Rob Dixon wrote:
On 21/10/2011 00:32, nac wrote:
I have corrected myself a bit, I think the script is now giving me what I
want, having said that, I guess it is not the best way ( even if there is
more than one way), again any pointer are welcome.
many thanks
Nat
#!/usr/bin/perl
use strict;
use warnings;
my @seq;
@seq=qw{^TGGCAGTGGAGG ^TGTCTGGCAGTG ^TG....GCAGTG TCTGTCTG TCTGGCAG
GCAGTGGA TGTCTGGC ^TGTCTGGC ^..TCTGGCAGTG ^TGTCTGGCAGTG ^TGCATGGC};
open (IN,"</Users/nac/Desktop/example.fastq") or die
"can't open in:$!";
open
(OUT,">>//Users/nac/Desktop/example.fastq\_class_COUNTED2.txt")
or die "can't open out: $!";
It is better to use lexical filehandles, and the three-parameter form
of open, so:
open my $in, '<', '/Users/nac/Desktop/example.fastq' or die "can't open in: $!";
open my $out, '>>', '//Users/nac/Desktop/example.fastq\_class_COUNTED2.txt' or die
"can't open out: $!";
(Is the double-slash in the output filename correct?)
my %final_hash;
while (<IN>) {
if (/^A|T|G|C/){
This will search for A at the start of the string, or T, G, or C
anywhere in the string, which is presumably not what you want. Also you
can save an indentation level using next:
next unless /^(?:A|T|G|C)/;
Probably better as:
next unless /^[ATGC]/;
John
--
Any intelligent fool can make things bigger and
more complex... It takes a touch of genius -
and a lot of courage to move in the opposite
direction. -- Albert Einstein
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