t/SearchIO/blastxml.t

   1 # -*-Perl-*- Test Harness script for Bioperl
   2 # $Id: SearchIO.t 14995 2008-11-16 06:20:00Z cjfields $
   3
   4 use strict;
   5
   6 BEGIN {
   7         use lib '.';
   8     use Bio::Root::Test;
   9
  10     test_begin(-tests => 391,
  11                            -requires_module => 'XML::SAX');
  12
  13         use_ok('Bio::SearchIO');
  14 }
  15
  16 my ($searchio, $result,$iter,$hit,$hsp);
  17
  18 # XML encoding/decoding done within XML::SAX now, though some parsers
  19 # do not work properly (XML::SAX::PurePerl, XML::LibXML::SAX)
  20
  21 eval {
  22         # test with RPSBLAST data first
  23         # this needs to be eval'd b/c the XML::SAX parser object is
  24         # instantiated in the constructor
  25         $searchio = Bio::SearchIO->new('-tempfile' => 1,
  26                    '-format' => 'blastxml',
  27                    '-file'   => test_input_file('ecoli_domains.rps.xml'),
  28                    '-blasttype' => 'blast',
  29                    '-verbose' => -1);
  30         # PurePerl works with these BLAST reports, so removed verbose promotion
  31         $result = $searchio->next_result;
  32         die if !defined $result;
  33 };
  34
  35 SKIP: {
  36         # this should be fixed with newer installations of XML::SAX::Expat, but as we
  37         # don't require a certain version (multiple backends can be used) we catch
  38         # and skip if needed
  39         if ($@ && $@ =~ m{Handler could not resolve external entity}) {
  40                 skip("XML::SAX::Expat does not work with XML tests; skipping",297);
  41         } elsif ($@) {
  42                 skip("Problem with XML::SAX setup: $@. Check ParserDetails.ini; skipping XML tests",297);
  43         }
  44         is($searchio->result_count, 1);
  45
  46         # basic ResultI data
  47         isa_ok($result, 'Bio::Search::Result::ResultI');
  48         is($result->database_name, '/data_2/jason/db/cdd/cdd/Pfam', 'database_name()');
  49         is($result->query_name,'gi|1786182|gb|AAC73112.1|','query_name()');
  50         is($result->query_description, '(AE000111) thr operon leader peptide [Escherichia coli]');
  51         is($result->query_accession, 'AAC73112.1');
  52         is($result->query_gi, 1786182);
  53         is($result->query_length, 21);
  54         is($result->algorithm, 'BLASTP');
  55         is($result->algorithm_version, 'blastp 2.1.3 [Apr-1-2001]');
  56
  57         # check parameters
  58         is($result->available_parameters, 8);
  59         is($result->get_parameter('matrix'), 'BLOSUM62');
  60         float_is($result->get_parameter('expect'), '1e-05');
  61         is($result->get_parameter('include'), 0);
  62         is($result->get_parameter('match'), 0);
  63         is($result->get_parameter('mismatch'), 0);
  64         is($result->get_parameter('gapopen'), 11);
  65         is($result->get_parameter('gapext'), 1);
  66         is($result->get_parameter('filter'), 'F');
  67
  68         # check statistics
  69         is($result->available_statistics, 5);
  70         is($result->database_entries, 0);
  71         is($result->database_letters, 0);
  72         is($result->get_statistic('hsplength'), 0);
  73         float_is($result->get_statistic('effectivespace'), 4.16497e+11);
  74         is($result->get_statistic('lambda'), 0.267);
  75         is($result->get_statistic('kappa'), 0.041);
  76         is($result->get_statistic('entropy'), 0.14);
  77
  78         # this result actually has a hit
  79         $result = $searchio->next_result;
  80
  81         # does the parser catch everything in the next result?
