CHANGELOG 3.89 KB
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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    - Removed PyDCA, which is outdated and introduces dependencies conflicts.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.

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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.

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v 1.3 beta, January 2021

The first uses of RNAnet by people from outside the development team happened between this 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 alignements 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 connexions 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', while '-' means 'nothing' or 'unknown'.