in reply to Re^2: seeking help for seek function
in thread seeking help for seek function

You use tell for SID834.56 when the file pointer is here: 
SID834.56    AGAAGTCGTACGATCA
[*]SID164.26    AGTCGATCATTATATATTCGCTAG

[download]
You want to use tell for SID834.56 when the file pointer is here: 
SID834.56    [*]AGAAGTCGTACGATCA
SID164.26    AGTCGATCATTATATATTCGCTAG

[download]
That's not easy to do, but it's easy and acceptable to use tell for SID834.56 when the file pointer is here: 
[*]SID834.56    AGAAGTCGTACGATCA
SID164.26    AGTCGATCATTATATATTCGCTAG

[download]

(i.e. before you read the line)

Replies are listed 'Best First'.
Re^4: seeking help for seek function
by pearly (Initiate) on Mar 25, 2010 at 09:57 UTC
    getting the correct position by using 
    my @indx;
my $pos = 0;

while(<FH1>){
    my ($id, $seq) = split /\t/;
    push(@indx, "$id\t$pos");
    $pos = tell FH1;
}

    [download]
    thanks for that !!! trying to read the correct line now...
[reply]
[d/l]
Re^4: seeking help for seek function
by Anonymous Monk on Mar 25, 2010 at 08:56 UTC
    i just noticed that. i want to use file pointer at the begining of everyline.but, when i use tell function, why does it point to the end of the line and not the begining?
[reply]
Re^4: seeking help for seek function
by pearly (Initiate) on Mar 25, 2010 at 09:01 UTC
    i just noticed that. i want to use file pointer at the begining of everyline.but, when i use tell function, why does it point to the end of the line and not the begining?
[reply]

      After you've read a line, the file pointer will naturally always be at the end of the line (= beginning of the next line). That is so because for every byte being read, the file pointer advances by one.

      Try this to get the correct positions: 

      my @indx;
my $pos = 0;

while(<FH1>){
    my ($id, $seq) = split /\t/;
    push(@indx, "$id\t$pos");
    $pos = tell FH1;
}

      [download]
[reply]
[d/l]

In Section Seekers of Perl Wisdom