  82         is($result->database_name, '/data_2/jason/db/cdd/cdd/Pfam', 'database_name()');
  83         is($result->query_name,'gi|1786183|gb|AAC73113.1|');
  84         is($result->query_description, '(AE000111) aspartokinase I, homoserine dehydrogenase I [Escherichia coli]');
  85         is($result->query_accession, 'AAC73113.1');
  86         is($result->query_gi, 1786183);
  87         is($result->query_length, 820);
  88         is($result->algorithm, 'BLASTP');
  89         is($result->algorithm_version, 'blastp 2.1.3 [Apr-1-2001]');
  90
  91         is($searchio->result_count, 2);
  92
  93         # check parameters
  94         is($result->available_parameters, 8);
  95         is($result->get_parameter('matrix'), 'BLOSUM62');
  96         float_is($result->get_parameter('expect'), '1e-05');
  97         is($result->get_parameter('include'), 0);
  98         is($result->get_parameter('match'), 0);
  99         is($result->get_parameter('mismatch'), 0);
 100         is($result->get_parameter('gapopen'), 11);
 101         is($result->get_parameter('gapext'), 1);
 102         is($result->get_parameter('filter'), 'F');
 103
 104         # check statistics
 105         is($result->available_statistics, 5);
 106         is($result->database_entries, 0);
 107         is($result->database_letters, 0);
 108         is($result->get_statistic('hsplength'), 0);
 109         float_is($result->get_statistic('effectivespace'), 3.82682e+07);
 110         is($result->get_statistic('lambda'), 0.267);
 111         is($result->get_statistic('kappa'), 0.041);
 112         is($result->get_statistic('entropy'), 0.14);
 113
 114         $hit = $result->next_hit;
 115         is($hit->name, 'gnl|Pfam|pfam00742');
 116         is($hit->description(), 'HomoS_dh, HomoS dehydrogenase');
 117         is($hit->accession, 'pfam00742');
 118         is($hit->ncbi_gi, ''); # not found
 119         is($hit->length, 310);
 120
 121         $hsp = $hit->next_hsp;
 122         is($hsp->query->seq_id, $result->query_name,'query name on HSP');
 123         is($hsp->query->seqdesc, $result->query_description,'query desc on HSP');
 124         is($hsp->hit->seq_id, $hit->name,'hitname');
 125         is($hsp->hit->seqdesc, $hit->description,'hitdesc');
 126         is($hsp->pvalue, undef);
 127         float_is($hsp->evalue, 1.46134e-90);
 128         is($hsp->score, 838);
 129         is($hsp->bits,327.405);
 130         is($hsp->query->start, 498);
 131         is($hsp->query->end,815);
 132         is($hsp->hit->start, 3);
 133         is($hsp->hit->end, 310);
 134         is($hsp->query->frame,0);
 135         is($hsp->hit->frame,0);
 136         is(sprintf("%.2f", $hsp->percent_identity), 37.73);
 137         is(sprintf("%.4f", $hsp->frac_identical('hit')), 0.3994);
 138         is(sprintf("%.4f", $hsp->frac_identical('query')), 0.3868);
 139         is(sprintf("%.4f",$hsp->query->frac_identical), 0.3868);
 140
 141         is(sprintf("%.4f",$hsp->frac_conserved('total')),0.5245);
 142         is(sprintf("%.4f",$hsp->frac_conserved('hit')),0.5552);
 143         is(sprintf("%.4f",$hsp->frac_conserved('query')),0.5377);
 144         # gaps should match calculated sequence indices for gaps and vice versa
 145         is($hsp->gaps('total'), $hsp->seq_inds('hit', 'gaps') + $hsp->seq_inds('query', 'gaps'));
 146         is($hsp->gaps('hit'), $hsp->seq_inds('hit', 'gaps'));
 147         is($hsp->gaps('query'), $hsp->seq_inds('query', 'gaps'));
 148         is($hsp->length('total'), 326);
 149         is($hsp->query_string, 'LRVCGVANSKALLTNVHGLNLENWQEELAQAKEPF-NLGRLIRLVKEYHLLN----PVIVDCTSSQAVAD-QYADFLREGFHVVTPNKKANTSSMDYYHQLRYAAEKSRRKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDE-GMSFSEATTLAREMGYTEPDPRDDLSGMDVARKLLILARET-GRELELADIEIEPVLPAEFNAEGDVAAFMANLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGENALAFYSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLS');
 150         is($hsp->hit_string, 'GVVTGITDSREMLLSRIGLPLEIWKVALRDLEKPRKDLGKLDLTDDAFAVVDDPDIDVVVELTGGIEVARELYLDALEEGKHVVTANKALNASHGDEYLAL---AEKSGVDVLYEAAVAGGIPIIKTLRELLATGDRILKIEGIFNGTTNFILSEMDEKGLPFSDVLAEAQELGYTEADPRDDVEGIDAARKLAILARIAFGIELELDDVYVEGISPITAEDISSADEFGYTLKLLDEAMRQRVEDAESGGEVLRYPTLIPE-------------DHPLASVKGSDNAVAVEGEAYG--PLMFYGPGAGAEPTASAVVADIVRIAR');
