[Bioperl-l] While running without stop

[debutant.bioperl]

hello, thank you very much Kevin for your reply. 
but it gives the same result, while  running without stop.

Kevin Brown-8 wrote:
> 
> This is a problem with accessing objects, IIRC.
> 
> Try doing something like:
> 
> my $in  = Bio::SeqIO->new(-file => $file , '-format' => 'fasta');
> while ( my $seq = $in->next_seq() )
> {
>     my $sequence = $seq->seq;
>     while ($sequence =~ m/(ATCGA)/){
> 	print "ATCGA commence à la position $-[1]\nse termine juste avant la
> position $+[1]\n";
> 	}
> }
> 
> Kevin Brown
> Center for Innovations in Medicine
> Biodesign Institute
> Arizona State University 
> 
>> -----Original Message-----
>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
>> bounces at lists.open-bio.org] On Behalf Of debutant.bioperl
>> Sent: Thursday, May 19, 2011 11:00 AM
>> To: Bioperl-l at lists.open-bio.org
>> Subject: [Bioperl-l] While running without stop
>> 
>> 
>> Hello all,
>> The following perl script looks for the pattern in each line (line of
>> the
>> fasta format that begins with">" : sequence).
>> 
>> .......................................................................
>> .....................................................................
>> #!/usr/bin/perl
>> use strict;
>> use warnings;
>> use Bio::SeqIO;
>> 
>> my $file = 'eee.txt';
>> my $in  = Bio::SeqIO->new(-file => $file , '-format' => 'fasta');
>> while ( my $seq = $in->next_seq() )
>> {
>>     while ($seq->seq =~ m/(ATCGA)/){
>> 	print "ATCGA commence à la position $-[1]\nse termine juste avant
>> la
>> position $+[1]\n";
>> 	}
>> }
>> .......................................................................
>> .....................................................................
>> 
>> the problem that the while of:
>> .......................................................................
>> ...........................
>> while ($seq->seq =~ m/(ATCGA)/){
>> 		print "ATCGA commence à la position $-[1]\nse termine juste
>> avant la
>> position $+[1]\n";
>> 	}
>> .......................................................................
>> ...........................
>> Runs continuously and always gives the same result.
>> 
>> ... ATCG commence Ó la position 172
>> se termine juste avant la position 176
>> ATCG commence Ó la position 172
>> se termine juste avant la position 176
>> ATCG commence Ó la position 172
>> se termine juste avant la position 176 ...
>> 
>> 
>> And if we use "if" instead of While he finds only the first pattern
>> (case),
>> otherwise, if more than one pattern in the same sequence, he finds only
>> the
>> first.
>> Please, have you any idea to fix this code so that:
>> While research patterns and ends.
>> Or
>> For If, when he finds a pattern he went to the next letter and not the
>> next
>> sequence and found many motifs per sequence.
>> Cordially
>> 
>> 
>> --
>> View this message in context: http://old.nabble.com/While-running-
>> without-stop-tp31658279p31658279.html
>> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
>> 
>> 
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> 
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