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.

    - 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.

    - 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)

    - 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'.