Re: Getting Lines 2,3, and 4 from FASTQ file's Chunk

Another simple solution:

use strict;
use warnings;


while(<DATA>)
{
    chomp;
    my $line = $_;

   # skip the first line of every chunk
   if ($line =~/^@/)
   {
   }

   # print the remaining lines
   else
   {
        print "$line\n";
   }
}


__DATA__
@SRR016086.1 308GJAAXX:2:1:911:957 length=36
CCCCCCCCCCACCCCCCCACACCACAAACACACCAC
+SRR016086.1 308GJAAXX:2:1:911:957 length=36
(IIIIIIII:&H68;I-3%/)*-/4$$')(0&$&,$
@SRR016086.2 308GJAAXX:2:1:916:735 length=36
AGATCAGTTTTGCACTCCACTTAAGTTTGTTCATAT
+SRR016086.2 308GJAAXX:2:1:916:735 length=36
I*IIIIIIIIIII%%CI()I2E6.I5;>+"=C+#%I
@SRR016086.3 308GJAAXX:2:1:908:956 length=36
CCCCCCCCCAACACAAAAACAAAATCCAAAACAATA
+SRR016086.3 308GJAAXX:2:1:908:956 length=36
II@III50I*9I+<00%.<9/,%-"$*2('&"&)""
[download]

Comment on Re: Getting Lines 2,3, and 4 from FASTQ file's Chunk Download Code

Replies are listed 'Best First'.
Re^2: Getting Lines 2,3, and 4 from FASTQ file's Chunk by johngg (Canon) on Apr 16, 2010 at 20:15 UTC
It is a simple solution but it would be even simpler if you avoided the un-necessary chomp and assignment to `$line`, and used an `unless` statement modifier. I don't know if it is safe to assume that every record begins with an "@" symbol. `while ( <DATA> ) { print unless m{^\@}; }` [download] I hope this is of interest. Cheers, JohnGG	[reply] [d/l] [select]
Re^2: Getting Lines 2,3, and 4 from FASTQ file's Chunk by Anonymous Monk on Mar 22, 2011 at 15:20 UTC
Skipping lines based on '@' at the start is dangerous as quality values (line 4) can be '@'!	[reply]