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  • Shaq
    Junior Member
    • Jun 2013
    • 5

    #1

    Bioperl MSG: seq doesn't validate fetch genbank from NCBI using GI

    I am trying to fetch genebank features, this code works for some GenbankIDs but not for this one as an example.
    use strict;
    use warnings;
    use Bio::SeqIO;
    use Bio:B::EUtilities;
    my $gi="385220095";
    my $factoryID = Bio:B::EUtilities->new(-eutil => 'efetch',
    -db =>'protein',
    -rettype=> 'gbwithparts',
    -email=> '[email protected]',
    -id=>$gi) ;
    my $gbfile="$gi.gbk";
    $factoryID->get_Response(-file =>$gbfile);
    my $seqio_object = Bio::SeqIO->new(-file =>"$gbfile",'protein');
    while ( my $seq_object=$seqio_object->next_seq){
    for my $feat_object ($seq_object->get_SeqFeatures) {
    my $sequence_string = $feat_object->spliced_seq->seq;
    }
    }
  • kmcarr
    Senior Member
    • May 2008
    • 1181

    #2
    If you really want someone to offer help you need to provide more information:

    - What do you expect the code to do if it works?
    - What is the code doing that your don't expect?
    - Are there any error messages output?
    - What have you already tried yourself to resolve the problem?

    P.S. When posting code snippets to this forum please enclose the code in 'CODE' tags and properly format it (e.g. indentation) so it is easier to read and understand.

    Code:
    #!/usr/bin/perl
    
    use strict;
    use warnings;
    use Bio::SeqIO;
    use Bio::DB::EUtilities;
    
    my $gi="385220095";
    my $factoryID = Bio::DB::EUtilities->new(-eutil => 'efetch',
    					-db =>'protein',
    					-rettype=> 'gbwithparts',
    					-email=> '[email protected]',
    					-id=>$gi);
    
    my $gbfile="$gi.gbk";
    $factoryID->get_Response(-file =>$gbfile);
    
    my $seqio_object = Bio::SeqIO->new(-file =>"$gbfile",'protein');
    
    while ( my $seq_object=$seqio_object->next_seq)	{
        for my $feat_object ($seq_object->get_SeqFeatures) {
            my $sequence_string = $feat_object->spliced_seq->seq;
        }
    }

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