Pattern location, Please help me

[happy2000]

Hello all,
The following perl script looks for the pattern in each line (fasta file). the problem that when they found a pattern (an occurrence) in a sequence, it goes directly to the next line without continuing to check if there are other pattern (an occurrence) in the same line .Please, can someone help me fix this script so that when it finds a pattern in a line going to the next letter and not to the next line. Essentially he can find many patterns in the same line.

#!/usr/bin/perl

use strict;
use warnings;

use Bio::SeqIO;

my $file = 'file.txt';
my $in = Bio::SeqIO->new(-file => $file, '-format' => 'fasta');

while (my $seq = $in->next_seq()) {
	if ($seq->seq =~ m/(ATCGA)/) {
		print "ATCGA commence à la position $-[1]\n";
		print "se termine juste avant la position $+[1]\n";
	}
}

please help me
thanks

[maasha]

What is your goal? Finding patterns or learning Perl?

If finding patterns - then use an appropriate tool - like scan_for_matches. If learning Perl - well, TMTOWTDI. How about index instead of regex? perldoc -f index.

Also, I should guess that Bioperl is equipped with pattern matching algorithms other than regex.


Cheers,


Martin

[happy2000]

Hello,
Thank you very much for your reply, my goal is Finding patterns and determination of position of patterns and id for the corresponding gene upstream sequence. Is there a tool that does this?
cordially