 151         is($hsp->homology_string, '  V G+ +S+ +L +  GL LE W+  L   ++P  +LG+L      + +++     V+V+ T    VA   Y D L EG HVVT NK  N S  D Y  L   AEKS    LY+  V  G+P+I+ L+ LL  GD ++K  GI +G+ ++I  ++DE G+ FS+    A+E+GYTE DPRDD+ G+D ARKL ILAR   G ELEL D+ +E + P           F   L  LD+    RV  A   G+VLRY   I E             + PL  VK  +NA+A     Y   PL+  G GAG + TA+ V AD++R   ');
 152         is(join(' ', $hsp->seq_inds('query', 'gap',1)), '532 548 562 649 690');
 153         is($hsp->ambiguous_seq_inds, '');
 154
 155         # one more
 156         $hit = $result->next_hit;
 157         isa_ok($hit,'Bio::Search::Hit::HitI');
 158
 159         my $results_left = 8;
 160         while( $result = $searchio->next_result ) { ok($result); $results_left--; }
 161         is($results_left, 0);
 162
 163         $searchio = Bio::SearchIO->new(-format => 'blastxml',
 164                                                                   -verbose => -1,
 165                                   -file => test_input_file('plague_yeast.bls.xml'));
 166
 167         $result = $searchio->next_result;
 168         is($searchio->result_count, 1);
 169         is($result->database_name, 'yeast.aa');
 170         is($result->query_name, 'gi|5763811|emb|CAB53164.1|');
 171         is($result->query_description,  'putative transposase [Yersinia pestis]');
 172         is($result->query_accession, 'CAB53164.1');
 173         is($result->query_gi, 5763811);
 174         is($result->query_length, 340);
 175
 176         $hit = $result->next_hit;
 177         ok(! $hit);
 178
 179         $searchio = Bio::SearchIO->new(-format => 'blastxml',
 180                                                                   -verbose => -1,
 181                                   -file => test_input_file('mus.bls.xml'));
 182
 183         $result = $searchio->next_result;
 184         is($searchio->result_count, 1);
 185         is($result->database_name,'Hs15_up1000');
 186         is($result->query_name,'NM_011441_up_1000_chr1_4505586_r');
 187         is($result->query_description,'chr1:4505586-4506585');
 188         is($result->query_accession,'NM_011441_up_1000_chr1_4505586_r');
 189         is($result->query_gi, '');
 190         is($result->query_length,'1000');
 191
 192         # check parameters
 193         is($result->available_parameters, 6);
 194         is($result->get_parameter('matrix'), undef); # not set
 195         float_is($result->get_parameter('expect'), 10);
 196         is($result->get_parameter('include'), undef); # not set
 197         is($result->get_parameter('match'), 1);
 198         is($result->get_parameter('mismatch'), -3);
 199         is($result->get_parameter('gapopen'), 5);
 200         is($result->get_parameter('gapext'), 2);
 201         is($result->get_parameter('filter'), 'D');
 202
 203         # check statistics
 204         is($result->available_statistics, 5);
 205         is($result->database_entries, 17516);
 206         is($result->database_letters, 17516000);
 207         is($result->get_statistic('hsplength'), 0);
 208         float_is($result->get_statistic('effectivespace'), 1.69255e+10);
 209         is($result->get_statistic('lambda'), 1.37407);
 210         is($result->get_statistic('kappa'), 0.710605);
 211         is($result->get_statistic('entropy'), 1.30725);
 212
 213         $hit = $result->next_hit;
 214         is($hit->name,'NM_001938_up_1000_chr1_93161154_f');
 215         is($hit->description,'chr1:93161154-93162153');
 216         is($hit->ncbi_gi, ''); # none reported
 217         is($hit->accession,'3153');
 218         is($hit->length,'1000');
 219
 220         # deal with new BLAST XML changes
 221         $searchio = Bio::SearchIO->new(-format => 'blastxml',
 222                                                                   -verbose => -1,
 223                                   -file => test_input_file('newblast.xml'));
 224
 225         $result = $searchio->next_result;
 226         is($searchio->result_count, 1);
 227         is($result->database_name,'nr');
 228         is($result->algorithm,'BLASTP');
 229         is($result->algorithm_version,'BLASTP 2.2.15 [Oct-15-2006]');
 230         # some XML::SAX parsers (PurePerl, XML::SAX::LibXML) don't decode entities
 231         # properly, not fixable using decode_entities()
 232         like($result->algorithm_reference, qr{Nucleic Acids Res} );
 233         is($result->query_name,'gi|15600734|ref|NP_254228.1|');
 234         is($result->query_description,'dihydroorotase [Pseudomonas aeruginosa PAO1]');
