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annotate phylogenies/beast_treeannotator.pl @ 0:5b9a38ec4a39 draft default tip

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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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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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1 #!/usr/bin/perl
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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2
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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3 my $treeannotator_path = '/home/galaxy/pkgs/BEAST172/bin/treeannotator';
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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4
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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5 my $input = $ARGV[0];
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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6 my $burnin = $ARGV[1];
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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7 my $Node_heights = $ARGV[2];
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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8
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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9 my $node_opt;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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10
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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11 if($Node_heights eq "0") {
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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12 $node_opt = "keep";
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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13 }
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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14 elsif($Node_heights eq "1") {
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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15 $node_opt = "median";
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16 }
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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17 elsif($Node_heights eq "2") {
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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18 $node_opt = "mean";
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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19 }
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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20
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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21 my $run = qx/$treeannotator_path -heights $node_opt -burnin $burnin $input out.tre 2>log.txt/;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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22
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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23 print $run;