2489-3115
Could not find nucleotides of chain 1 in annotation 7ane.json. Either there is a problem with 7ane mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
7ane_1_1_1904-2468
Could not find nucleotides of chain 1 in annotation 7ane.json. Either there is a problem with 7ane mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
6uz7_1_8_2140-2825
Could not find nucleotides of chain 8 in annotation 6uz7.json. Either there is a problem with 6uz7 mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
......@@ -3,7 +3,7 @@
# run it one or twice a year, otherwise, the faster update runs should be enough.
cd /home/lbecquey/Projects/RNANet
rm -rf latest_run.log errors.txt
rm -rf latest_run.log errors.txt known_issues.txt known_issues_reasons.txt
# Run RNANet
bash -c 'time python3.8 ./RNAnet.py --3d-folder /home/lbecquey/Data/RNA/3D/ --seq-folder /home/lbecquey/Data/RNA/sequences/ --from-scratch --ignore-issues -r 20.0 --no-homology --redundant --extract' > latest_run.log 2>&1
......