added partition-graph script + tests
added output-partitions & associated tests; pmap files now contain format info.
chmod +x all scripts.
removed leftover gunk
added extract-partitions
added python-dev installation to doc
fixed partition-graph string/int comparison
added check to make sure file is open
switched to using screed.open
Merge branch 'refactor' of github.com:ctb/khmer into refactor
refactored partitioning a bit to use merge-partitions
knot/artifact removal scripts
cleanup of command line interface.
changed default min-partition-size to 5
updated partitioning and scripts docs
Merge branch 'refactor' of github.com:ctb/khmer into refactor
added collect_high_abundance_kmers code
ignore shutil.rmtree errors in tests
Merge branch 'refactor' of github.com:ctb/khmer into refactor
added stoptags arguments to make-initial; noted inconsistency in find-knots treatment of stoptags