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  • BioPerl Issues

    I am having issues with a BioPerl script. I have a blastxml file from a blastx blast and the original multifasta file containing the original nucleotides sequences.

    I want to take the blast result (ie. the blast description) and annotated my multifasta file.

    I have written 2 while loops that extract the blast descriptions as well as the nucleotide sequence from the multifasta file.

    My problem is that I cannot incorporate one of the while loops into the other without loosing the loop property of one of the loops.

    See script below:


    use warnings;
    use strict;
    use Bio::SearchIO;
    use Bio::SeqIO;


    my $search_in = Bio::SearchIO->new(-format => 'blastxml', -file => "$ARGV[0]");
    while (my $result = $search_in->next_result) {
    while (my $hit = $result->next_hit) {
    while (my $hsp = $hit->next_hsp) {
    my $qd = $hit->description;
    print $qd, "\n";
    }
    }
    }

    my $seqio = Bio::SeqIO->new(-format => 'fasta', -file => "$ARGV[1]");
    while (my $seqobj = $seqio->next_seq) {
    my $nuc = $seqobj->seq();
    print $nuc, "\n";
    }

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