Mercurial > repos > dereeper > sniplay
view Rooting/Rooting.pl @ 1:420b57c3c185 draft
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author | dereeper |
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date | Fri, 10 Jul 2015 04:39:30 -0400 |
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#!/usr/bin/perl use strict; use Switch; use Getopt::Long; use Bio::SeqIO; use Cwd ; use FindBin qw ( $Bin $Script ); my $CURRENT_DIR = $Bin; my $ROOTING_EXE = "java -jar ". $CURRENT_DIR . "/Rootings_54.jar"; my $usage = qq~Usage:$0 <args> [<opts>] where <args> are: -i, --input <newick input> -o, --output <newick output> ~; $usage .= "\n"; my ($input,$outfile); GetOptions( "input=s" => \$input, "output=s" => \$outfile ); die $usage if ( !$input || !$outfile); my $treefile = $input; # replace negative values by 0 open(T,$treefile); open(T2,">$treefile.2"); while(<T>) { my $line = $_; $line =~s/\-\d+\.*\d*\,/0,/g; $line =~s/\-\d+\.*\d*\)/0\)/g; print T2 $line; } close(T); close(T2); my $rooting_command = $ROOTING_EXE . " -input $treefile.2 -output $treefile.all -midpoint $treefile.midpoint >>$treefile.rooting.log 2>&1"; system($rooting_command); unlink("$treefile.all"); unlink("$treefile.2"); rename("$treefile.midpoint",$outfile);