Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • Pattern location, Please help me

    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.
    Code:
    #!/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

  • #2
    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

    Comment


    • #3
      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

      Comment

      Latest Articles

      Collapse

      • seqadmin
        Genetic Variation in Immunogenetics and Antibody Diversity
        by seqadmin



        The field of immunogenetics explores how genetic variations influence immune responses and susceptibility to disease. In a recent SEQanswers webinar, Oscar Rodriguez, Ph.D., Postdoctoral Researcher at the University of Louisville, and Ruben Martínez Barricarte, Ph.D., Assistant Professor of Medicine at Vanderbilt University, shared recent advancements in immunogenetics. This article discusses their research on genetic variation in antibody loci, antibody production processes,...
        11-06-2024, 07:24 PM
      • seqadmin
        Choosing Between NGS and qPCR
        by seqadmin



        Next-generation sequencing (NGS) and quantitative polymerase chain reaction (qPCR) are essential techniques for investigating the genome, transcriptome, and epigenome. In many cases, choosing the appropriate technique is straightforward, but in others, it can be more challenging to determine the most effective option. A simple distinction is that smaller, more focused projects are typically better suited for qPCR, while larger, more complex datasets benefit from NGS. However,...
        10-18-2024, 07:11 AM

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by seqadmin, 11-01-2024, 06:09 AM
      0 responses
      29 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 10-30-2024, 05:31 AM
      0 responses
      21 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 10-24-2024, 06:58 AM
      0 responses
      26 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 10-23-2024, 08:43 AM
      0 responses
      57 views
      0 likes
      Last Post seqadmin  
      Working...
      X