|
1
|
1 #!/usr/bin/perl
|
|
|
2
|
|
|
3 use strict;
|
|
|
4 use Switch;
|
|
|
5 use Getopt::Long;
|
|
|
6 use Bio::SeqIO;
|
|
|
7 use Cwd ;
|
|
|
8 use FindBin qw ( $Bin $Script );
|
|
|
9
|
|
|
10 my $CURRENT_DIR = $Bin;
|
|
|
11
|
|
|
12 my $ROOTING_EXE = "java -jar ". $CURRENT_DIR . "/Rootings_54.jar";
|
|
|
13
|
|
|
14 my $usage = qq~Usage:$0 <args> [<opts>]
|
|
|
15 where <args> are:
|
|
|
16 -i, --input <newick input>
|
|
|
17 -o, --output <newick output>
|
|
|
18 ~;
|
|
|
19 $usage .= "\n";
|
|
|
20
|
|
|
21 my ($input,$outfile);
|
|
|
22
|
|
|
23
|
|
|
24 GetOptions(
|
|
|
25 "input=s" => \$input,
|
|
|
26 "output=s" => \$outfile
|
|
|
27 );
|
|
|
28
|
|
|
29
|
|
|
30 die $usage
|
|
|
31 if ( !$input || !$outfile);
|
|
|
32
|
|
|
33 my $treefile = $input;
|
|
|
34
|
|
|
35
|
|
|
36 # replace negative values by 0
|
|
|
37 open(T,$treefile);
|
|
|
38 open(T2,">$treefile.2");
|
|
|
39 while(<T>)
|
|
|
40 {
|
|
|
41 my $line = $_;
|
|
|
42 $line =~s/\-\d+\.*\d*\,/0,/g;
|
|
|
43 $line =~s/\-\d+\.*\d*\)/0\)/g;
|
|
|
44 print T2 $line;
|
|
|
45 }
|
|
|
46 close(T);
|
|
|
47 close(T2);
|
|
|
48
|
|
|
49 my $rooting_command = $ROOTING_EXE . " -input $treefile.2 -output $treefile.all -midpoint $treefile.midpoint >>$treefile.rooting.log 2>&1";
|
|
|
50 system($rooting_command);
|
|
|
51
|
|
|
52 unlink("$treefile.all");
|
|
|
53 unlink("$treefile.2");
|
|
|
54 rename("$treefile.midpoint",$outfile);
|
|
|
55
|
|
|
56
|
|
|
57
|
|
|
58
|
|
|
59
|
