Allow for - in dot-bracket
Outline remove pseudoknots
Rework Format into Writer.
Writer now can write to files and no longer has a str() method. In addition it
has default behaviour which it did not before. It now simple returns
str(parser._pairs).
Add a class to format a parser into a connect style string.
I've also modified the parser to accept more header types.
Make dot_bracket.Writer a new style formatter
Add sequence as optional paramter to parsers.
Also make the Connect parser send this argument. This fixes failures caused by
setting a default sequence property in the base parser.
Ignore tmp/
Replace rake with fabric
Tinker with connect parser
Basic RemovePseudoknots wrapper
Let connect parser roundtrip without sequence
Add note about DATADIR.
Clean up imports
Fix indenting.
Make test the default task.
Rework all folders to new interface.
All folders are now callable objects and use the wrapper in utils.wrapper. This
provides a uniform interface and exceptions for all wrappers.
Make ResultSet more list-like
Add dialects to DotBracket parsers.

The dot bracket parser now understands dialects. Dialects just define what is a
pair, pseudoknot, unpaired, etc. This allows it to parse either Rfam or generic
dot bracket strings. We can't do both becuase Rfam may use {} as a pair while in
general this means a pseudoknot. Dialects solve this.
Add example for RemovePseudoknots
Change default generic dialect.
Generic dialect for dot-bracket should now parse rfam like or non-rfam
structures.  Note that it will not parse all valid rfam structures correctly as
rfam allows using {} to indicate a pair instead of a pseudoknot. To be really
sure to parse rfam correctly then the rfam dialect should be used, otherwise
generic will probably work.