Mercurial > repos > ucsb-phylogenetics > osiris_phylogenetics

annotate alignment/prank.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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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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0
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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 $input = $ARGV[0];
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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4 my $format = $ARGV[1];
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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5 my $missing = $ARGV[2];
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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6 my $output = "output";
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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7 my $fparam;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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8
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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9 if($missing eq 'yes'){
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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10 $fparam = "-F";
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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11 }else{
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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12 $fparam = "";
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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 my $run = qx/prank -d=$input -o=$output -f=$format $fparam/;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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15 print $run;