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Writing a Perl Script that processes multiple files

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Top Forums Shell Programming and Scripting Writing a Perl Script that processes multiple files
# 8  
Old 10-05-2011
Just like that other variable you declared there, you have to declare a 'my $N' and 'my $filename' because you have -w forced on.

---------- Post updated at 12:18 PM ---------- Previous update was at 12:15 PM ----------

That 'd' you deleted meant something:
Code:
$filename=sprintf("/cchome/perm/pedigree/250.1chr%.ped", $N);

Code:
$filename=sprintf("/cchome/perm/pedigree/250.1chr%d.ped", $N);

'%d' means 'substitute integer'. '%.p' means 'print memory pointer', I think.
Last edited by Corona688; 10-05-2011 at 03:26 PM..
This User Gave Thanks to Corona688 For This Post:
evelibertine
# 9  
Old 10-05-2011
Thanks, that partially solved the problem. So I modified my further and now it looks like this:


Code:
#!/usr/local/bin/perl  -w
use Carp;
my @file;


for($N=1; $N<=22; $N++)
{
        $filename=sprintf("250.1chr%d.ped", $N);
        if(!open(FILE, "<${filename}"))
        {
                print STDERR "Couldn't open ${filename}\n";
        }
    else
    {
    my $pheno_tmp = "";
        $pheno_tmp = $filename;

        if ($pheno_tmp =~ /(.+)chr/)
        {
                $pheno_tmp = $1;
        }
    else
    {
                $pheno_tmp = "Undef";
        }
    open (IN,"/cchome/perm/pedigree/output/$filename")   ||
die "cannot open input
file $filename";
        while (<IN>)
        {
    if ($_ =~ /Testing marker:/){chomp($_); my @marker = split(/\s+/,$_); my $marker = $marker[2]; print OUT $pheno_tmp, "\t", $marker,"\t";}   $
        if ($_ =~ /probands/){chomp($_); my @pvalue = split(/\s+/,$_);
        my $Rsq = $pvalue[5]; my $pvalue = $pvalue[7]; print OUT "$Rsq\t$pvalue";print OUT "\n";}      #change the keywords;
        }
    close (IN);

}
close(FILE);
}
close (OUT);

Now I'm getting a diff error message. It says:

Code:
print() on unopened filehandle OUT at getout.pl line 33, <IN> line 120086.
print() on unopened filehandle OUT at getout.pl line 33, <IN> line 120086.
print() on unopened filehandle OUT at getout.pl line 31, <IN> line 120088.
print() on unopened filehandle OUT at getout.pl line 33, <IN> line 120092.
print() on unopened filehandle OUT at getout.pl line 33, <IN> line 120092.
print() on unopened filehandle OUT at getout.pl line 31, <IN> line 120094.
print() on unopened filehandle OUT at getout.pl line 33, <IN> line 120098.
print() on unopened filehandle OUT at getout.pl line 33, <IN> line 120098.
print() on unopened filehandle OUT at getout.pl line 31, <IN> line 120100.
print() on unopened filehandle OUT at getout.pl line 33, <IN> line 120104.
print() on unopened filehandle OUT at getout.pl line 33, <IN> line 120104.

Moderator's Comments:
Mod Comment
Please use code tags when posting data and code samples!


---------- Post updated at 01:34 PM ---------- Previous update was at 01:27 PM ----------

Actually I solved the problem I think. I needed to open filehandle OUT. Thank you so much Smilie
Last edited by vgersh99; 10-05-2011 at 03:34 PM.. Reason: once again - please use code tags!
# 10  
Old 10-05-2011
You're not closing FILE anywhere. You should close FILE if you succeed in opening it. Otherwise you're opening 22 separate files and leaving them open.

In fact, why not use FILE in the first place instead of reopening it in IN ?
# 11  
Old 10-05-2011
Quote:
Originally Posted by Corona688
I keep forgetting perl doesn't have continue. That's annoying, it has everything else you could think of...
Perl has "next" and "last" instead:

Code:
$
$
$ # "next" skips current iteration and goes on to the next iteration
$
$ perl -le 'for $i (1..10)
           {
             next if $i%4 == 0;
             print $i
           }'
1
2
3
5
6
7
9
10
$
$
$ # "last" skips current iteration and exits the loop altogether
$
$ perl -le 'for $i (1..10)
           {
             last if $i%4 == 0;
             print $i
           }'
1
2
3
$
$
$

tyler_durden
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