Hi Perlmonks.

How to get rid of extra spaces before the input separator \r\n ?
I have a flat file input separated by \r\n.,
Sample input : 
FEATURE              /group=" "
                 /translation="MMSKLGVLLT ICLLLFPLTA VQLDGDQPAD LPALRT
+QDIA
             TDHSPWFDPV KRCCSRYCYI CIPCCPN"
                     /disulfide="9,19"
                     /disulfide="13,24"
                     /hydroxylation="10"
                     /hydroxylation="11"
                     /post_trans_mod="

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For a few input lines, there are extra spaces before the \r\n, for eg : 
Input:  
                     /disulfide="13,24"\r\n
                     /hydroxylation="10"   \r\n 
                     /hydroxylation="11"\r\n
Output:
Disulfide       "13,24"
Hydroxylation   "10"   Hydroxylation    "11" 

Desired output:
Disulfide       "13,24"
Hydroxylation   "10"   
Hydroxylation    "11"

[download]
This cause trouble in my program even though I have check for extra spaces in my regex. This is part of my working program : 
#!/usr/bin/perl -w
use strict;

#initialize all the variable, initialize flags to 0 and line to ''
my $last;
my $file1="$ARGV[0]";
my $result=">".$ARGV[1];   
my $flag=0;
my $templine='';

open(INFO1,$file1) or die "Can't open $file1.\n";   
open(OUT,$result) or die "Can't open $result.\n";  

foreach(<INFO1>)
{
     if(/\s*\t*\s*\/(.*)=(.*)\s*\r/){
        my $feature=$1;
        my $value=$2;
        if(($value !~ /" "/) && ($value !~ /""/)){
            print OUT ucfirst($feature),"\t$value";
            $last=chop($value);
            if($last eq "\""){ #if last element="
                print OUT "\n";
                $flag=0; }
            else {
                $flag=1; }
           }
        }      
    elsif(/\s*(.*)\s*\r/ && $flag==1){
        $templine=$1;
        print OUT " $1";
        $last=chop($templine);
        if($last eq '"'){
            print OUT "\n";
            $flag=0;
        }
    }                   
}
close(INFO1) or die "Can't close $file1.\n";  
close(OUT) or die "Can't open $result.\n";

[download]
I use flag in case the item consists of more than one line. The entry is always quoted, so I use the " to check whether it is already the end of the item.
What should I do since it's not possible for me to check the input files and remove the extra spaces.

Thank you in advanced.
Regards

Agustina

In reply to extra spaces before \r\n by agustina_s

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