Make an initial pass at a data structure

[hyanwong]

This sets up a table structure very roughly like that in tskit, but without any attempts at efficiency. I have attempted to mirror the tskit functions like add_row etc, so that it is easy to port e.g. the WF simulator from tskit-dev/tutorials#254 to a GIG version (see #16 (comment))

There's a lot missing here (it just deals with the table interface, and only a few tables at that), but one of the interesting things that you can do is convert a tree sequence into a GIG, using e.g.

import msprime
from GeneticInheritanceGraph import TableCollection
ts = msprime.sim_ancestry(10, sequence_length=1000)
GIGtables = TableCollection.from_tree_sequence(ts)

What do you think @duncanMR ?

[hyanwong]

I'm sure we will soon want to be able to access the table data by columns as well as rows, returning numpy arrays, e.g. we should be able to do

print((tables.intervals.parent_left - tables.intervals.parent_right).mean()

[duncanMR]

This is a great start! Besides the access by columns functions, I'll also work on implementing a function to add rows to the IntervalTable for a particular SV type. For example, something like add_structural_variant(type='deletion', interval=(0,2)). We'll need this to implement add_inheritance_paths in #16.

[hyanwong]

Shall I merge it, then? This is just a provisional API: we can replace all the structure underneath invisibly, I hope.

[duncanMR]

Shall I merge it, then? This is just a provisional API: we can replace all the structure underneath invisibly, I hope.

Yes, go for it!

[hyanwong]

Yes, go for it!

Done, and I stole the formatting from tskit(!):