Re: need help for Getopt::Long; --resolved

[Shiping Wang]

At 10:46 AM 3/25/2005 -0600, Shiping Wang wrote:

Hi, I have problem to match array defined in Getopt::Long and transfer to new file:
If I do:
try.pl --InputData sample.txt --Trait=_BMI --covars=age, _DBP, _SBP --Race=Others
with this file:
GFAMID GDADID GMOMID ID SEX HYT3 _SBP _DBP _BMI RACE AGE _HTMED antiht

How can I get it to new file like this:

A       HYT3
C       _SBP
C       _DBP
T       _BMI
S       RACE
C       AGE
S       _HTMED
S       antiht

Thanks!!!

SW

###############################################################################

#!/usr/local/bin/perl
# try.pl
use warnings;
use strict;
use Getopt::Long;
my $inputData =' ';
my $trait= ' ';
my $race;
my @covars;
my $result = GetOptions("InputData=s" => \$inputData,
"Trait=s" => \$trait,
"Race=s" => \$race,

"Covars=s" => [EMAIL PROTECTED]
);
my @covarlist = split(/,/, @covars);
if(!$inputData){
exit();
}
#die "you must specify all parameters\n\t--Trait --Race --Covars\n" unless(define $trait || define $race || define @covars);
my $oriname = (split/\./, $inputData)[0];
my $outname;
if ($race){
$outname = "$oriname\_$race";
} else{
$outname = "$oriname";
}

open (outDat, ">$outname.dat") or die $!;
open (inPed, "$inputData") or die $!;

my $header = <inPed>;
chomp $header;
my @headline = split/\t/, $header;

        my @ped_n_trait = @headline[0, 3, 1, 2, 4..12];
        my %vartype;

### not working

        foreach my $i (@ped_n_trait[5..12]){
                if ($i eq 'HYT3'){
                        $vartype{$i} = 'A';
                }elsif ($i eq "$trait"){
                        $vartype{$i} = 'T';
                }else{
                        $vartype{$i} = 'S';
                        for(@covarlist){
                                if($_ eq "$i"){
                                        $vartype{$_} = 'C';
                                }
                        }

                }
        }

### working, maybe better way to it ###

        foreach my $i (@ped_n_trait[5..12]){
                if ($i eq 'HYT3'){
                        $vartype{$i} = 'A';
                }elsif ($i eq "$trait"){
                        $vartype{$i} = 'T';
                }else{

                        for(@covarlist){
                          if($_ eq "$i"){
                                $vartype{$i} = 'C';
                        }
                        $vartype{$i} = 'S' if (!$vartype{$i});
                }

                }
        }

        for (@ped_n_trait[5..12]){
                print outDat "$vartype{$_}\t$_\n";
        }

close outDat;

close inPed;

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