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annotate phylostatistics/ses-mpd-galaxy.r @ 0:5b9a38ec4a39 draft default tip

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