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t/SearchIO/blastxml.t  view on Meta::CPAN

    is($hsp->pvalue, undef);
    float_is($hsp->evalue, 1.46134e-90);
    is($hsp->score, 838);
    is($hsp->bits,327.405);
    is($hsp->query->start, 498);
    is($hsp->query->end,815);
    is($hsp->hit->start, 3);
    is($hsp->hit->end, 310);
    is($hsp->query->frame,0);
    is($hsp->hit->frame,0);
    is(sprintf("%.2f", $hsp->percent_identity), 37.73);
    is(sprintf("%.4f", $hsp->frac_identical('hit')), 0.3994);
    is(sprintf("%.4f", $hsp->frac_identical('query')), 0.3868);
    is(sprintf("%.4f",$hsp->query->frac_identical), 0.3868);

    is(sprintf("%.4f",$hsp->frac_conserved('total')),0.5245);
    is(sprintf("%.4f",$hsp->frac_conserved('hit')),0.5552);
    is(sprintf("%.4f",$hsp->frac_conserved('query')),0.5377);
    # gaps should match calculated sequence indices for gaps and vice versa
    is($hsp->gaps('total'), $hsp->seq_inds('hit', 'gaps') + $hsp->seq_inds('query', 'gaps'));
    is($hsp->gaps('hit'), $hsp->seq_inds('hit', 'gaps'));

t/SearchIO/blastxml.t  view on Meta::CPAN

                        is($hsp->query->end, 155);
                        is($hsp->hit->start, 475);
                        is($hsp->hit->end, 617);
                        is($hsp->length('total'), 153);
                        is($hsp->start('hit'), $hsp->hit->start);
                        is($hsp->end('query'), $hsp->query->end);
                        is($hsp->strand('sbjct'), $hsp->subject->strand);# alias for hit
                        float_is($hsp->evalue, 0.000286309);
                        is($hsp->score, 86);
                        is($hsp->bits, 37.7354);
                        is(sprintf("%.1f",$hsp->percent_identity), 20.9);
                        is(sprintf("%.4f",$hsp->frac_identical('query')), 0.2105);
                        is(sprintf("%.3f",$hsp->frac_identical('hit')), 0.224);
                        is($hsp->gaps('total'), 11);
                        $hsps_left--;
                    }
                    is($hsps_left, 0);
                }
                last if( $hit_count++ > @valid_hit_data );
            }
        }

t/SearchIO/blastxml.t  view on Meta::CPAN

                        is($hsp->query->end, 181);
                        is($hsp->hit->start, 304);
                        is($hsp->hit->end, 432);
                        is($hsp->length('total'), 129);
                        is($hsp->start('hit'), $hsp->hit->start);
                        is($hsp->end('query'), $hsp->query->end);
                        is($hsp->strand('sbjct'), $hsp->subject->strand);# alias for hit
                        float_is($hsp->evalue, 0.0242028);
                        is($hsp->score, 73);
                        is($hsp->bits, 32.7278);
                        is(sprintf("%.1f",$hsp->percent_identity), '24.0');
                        is(sprintf("%.4f",$hsp->frac_identical('query')), '0.2605');
                        is(sprintf("%.3f",$hsp->frac_identical('hit')), '0.240');
                        is($hsp->gaps, 10);
                        $hsps_left--;
                    }
                    is($hsps_left, 0);
                }
                last if( $hit_count++ > @valid_hit_data );
            }
        }