add experimental support for .sra input file format
bugfix for sra input file format support
bettered sra extraction
improved parameter checking
bugfix
first unit test: 16S pipeline with fasta input
more work in -f of sra files
manual merge commit
add ability to read alignment from nhmmer directly rather than going through pynast
searching SRA files in protein mode debugged, v0.3.1
v0.3.1, DRY the version number specification
bugfix 16S, more errors shown for hmmsearch step
biopython assert hack
code cleanup
replaced getorf with OrfM, added protein unit test
typo and fxtract call fixup
discourage use of reverse reads
0.3.3
Merged unit testing with master
Merge branch 'wwood-unit_testing'