Tags give the ability to mark specific points in history as being important
-
v 1.5 beta, April 2021
FEATURE CHANGES
- New option
--stats-opts="..."
allows to pass options to the automatic run of statistics.py (when-s
is used) - Removed support for 3'->5' Rfam hits, they are now completely ignored. They concern the opposite strand, which is unresolved in 3D.
- Removed PyDCA, which is outdated and introduces dependencies conflicts. Code may be adapted later.
- A new column in align_column table,
index_small_ali
, gives the index of the nucléotide in the "3d only" alignment. - 3D distance matrices are now computed only for match positions (match to the covariance model)
BUG CORRECTIONS
- Corrected a bug which skipped angle conversions from degrees (DSSR) to radians if nucleotides where renumbered.
v 1.4 beta, March 2021
Khodor Hannoush joins the development of RNANet.
FEATURE CHANGES
- SINA is now used only if you pass the option
--sina
, Infernal is used by default even for rRNAs. - A new option
--cmalign-opts="..."
allows to customize your cmalign runs, e.g. with--cyk
. The default is no option. - RNANet makes use of PyDCA to compute DCA-related features on the alignments (descriptions to come in the Database.md)
- statistics.py now fully supports the computation of 3D distance matrices, with average and standard deviation by RNA family
- Now RNANet considers only the equivalence class representative structure by default. To consider all members of an equivalence class (like before), use the
--redundant
option.
TECHNICAL CHANGES
- cmalign is not run with
--cyk
anymore by default, and now requires huge amounts of RAM if launched with the default options. - Moving to a 60-core/128GB server for our internal runs.
- New option
-
v1.3-beta January 2021 update (v1.3-beta)
v1.3-beta, January 2021
The first uses of RNAnet by people from outside the development team happened last December. A few feedback allowed to identify issues and useful information to add.
FEATURE CHANGES
- Sequence alignments of the 3D structures mapped to a family are now provided.
- Full alignments with Rfam sequences are not provided, but you can ask us for the files.
- Two new fields in table 'family': ali_length and ali_filtered_length. They are the MSA lengths of the alignment with and without the Rfam sequences.
- Gap replacement by consensus (--fill-gaps) has been removed. Now, the gap percentage and consensus are saved in the align_column table and the datapoints in CSV format, in separate columns. Consensus is one of ACGUN-, the gap being chosen if >75% of the sequences are gaps at this position. Otherwise, A/C/G/U is chosen if >50% of the non-gap positions are A/C/G/U. Otherwise, N is the consensus.
TECHNICAL CHANGES
- SQLite connections are now all in WAL mode by default (previously, only the writers used WAL mode, but this is useless)
- Moved to Python3.9 for internal testing.
- Latest version of BioPython is now supported (1.78)
BUG CORRECTIONS
- When an alignment file is updated in a newer run of RNANet, all the re_mappings are now re-computed for this family. Previously, the remappings were computed only for the newly added sequences, while the alignment actually changed even for chains added in past runs.
- Changed the ownership and permissions of files produced by the Docker container. They were previously owned by root and the user could not get access to them.
- Modified nucleotides were not always correctly transformed to N in the alignments (and nucleotide.nt_align_code fields). Now, the alignments and nt_align_code (and consensus) only contain "ACGUN-" chars. Now, 'N' means 'other' or 'any', while '-' means 'nothing' or 'unknown'.