 235         is($result->query_accession,'NP_254228.1');
 236         is($result->query_gi, 15600734);
 237         is($result->query_length,'445');
 238
 239         # check parameters
 240         is($result->available_parameters, 4);
 241         is($result->get_parameter('matrix'), 'BLOSUM62');
 242         float_is($result->get_parameter('expect'), 10);
 243         is($result->get_parameter('include'), undef); # not set
 244         is($result->get_parameter('match'), undef);   # not set
 245         is($result->get_parameter('mismatch'), undef);# not set
 246         is($result->get_parameter('gapopen'), 11);
 247         is($result->get_parameter('gapext'), 1);
 248         is($result->get_parameter('filter'), undef);  # not set
 249
 250         # check statistics
 251         is($result->available_statistics, 5);
 252         is($result->database_entries, 4299737);
 253         is($result->database_letters, 1479795817);
 254         is($result->get_statistic('hsplength'), 0);
 255         float_is($result->get_statistic('effectivespace'), 0);
 256         is($result->get_statistic('lambda'), 0.267);
 257         is($result->get_statistic('kappa'), 0.041);
 258         is($result->get_statistic('entropy'), 0.14);
 259
 260         $hit = $result->next_hit;
 261         is($hit->name,'gi|15600734|ref|NP_254228.1|');
 262         is($hit->description,'dihydroorotase [Pseudomonas aeruginosa PAO1] '.
 263            '>gi|107104643|ref|ZP_01368561.1| hypothetical protein PaerPA_01005722 '.
 264            '[Pseudomonas aeruginosa PACS2] >gi|9951880|gb|AAG08926.1|AE004966_8 '.
 265            'dihydroorotase [Pseudomonas aeruginosa PAO1]');
 266         is($hit->accession,'NP_254228');
 267         is($hit->length,'445');
 268         $hsp = $hit->next_hsp;
 269         is($hsp->query->seq_id, $result->query_name,'query name on HSP');
 270         is($hsp->query->seqdesc, $result->query_description,'query desc on HSP');
 271         is($hsp->hit->seq_id, $hit->name,'hitname');
 272         is($hsp->hit->seqdesc, $hit->description,'hitdesc');
 273         is($hsp->pvalue, undef);
 274         float_is($hsp->evalue, 0);
 275         is($hsp->score, 2251);
 276         is($hsp->bits,871.692);
 277         is($hsp->query->start, 1);
 278         is($hsp->query->end,445);
 279         is($hsp->hit->start, 1);
 280         is($hsp->hit->end, 445);
 281         is($hsp->query->frame,0);
 282         is($hsp->hit->frame,0);
 283
 284         $result = $searchio->next_result;
 285         is($searchio->result_count, 2);
 286         is($result->database_name,'nr');
 287         is($result->algorithm,'BLASTP');
 288         is($result->algorithm_version,'BLASTP 2.2.15 [Oct-15-2006]');
 289         like($result->algorithm_reference, qr{Nucleic Acids Res} );
 290         is($result->query_name,'gi|15598723|ref|NP_252217.1|');
 291         is($result->query_description,'dihydroorotase [Pseudomonas aeruginosa PAO1]');
 292         is($result->query_accession,'NP_252217.1');
 293         is($result->query_gi, 15598723);
 294         is($result->query_length,'348');
 295
 296         # check parameters
 297         is($result->available_parameters, 4);
 298         is($result->get_parameter('matrix'), 'BLOSUM62');
 299         float_is($result->get_parameter('expect'), 10);
 300         is($result->get_parameter('include'), undef); # not set
 301         is($result->get_parameter('match'), undef);   # not set
 302         is($result->get_parameter('mismatch'), undef);# not set
 303         is($result->get_parameter('gapopen'), 11);
 304         is($result->get_parameter('gapext'), 1);
 305         is($result->get_parameter('filter'), undef);  # not set
 306
 307         # check statistics
 308         is($result->available_statistics, 5);
 309         is($result->database_entries, 4299737);
 310         is($result->database_letters, 1479795817);
 311         is($result->get_statistic('hsplength'), 0);
 312         float_is($result->get_statistic('effectivespace'), 0);
 313         is($result->get_statistic('lambda'), 0.267);
 314         is($result->get_statistic('kappa'), 0.041);
 315         is($result->get_statistic('entropy'), 0.14);
 316
 317         $hit = $result->next_hit;
 318         is($hit->name,'gi|15598723|ref|NP_252217.1|');
 319         is($hit->description,'dihydroorotase [Pseudomonas aeruginosa PAO1] '.
