[bip] bhutils 0.1.2 released

[Brandon King]

Hi All,

I recently ripped out some useful utilities out of the BioHub 
<http://woldlab.caltech.edu/biohub/> project an put them in there own 
smaller package which can be reused elsewhere. The package is called 
bhutils (BioHub Utils) and it is LGPL'd as they were ripped form BioHub 
which is LGPL'd.

Currently BlastDB and BlastHandler modules have a requirement of 
BioPython, but I hope that requirement will go away in the future. I 
believe the rest of the modules use builtin Python modules.

Hopefully some of these modules will be useful to others. Regardless, 
they are more easily available now. By the way, I will write up example 
uses for the modules if anyone is interested.

Website: http://woldlab.caltech.edu/html/bhutils/

Summary of package modules:

bhutils.BlastDB:
 * Allows for easy blasting (wrapper around biopython's blast utils)
 * Contains code for generating a blast database (i.e. formatdb
   commandline) given a list of fasta files. (See bhutils.Fasta for
   useful fasta handling code).

bhutils.BlastHandler:
 * Filter classes which take the output from BlastDB module and filter
   the results. Like only return results that have n-mismatches.

bhutils.Blat:
 * Util for using blat.
 * Util for creating nibs (blat db files) from list of fasta files.
 * Blat parser

bhutils.DirectoryBuilder:
 * Given a path, builds a directory tree (more like a branch).

bhutils.Decompress:
 * Allows decompression of files from Python (.zip, bzip2, tar,
   gzip). Uses one function to decompress all compression types from
   within Python. No need to import individual types of decompression
   modules. (Used included Python modules for actual decompression).

bhutils.DownloadUtil:
 * A utility to download one or many files from http or ftp. Can use
   wildcards. on linux where wget exists, it uses wget otherwise it
   falls back to modules included with Python.

bhutils.Fasta
 * Disk based Fasta reader.
 * Only retrieves sequence when getSequence*() functions are
   called. (Seeks to correct locations in the file base on a
   precalculated indexing of the fasta file).
 * Can write list of FastaSequence objects to FASTA file with multiple
   FASTA sequences in it.

bhutils.SequenceUtils:
 * ReverseComplement code


-Brandon King
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