biocore/scikit-bio — pull request #235 by ElDeveloper (2014-03-29 08:22:10+00:00)
Title: Port Rfam and Clustal parsers ⚠️Not ready for merge⚠️

This pull request still needs to add the appropriate documentation and some more clean-up. However before I continue to move forward I wanted to bring up the cluttering that `skbio/parse/sequences` is becoming. Currently the FASTA and FASTQ parsers are living under this module and with this pull request the `Rfam` parser and other accompanying functions will be living there as well, what I think would be nice is if we took a similar approach to what @Jorge-C took for the ordination sub package i. e. where each method is in its own module but all methods become accessible via the `__init__.py` file using the `__all__` variable.

What I'm thinking about is to separate sequences.py into three modules (`fasta.py`, `fastq.py` and `rfam.py`) and making all the parsers available via `sequences.py` using the `__all__` variable so the imports remain the same but the organization is a bit better.

You could then do:

```python
# this would be the recommended way
from skbio.parse.sequences import parse_fasta

# however, if you wanted, you could still do
from skbio.parse.fasta import parse_fasta
```

Thoughts? Once we resolve this, I'll begin working on the docs.