I have a file where the rows correspond to individuals and the columns are about 106 variables. Each variable is coded as either ACGT, and "missing" is coded as blank. This is a tab delimited file. I'm trying to replace all blanks (" ") with 0. The simple script I have is only replacing some of the blanks. Please help me figure out what's wrong with the script, so that every blank could be replaced by zero. Thanks!!!!

#!/usr/local/bin/perl
print "What file would you like to edit?";
$filename= <STDIN>;
open (TEXT, "$filename") || die "Can't open";
open (OUT, ">gd_53d.out" || die "Can't Open");
$var = " ";
while ($var ne "")
{
$var = <TEXT>;
if ($var eq "\t\t")
{
print OUT "\t\t";
next;
}
$var =~s/\t\t/\t0\t/gi;
print OUT $var;
}
close TEXT;
close OUT;
exit;

You can't use sed?

doesn't work.

example format of file:

id a1 a2
1 A B
2 A B
3
4 A B


Even the following perl code only replaces some of the blanks with 0.

#!/usr/local/bin/perl
open (TEXT, "gd_53.txt" || die "Can't open");
open (OUT, ">gd_53b.out" || die "Can't Open");
undef($/);
$var = <TEXT>;
$var =~ s/\t\t/\t0\t/g;
print OUT $var;
exit;

thanks!

Ae you sure the delimiter is tabs? Try \s+ instead of \t:

/\s+/[-0-]/g

the [- -] is just visual stuff to help you see what is happening, that can be removed after you get the substitution working properly.