Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • BioPerl installation and execution problem

    I have installed activeperl in windows xp.
    through Perl Package Manager i have installed BioPerl repositories.
    but while trying to execute BioPerl program..
    #!/usr/bin/env perl
    use Bio::Seq;
    use Bio::SeqIO;

    # create a sequence object of some DNA
    my $seq = Bio::Seq->new(-id => 'testseq', -seq => 'CATGTAGATAG');

    # print out some details about it
    print "seq is ", $seq->length, " bases long\n";
    print "revcom seq is ", $seq->revcom->seq, "\n";

    # write it to a file in Fasta format
    my $out = Bio::SeqIO->new(-file => '>testseq.fsa', -format => 'Fasta');
    $out->write_seq($seq);

    the following error is coming

    Cant locate Bio/Seq.pm in @INC <INC contains : C:/Perl/site/lib C:/Perl/lib.> at C:\Perl\bin\Sequence.pl line1.
    BEGIN failed--compilation aborted at C:\Perl\bin\Sequence.pl line1.

    what is the problem here??

    How to identify whether BioPerl is installed or not???

    Please guide me....

    thanks & Regards

  • #2
    That error you see "Can't locate Bio/Seq.pm ..." means that Perl cannot find BioPerl in the standard places that libraries are installed (referred to as PERL5LIB or @INC). You might want to review the install process to ensure that it was successful and try to find out if it was installed somewhere other than what is listed in that error message. If you are using a package manager then it will probably install in a standard location, so the installation likely did not succeed. I should warn that I have no experience with Windows and PPM, but what you are seeing is a standard complaint from Perl. If you can't find a solution, you could try sending your message to the BioPerl listserv, as there are sure to be people there with experience installing on Windows.

    Comment

    Latest Articles

    Collapse

    • seqadmin
      Exploring the Dynamics of the Tumor Microenvironment
      by seqadmin




      The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...
      07-08-2024, 03:19 PM
    • seqadmin
      Exploring Human Diversity Through Large-Scale Omics
      by seqadmin


      In 2003, researchers from the Human Genome Project (HGP) announced the most comprehensive genome to date1. Although the genome wasn’t fully completed until nearly 20 years later2, numerous large-scale projects, such as the International HapMap Project and 1000 Genomes Project, continued the HGP's work, capturing extensive variation and genomic diversity within humans. Recently, newer initiatives have significantly increased in scale and expanded beyond genomics, offering a more detailed...
      06-25-2024, 06:43 AM

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by seqadmin, 07-16-2024, 05:49 AM
    0 responses
    22 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 07-15-2024, 06:53 AM
    0 responses
    30 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 07-10-2024, 07:30 AM
    0 responses
    40 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 07-03-2024, 09:45 AM
    0 responses
    205 views
    0 likes
    Last Post seqadmin  
    Working...
    X