matsen/pplacer — Issue #214: overlap graph (perhaps as part of `islands`)
Author: matsen
Created: 2012-01-27 01:34:36+00:00
State: open
Labels: top-ish

We would like to spit out the weighted overlap graph (unweighted version
described in mass_islands.ml).

That is, if the placement distributions of reads i and j overlap (i.e.
share an edge) then they get connected in the graph. The weight assigned
to that edge is

\sum_e d(i)_e d(j)_e

where d(i)_e is the probability mass of read i on edge e (and the sum is
over all edges, but we clearly only have to look at edges where both are
nonzero).

The output should be in [ABC format](http://micans.org/mcl/), i.e.

"The input is then a file or stream in which each line encodes an edge
in terms of two labels (the 'A' and the 'B') and a numerical value (the
'C'), all separated by white space."

So something like

read1 read2 0.3
read3 read4 0.4

We will then want to feed these graphs to the `mcl` binary-- please
check to make sure that it properly executes using the guppy output. I
haven't installed it yet (though it's avail using apt-get for
Debianesque systems).

I would be happy for this to be its own subcommand: `guppy ograph`, or a
flag to `islands`, though that might get a bit complex if this thing is
going to have flags of its own.

[MCL site](http://micans.org/)