Mercurial > repos > ucsb-phylogenetics > osiris_phylogenetics
comparison phylostatistics/ses-mpd-galaxy.r @ 0:5b9a38ec4a39 draft default tip
First commit of old repositories
| author | osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> |
|---|---|
| date | Tue, 11 Mar 2014 12:19:13 -0700 |
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| -1:000000000000 | 0:5b9a38ec4a39 |
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| 1 #!/sw/math/R-2.15.3-shlib/bin/Rscript | |
| 2 | |
| 3 # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | |
| 4 # NOTE: since picante is licensed under the GPL, and this program relies on | |
| 5 # picante, the program is licensed under the GPL regardless | |
| 6 # | |
| 7 # See: http://cran.r-project.org/web/packages/picante/picante.pdf, | |
| 8 # http://www.gnu.org/licenses/old-licenses/gpl-2.0-faq.html#IfLibraryIsGPL | |
| 9 # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | |
| 10 | |
| 11 library('picante') | |
| 12 | |
| 13 args <- commandArgs(trailingOnly = TRUE) | |
| 14 | |
| 15 sample <- read.table(file = args[1]) | |
| 16 tree <- read.tree(file = args[2]) | |
| 17 | |
| 18 # get community data matrix of sample | |
| 19 comm <- sample2matrix(sample) | |
| 20 # get phylogenetic distance matrix of tree | |
| 21 phydist <- cophenetic(tree) | |
| 22 | |
| 23 # finally, run the processed info through ses.mpd to get the result we want | |
| 24 result <- ses.mpd(comm, phydist) | |
| 25 | |
| 26 # capture result and output to file | |
| 27 out <- capture.output(result) | |
| 28 cat(out, file = args[3], sep = "\n") |