 320            '>gi|6226683|sp|P72170|PYRC_PSEAE Dihydroorotase (DHOase) '.
 321            '>gi|9949676|gb|AAG06915.1|AE004773_4 dihydroorotase [Pseudomonas aeruginosa PAO1] '.
 322            '>gi|3868712|gb|AAC73109.1| dihydroorotase [Pseudomonas aeruginosa]');
 323         is($hit->ncbi_gi, 15598723);
 324         is($hit->accession,'NP_252217');
 325         is($hit->length,'348');
 326         $hsp = $hit->next_hsp;
 327         is($hsp->query->seq_id, $result->query_name,'query name on HSP');
 328         is($hsp->query->seqdesc, $result->query_description,'query desc on HSP');
 329         is($hsp->hit->seq_id, $hit->name,'hitname');
 330         is($hsp->hit->seqdesc, $hit->description,'hitdesc');
 331         is($hsp->pvalue, undef);
 332         float_is($hsp->evalue, 0);
 333         is($hsp->score, 1780);
 334         is($hsp->bits,690.263);
 335         is($hsp->query->start, 1);
 336         is($hsp->query->end,348);
 337         is($hsp->hit->start, 1);
 338         is($hsp->hit->end, 348);
 339         is($hsp->query->frame,0);
 340         is($hsp->hit->frame,0);
 341
 342         # PSIBLAST XML parsing
 343
 344         $searchio = Bio::SearchIO->new('-tempfile' => 1,
 345                    '-format' => 'blastxml',
 346                    '-file'   => test_input_file('psiblast.xml'),
 347                    '-blasttype' => 'psiblast');
 348
 349         $result = $searchio->next_result;
 350         is($searchio->result_count, 1);
 351         is($result->database_name, 'AL591824.faa');
 352         is($result->algorithm, 'BLASTP');
 353         like($result->algorithm_version, qr/2\.2\.16/);
 354         is($result->query_name, 'gi|1373160|gb|AAB57770.1|');
 355         is($result->query_accession, 'AAB57770.1');
 356         is($result->query_gi, '1373160');
 357         is($result->query_length, 173);
 358
 359         # check parameters
 360         is($result->available_parameters, 6);
 361         is($result->get_parameter('matrix'), 'BLOSUM62');
 362         float_is($result->get_parameter('expect'), 10);
 363         is($result->get_parameter('include'), 0.002);
 364         is($result->get_parameter('match'), undef);   # not set
 365         is($result->get_parameter('mismatch'), undef);# not set
 366         is($result->get_parameter('gapopen'), 11);
 367         is($result->get_parameter('gapext'), 1);
 368         is($result->get_parameter('filter'), 'F');
 369
 370         # check statistics
 371         is($result->available_statistics, 5);
 372         is($result->database_entries, 2846);
 373         is($result->database_letters, 870878);
 374         is($result->get_statistic('hsplength'), 75);
 375         float_is($result->get_statistic('effectivespace'), 6.44279e+07);
 376         is($result->get_statistic('lambda'), 0.267);
 377         is($result->get_statistic('kappa'), 0.0475563);
 378         is($result->get_statistic('entropy'), 0.14);
 379
 380         my $iter_count = 0;
 381         my @valid_hit_data = ( [ 'gi|16411294|emb|CAC99918.1|', 183, 'CAC99918', 16411294, '4.5377e-56', 209.92],
 382                                    [ 'gi|16409584|emb|CAD00746.1|', 648, 'CAD00746', 16409584, '0.000286309', 37.7354],
 383                                    [ 'gi|16411285|emb|CAC99909.1|', 209, 'CAC99909', 16411285, '0.107059', 29.261]);
 384         my @valid_iter_data = ( [ 16, 16, 0, 2, 14, 0, 0, 0, 0],
 385                                 [ 16, 8, 8, 0, 8, 0, 2, 0, 6]);
 386
 387         while (my $iter = $result->next_iteration) {
 388                 $iter_count++;
 389                 my $di = shift @valid_iter_data;
 390                 is($iter->number, $iter_count);
 391                 is($iter->num_hits, shift @$di);
 392                 is($iter->num_hits_new, shift @$di);
 393                 is($iter->num_hits_old, shift @$di);
 394                 is(scalar($iter->newhits_below_threshold), shift @$di);
 395                 is(scalar($iter->newhits_not_below_threshold), shift @$di);
 396                 is(scalar($iter->newhits_unclassified), shift @$di);
 397                 is(scalar($iter->oldhits_below_threshold), shift @$di);
