Partial commit
Add missing import and change constructor
Merge branch 'master' of git://github.com/biocore/scikit-bio into port-rfam
STY: Make code adhere to the project standards
MAINT: Remove irrelevant Exceptions
TST: Add tests for clustal

These tests were directly ported from the test suite in cogent. Some
clean-up took place but there was nothing major, most of it was PEP-8
related.
TST: Add tests for the Rfam related code
TST: Add tests for utility functions in Rfam

The following functions were untested in skbio but were tested in
pycogent, the test-cases were ported over and a few minor changes were
made to take advantage of TestCase object:
    - is_rfam_header_line
    - is_rfam_structure_line
    - is_rfam_seq_line

Five failures remain.
BUG: Change Sequence to BiologicalSequence

Making this change required that the output of any BiologicalSequence
object be casted to a string to ensure backwards compatibility
API: Update use of the skbio API
API: SequenceCollection does not provide NamedSeqs

This is a property that the previous SequenceCollection objects did
provide (in cogent).
TST API: Fix broken test because of deprecated API

This test relied on counting the number of sequences in the alignment
object, the new API provides a sequence_count method that makes this
more straight forward.
API: Update use of Sequence API

The parsed fasta records in SequenceCollection split the identifiers on
blankspaces to retrieve the description of each sequences, this is
required the code to be updated because it was previously checking for
an identifer plus description combo.
TST: clean up tests for MinimalRfamParser
MAINT: Use BiologicalSequence instead of DNA
STY: Re-order import statments
TST: Fix all remaining failing tests

Making a better use of the Alignment object yields cleaner code overall.
API; Improve the usage of the core objects

These changes avoid the need of creating the sequence collection objects
starting off of FASTA records.
STY: Change files to be PEP8 compliant
bug fix, find cache was not forced to be at the root