chopping new line while counting length

sugar has asked for the wisdom of the Perl Monks concerning the following question:

Dear monks, This query is also with reference to the post "printing the length of string variables". the program works for single line string, but not for multiple lines. However, there is a chomp for the strings which doesnt seem to work i think. Please guide.

printing the length of string variables

use strict;
use warnings;

my ($head);

while(<DATA>){
     my ($x, $str, $len, $s);
     $s = $_;

     if($s=~m/^>/){
        chomp($s);
        ($head)=(split(/ /,$s))[0];
     }
     else{ 
        chomp($s);
        $len=length($s);
     }
     print "$head length=$len\n$s\n" if($s !~m/^>/);
}

__DATA__
>IDnumber1 length=350
AGCTG
AAGTCGCT
>IDnumber2 length=350
AGAACGT
ACC
>IDnumber3 length=350
AGC
ACTTCGCTAACT


Expected output:
-----------------
>IDnumber1 length=13
AGCTGAAGTCGCT
>IDnumber2 length=10
AGAACGTACC
>IDnumber3 length=15
AGCACTTCGCTAACT
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Comment on chopping new line while counting length Download Code

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Re: chopping new line while counting length by ikegami (Patriarch) on Jan 15, 2009 at 10:00 UTC
[ Link to other thread for reference: printing the length of string variables ] The following uses a single-line lookahead, and it happens to only keep one sequence in memory at a time. `use strict; use warnings; my $fh = \*DATA; my $line = <$fh>; while (defined($line)) { my $head = $line; $line = <$fh>; die("Premature EOF\n") if !defined($line); chomp( my $seq = $line ); for (;;) { $line = <$fh>; last if !defined($line) \|\| $line =~ /^>/; chomp( $seq .= $line ); } my $len = length($seq); $head =~ s/(length=)\d+/$1$len/; print("$head$seq\n"); } __DATA__ >IDnumber1 length=350 AGCTG AAGTCGCT >IDnumber2 length=350 AGAACGT ACC >IDnumber3 length=350 AGC ACTTCGCTAACT` [download]	[reply] [d/l]
Re: chopping new line while counting length by johngg (Canon) on Jan 15, 2009 at 10:21 UTC
A few points about your code spring to mind. Inside the `while` loop you have `if` and `else` code branches. The first thing you do in each is `chomp` the string. It would make more sense to do the `chomp` before the `if`. You assign `$_` to `$s`. If you are doing this for readability then choose a variable name that is more meaningful, otherwise just operate on `$_`. You are having difficulty with multiple-line data because you operate on each data line individually rather than accumulating the data lines then processing them all once you reach the next header. What do you do to process the last data item when you reach end of file? I think this code will do what you want. I have moved the process of getting the data length and printing the item into a subroutine. `use strict; use warnings; my $header = q{}; my $dataAccumulator; while( <DATA> ) { chomp; if( m{^>} ) { printDataItem() if $header; ( $header ) = m{^.(\S+)}; $dataAccumulator = q{}; } else { $dataAccumulator .= $_; } } printDataItem(); sub printDataItem { print qq{>$header length=}, length $dataAccumulator, qq{\n$dataAccumulator\n}; } __DATA__ >IDnumber1 length=350 AGCTG AAGTCGCT >IDnumber2 length=350 AGAACGT ACC >IDnumber3 length=350 AGC ACTTCGCTAACT` [download] The output. `>IDnumber1 length=13 AGCTGAAGTCGCT >IDnumber2 length=10 AGAACGTACC >IDnumber3 length=15 AGCACTTCGCTAACT` [download] I hope this is of use. Cheers, JohnGG Update: Corrected typo.	[reply] [d/l] [select]
Re: chopping new line while counting length by andye (Curate) on Jan 15, 2009 at 11:51 UTC
An alternative way to do it: `#!/usr/bin/perl -w undef $/; use strict; $_ = <DATA>; while (m/\G(>IDnumber\d+ length=)350\n([^\n]+)\n([^\n]+)\n/g) { print $1.length($2.$3)."\n$2$3\n"; } __DATA__ >IDnumber1 length=350 AGCTG AAGTCGCT >IDnumber2 length=350 AGAACGT ACC >IDnumber3 length=350 AGC ACTTCGCTAACT` [download] Hope that's helpful to you. Best wishes, andye	[reply] [d/l]