Mercurial > repos > dereeper > sniplay
diff 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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Rooting/Rooting.pl Fri Jul 10 04:39:30 2015 -0400 @@ -0,0 +1,59 @@ +#!/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); + + + + +