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21 | * [UPCOMING] Possibly, automated detection of HLs and ILs from the 3D Motif Atlas (BGSU). Maybe. Their own website already does the job. | 21 | * [UPCOMING] Possibly, automated detection of HLs and ILs from the 3D Motif Atlas (BGSU). Maybe. Their own website already does the job. |
22 | * A field estimating the quality of the sequence alignment in table family. | 22 | * A field estimating the quality of the sequence alignment in table family. |
23 | * Possibly, more metrics about the alignments coming from Infernal. | 23 | * Possibly, more metrics about the alignments coming from Infernal. |
24 | +* Move to SILVA LSU release 138 | ||
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... | @@ -1072,8 +1072,8 @@ class Pipeline: | ... | @@ -1072,8 +1072,8 @@ class Pipeline: |
1072 | elif opt == "--from-scratch": | 1072 | elif opt == "--from-scratch": |
1073 | warn("Deleting previous database and recomputing from scratch.") | 1073 | warn("Deleting previous database and recomputing from scratch.") |
1074 | subprocess.run(["rm", "-rf", | 1074 | subprocess.run(["rm", "-rf", |
1075 | - # path_to_3D_data + "annotations", # DEBUG : keep the annotations ! | 1075 | + path_to_3D_data + "annotations", |
1076 | - # path_to_3D_data + "RNAcifs", # DEBUG : keep the cifs ! | 1076 | + path_to_3D_data + "RNAcifs", |
1077 | path_to_3D_data + "rna_mapped_to_Rfam", | 1077 | path_to_3D_data + "rna_mapped_to_Rfam", |
1078 | path_to_3D_data + "rnaonly", | 1078 | path_to_3D_data + "rnaonly", |
1079 | path_to_seq_data + "realigned", | 1079 | path_to_seq_data + "realigned", | ... | ... |
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