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# -*-Perl-*- mode
use strict;
BEGIN {
# to handle systems with no installed Test module
# we include the t dir (where a copy of Test.pm is located)
# as a fallback
eval { require Test; };
if( $@ ) {
use lib 't';
}
use Test;
plan tests => 11;
}
use Bio::Tools::BPlite::Iteration;
use Bio::Tools::BPpsilite;
use Bio::Root::IO;
my $report = Bio::Tools::BPpsilite->new(-file=>Bio::Root::IO->catfile("t","data", "psiblastreport.out"));
ok $report;
ok $report->query =~ /DICDI/;# " query not found";
ok $report->database =~ /swissprot/i;# " database name not found";
my $total_iterations = $report->number_of_iterations;
ok $total_iterations, 2, " wrong total iteration number";
my $last_iteration = $report->round($total_iterations);
my $oldhitarray_ref = $last_iteration->oldhits;
# Process initial newly identified hit only
my ($sbjct, $id, $new_hsp, @is_old);
HIT: while($sbjct = $last_iteration->nextSbjct) {
$id = $sbjct->name;
@is_old = grep /\Q${id}\E/, @$oldhitarray_ref;
next HIT if (@is_old);
$new_hsp = $sbjct->nextHSP;
ok $new_hsp->score, 1097, " HSP score not found";
last HIT;
}
$report->close();
close FH;
# Verify parsing of PHI-PSI Blast reports
open FH, Bio::Root::IO->catfile("t","data","phipsi.out");
my $report2 = Bio::Tools::BPpsilite->new(-fh=>\*FH);
ok $report2;
ok $report2->pattern, "P-E-E-Q", " wrong phi pattern";
ok $report2->query_pattern_location->[1], 120, " wrong phi pattern location";
$total_iterations = $report2->number_of_iterations;
ok $total_iterations, 2, " wrong total iteration number in phiblast report";
my $last_iteration2 = $report2->round($total_iterations);
my $sbjct2 = $last_iteration2->nextSbjct;
ok $last_iteration2->newhits->[1] =~ /ARATH/;# " Hit not found in phiblast report";
my $hsp2 = $sbjct2->nextHSP;
ok $hsp2->hit->end, 343, " HSP start not found in phiblast report";
$report2->close();
close FH;
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