Modified a single line in parse_classic_otu_table to allow it to correctly parse classic tab delimited OTU tables that do not have a leading comment line (fixes issue #678). Added a specific test for this case in test_parse_classic_otu_table. Ran all_tests.py to make sure it didn't break anything down stream and it appears not to have. The specific case I am resolving with this commit is where you sumbit a classic OTU table instead of a summarized OTU table to make_3d_plots.py as the biplot otu table (the -t option).
Fix for issue #677
I changed the behavior of beta_diversity.py -r xxx using unifrac-like measures to now only warn the user when there's no information on a sample (no counts in an otu table, or none that match the phylogenetic tree. Those comparisons are meaningless, but when two samples are absent any information, they now return a distance of 1 with -r, but 0 without the -r flag (i.e., computing the whole matrix). This is tricky to change, and I think since we clearly list those distances as meaningless, it's a non-ideal but ok approach.
Fix for issue #677
Merge pull request #682 from justin212k/676

fixing issue #676.  beta_diversity.py -r now only warns when run on samples with no data
Merge pull request #681 from wdwvt1/parse_otu_table_fix

Modified a single line in parse_classic_otu_table to allow it to correct...
Addressing comments for merge
Addressing last comments for merge
Fixing typo
Merge pull request #683 from antgonza/fix_issue_#677

Fix issue #677
Merge branch 'master' of https://github.com/qiime/qiime