mirror of
http://43.156.76.180:8026/YuuMJ/EukPhylo.git
synced 2025-12-28 03:40:25 +08:00
66 lines
1.6 KiB
Perl
66 lines
1.6 KiB
Perl
#!/usr/local/bin/perl
|
|
use strict;
|
|
|
|
###############################################################################################################
|
|
# Works together (or rather after) the script names2codeFasta.pl. Takes a tree created based on
|
|
# a fasta file with codes, and reverts the codes to the names. Required input is a code file which is created by
|
|
# names2codeFasta.pl
|
|
# ** very useful for working with all phyml and such, since these programs chop the name to 10 chars
|
|
###############################################################################################################
|
|
|
|
|
|
die "Usage: code2name.pl CODE_FILE TREE_FILE NEW_FILE NAME_LENGTH" if (scalar(@ARGV) < 3);
|
|
my $code2nameFile = $ARGV[0];
|
|
my $treeFile = $ARGV[1];
|
|
my $newFile = $ARGV[2];
|
|
my $nameLength = 30;
|
|
if (defined $ARGV[3]) {
|
|
$nameLength = $ARGV[3];
|
|
}
|
|
|
|
|
|
|
|
my %names2code;
|
|
my @fields;
|
|
|
|
|
|
open FH, "<$code2nameFile";
|
|
#my $line;
|
|
while (my $line=<FH>){
|
|
$line =~ /(.+)\t(\d+)/;
|
|
my $code = $2;
|
|
my $name = $1;
|
|
$name =~ s/[\[\]\,\:\;\(\)]/_/g; #remove characters that are newick format associated
|
|
if ($name =~ m/(.*\|.{$nameLength})/) {
|
|
$name = $1;
|
|
}
|
|
$names2code{$code}=$name;
|
|
print "$code $name\n";
|
|
}
|
|
|
|
close FH;
|
|
|
|
open TREE, "<$treeFile";
|
|
open NEWTREE, ">$newFile";
|
|
|
|
my $full_tree = "";
|
|
my $line2;
|
|
while ($line2 = <TREE>){ # this assumes there are bootstrap values on the input tree
|
|
chomp $line2;
|
|
$full_tree.=$line2;
|
|
|
|
}
|
|
|
|
@fields = split(/:/, $full_tree);
|
|
|
|
foreach my $field (@fields) {
|
|
if ($field =~ /[\,\(](\d+)$/) { # a leaf comes either after a "(" or a ","
|
|
$field =~ s/(\d+)$/$names2code{$1}/;
|
|
}
|
|
|
|
print NEWTREE "$field:";
|
|
|
|
}
|
|
|
|
print NEWTREE "\n";
|