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9
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1 #!/usr/bin/perl
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2
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3 use strict;
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4 use Getopt::Long;
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5 use Bio::SeqIO;
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6 use Cwd ;
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7 use FindBin qw ( $Bin $Script );
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8
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9 my $CURRENT_DIR = $Bin;
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10
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11 my $ROOTING_EXE = "java -jar ". $CURRENT_DIR . "/Rootings_54.jar";
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12
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13 my $usage = qq~Usage:$0 <args> [<opts>]
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14 where <args> are:
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15 -i, --input <newick input>
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16 -o, --output <newick output>
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17 ~;
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18 $usage .= "\n";
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19
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20 my ($input,$outfile);
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21
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22
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23 GetOptions(
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24 "input=s" => \$input,
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25 "output=s" => \$outfile
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26 );
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27
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28
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29 die $usage
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30 if ( !$input || !$outfile);
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31
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32 my $treefile = $input;
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33
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34
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35 # replace negative values by 0
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36 open(T,$treefile);
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37 open(T2,">$treefile.2");
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38 while(<T>)
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39 {
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40 my $line = $_;
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41 $line =~s/\-\d+\.*\d*\,/0,/g;
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42 $line =~s/\-\d+\.*\d*\)/0\)/g;
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43 print T2 $line;
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44 }
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45 close(T);
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46 close(T2);
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47
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48 my $rooting_command = $ROOTING_EXE . " -input $treefile.2 -output $treefile.all -midpoint $treefile.midpoint >>$treefile.rooting.log 2>&1";
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49 system($rooting_command);
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50
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51 unlink("$treefile.all");
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52 unlink("$treefile.2");
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53 rename("$treefile.midpoint",$outfile);
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54
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55
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56
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57
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58
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