Hi,
I'm trying to get this program to work and it works up until the last two lines
(substitution) which gives a syntax error...any idea what might be the problem?
thanks,
kathryn
#!/usr/bin/perl -w
use warnings;
use Bio::Seq;
use Bio::SeqIO;
#initialize id and fasta files
my $codefile = $ARGV[0];
my $treefile = $ARGV[1];
#open alignment list and create a global hash of tree codes with species name
as
#open gi id file and assign file handle
open(ID,$codefile)|| die "can't open id file: $!\n";
#initialize hash
my(@ID);
my %id_global;
my $id;
while (<ID>){
#split on spaces
my @ID = split(/\s+/);
#print "ID->".$ID[0]."<-\n"."Code->".$ID[1]."<-\n";
#get rid of carriage returns
chomp;
#define id as the code number
my $id = $ID[1];
#print "ID->".$id."<-\n";
#create a global hash with code number as key and species name as value
$id_global{$id}= $ID[0];
#print $id."VALUE->".$id_global{$id}."<-\n";
}
#test that keys loaded to global hash with correct value
#foreach my $key (keys %id_global){
#print "KEY->".$key."<-->VALUE->".$id_global{$key}."<-\n";
#}
#open treefile and while through it, substituting species name value when key
found in file.
open (TREE,$treefile)|| die "can't open tree file: $\n";
while (<TREE>){
foreach my $code (keys %id_global){
#print "CODE->".$code."<-VALUE->".$id_global{$code}."\n";
$line = $_;
#if ($line =~ m/(.*)$code([\D])/) {print "MATCH"."
".$code."VALUE->".$id_global{$code}."<-\n";}
#else {print "NO MATCH"." ".$code."<-\n";} #works,matches all values w/right
val
$line=~ s/(.*)$code([/D])/$1$id_global{$code}$2/;
print $line;
}
}
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