II.5 - Agrogenom genomic blocks of evolutionary events (first pass)

Blocks of evolutionary events ( gene duplication, D, or transfer, T) involving several neighbour genes ; this is a first pass of running the script getblockevents.py to find congruent neighbouring events across gene family trees.This will allow (at the next step) to pick the optimal events amongst the set of mutually exclusive events retained as possible for a gene tree node at the previous step (see item #II.4).

getblockevents_out.l.*/ folders are results of parallel jobs searching for neighbouring genes in extant ("leaf") genomes involved in similar events, i.e. leaf blocks; each job searched separately within a set of replicon (or contigs). This search is performed with a greedy algorithm covering chromosome; "gap" genes without signal for a congruent event are first allowed, and then tested for compatibility and eventually rejected if negative.
getblockevents_out.a.*/ folder is the result of the single job that searched for leaf blocks linking to the same events in gene trees, to reconstruct the one ancestral block of genes from which descend the extant blocks of co-evolved gene.

The file structure in getblockevents_out.l.*/ folders is similar:- blocks/ folder: one file per replicon listing genes involved in a block- before_split_blocks.stats file: stats on blocks generated by the greedy algorithm recognizing similar events based on their event characteristics, i.e. the sets of possible recipient and donor species;- transferred_blocks.stats file: stats on blocks after the compatibility of common events with gap gene trees was checked and incopatibility resolved by splitting the initial blocks into several blocks.
[omitted here for space sake, several Gb altogether]:- block_trees/ folder: the gene trees associated to the block events - replicon.shelve file: the serialized Python objects containing all the genes borne by a replicon/contig and the event block that link them.
file structure in getblockevents_out.a.*/:- ancestral_blocks file: list of all ancestral blocks and the leaf blocks they link to;
[similar files as described above for leaf blocks]- blocks_events.mat file: summary of block events recorded between donor and recipient (ancestral) species pairs[omitted here for space sake, several Gb for 1 file]:- ancblocks.shelve file:the serialized Python objects containing all the ancestral blocks and the leaf blocks linked to them