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matsen / pplacer

Phylogenetic placement and downstream analysis
http://matsen.fredhutch.org/pplacer/
GNU General Public License v3.0
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CSV flag not working? #347

Closed matsen closed 8 years ago

matsen commented 8 years ago

Here is the original report:

I am using the guppy unifrac function to analyse a number of jplace files and would benefit from having it output a csv instead of a padded matrix. The command I'm using is as follows: guppy unifrac --csv --out-dir [my out dir] [jplace1, jplace2, jplace2, ...] -o [out.csv] I generalized the flag inputs in this case. I can't attach my files because they are to large. I can get it to output to the file, but the format is still a padded matrix, even with the '--csv' flag. What am I missing? Also, I am using the most recent version of guppy.

matsen commented 8 years ago

It turns out that the --csv flag works fine, but it needs to be used in conjunction with the --list-out option.