[Biopython] StockholmIO replaces "." with "-", why?

[Bryan Lunt]

Greetings All!

It looks like line 364 of Bio.AlignIO.StockholmIO reads:

seqs[id] += seq.replace(".","-")

So when you load into memory alignments that mark gaps created to
allow alignment to inserts with ".", (such as PFam alignments or the
output of hmmer) that information is lost.

I know there must be a good reason for this, but I am finding it a
problem on my end..

-Bryan Lunt