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  • Bioperl 解析blast的输出结果

    用bioperl 解析blast的默认输出结果, 整理成-m8格式的输出

    #!/usr/bin/perl
    
    use Bio::SearchIO;
    my ($blast) = @ARGV;
    my $searchio = new Bio::SearchIO(-format => "blast",
                                     -file   => "test.bls");
    
    while (my $result = $searchio->next_result) {
        while (my $hit = $result->next_hit) {
            while (my $hsp = $hit->next_hsp) {
                my $query_name   = $result->query_name;
                my $query_length = $result->query_length;
                my $align        = $hsp->homology_string;
                $align           =~ s/ /0/g;
                my $hit_name     = $hit->name;
                my $identity     = sprintf "%0.2f", $hsp->frac_identical * 100;
                my $mismatch     =()= $hsp->seq_inds('hit','nomatch');
                my $gaps         = $hsp->gaps;
                my $align_length = $hsp->hsp_length;
                my $query_start  = $hsp->start('query');
                my $query_end    = $hsp->end('query');
                my $hit_start    = $hsp->start('hit');
                my $hit_end      = $hsp->end('hit');
                my $evalue       = $hsp->evalue;
                my $bit_score    = $hsp->bits;
                print qq{$query_name	$hit_name	$identity	$align_length	$mismatch	$gaps	$query_start	$query_end	$hit_start	$hit_end	$evalue	$bit_scoren};
            }
        }
    }
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  • 原文地址:https://www.cnblogs.com/xudongliang/p/5120762.html
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