 398                 is(scalar($iter->oldhits_newly_below_threshold), shift @$di);
 399                 is(scalar($iter->oldhits_not_below_threshold), shift @$di);
 400                 my $hit_count = 0;
 401                 if ($iter_count == 1) {
 402                         while( my $hit = $result->next_hit ) {
 403                                 my $d = shift @valid_hit_data;
 404                                 is($hit->name, shift @$d);
 405                                 is($hit->length, shift @$d);
 406                                 is($hit->accession, shift @$d);
 407                                 is($hit->ncbi_gi, shift @$d);
 408                                 float_is($hit->significance, shift @$d);
 409                                 is($hit->bits, shift @$d );
 410                                 if( $hit_count == 1 ) {
 411                                         my $hsps_left = 1;
 412                                         while( my $hsp = $hit->next_hsp ){
 413                                                 is($hsp->query->start, 4);
 414                                                 is($hsp->query->end, 155);
 415                                                 is($hsp->hit->start, 475);
 416                                                 is($hsp->hit->end, 617);
 417                                                 is($hsp->length('total'), 153);
 418                                                 is($hsp->start('hit'), $hsp->hit->start);
 419                                                 is($hsp->end('query'), $hsp->query->end);
 420                                                 is($hsp->strand('sbjct'), $hsp->subject->strand);# alias for hit
 421                                                 float_is($hsp->evalue, 0.000286309);
 422                                                 is($hsp->score, 86);
 423                                                 is($hsp->bits, 37.7354);
 424                                                 is(sprintf("%.1f",$hsp->percent_identity), 20.9);
 425                                                 is(sprintf("%.4f",$hsp->frac_identical('query')), 0.2105);
 426                                                 is(sprintf("%.3f",$hsp->frac_identical('hit')), 0.224);
 427                                                 is($hsp->gaps('total'), 11);
 428                                                 $hsps_left--;
 429                                         }
 430                                         is($hsps_left, 0);
 431                                 }
 432                                 last if( $hit_count++ > @valid_hit_data );
 433                         }
 434                 }
 435         }
 436         is(@valid_hit_data, 0);
 437         is(@valid_iter_data, 0);
 438         is($iter_count, 2);
 439
 440         $result = $searchio->next_result;
 441         is($searchio->result_count, 2);
 442         is($result->database_name, 'AL591824.faa');
 443         is($result->algorithm, 'BLASTP');
 444         like($result->algorithm_version, qr/2\.2\.16/);
 445         is($result->query_name, 'gi|154350371|gb|ABS72450.1|');
 446         is($result->query_accession, 'ABS72450.1');
 447         is($result->query_gi, '154350371');
 448         is($result->query_length, 378);
 449
 450         # check parameters
 451         is($result->available_parameters, 6);
 452         is($result->get_parameter('matrix'), 'BLOSUM62');
 453         float_is($result->get_parameter('expect'), 10);
 454         is($result->get_parameter('include'), 0.002);
 455         is($result->get_parameter('match'), undef);   # not set
 456         is($result->get_parameter('mismatch'), undef);# not set
 457         is($result->get_parameter('gapopen'), 11);
 458         is($result->get_parameter('gapext'), 1);
 459         is($result->get_parameter('filter'), 'F');
 460
 461         # check statistics
 462         is($result->available_statistics, 5);
 463         is($result->database_entries, 2846);
 464         is($result->database_letters, 870878);
 465         is($result->get_statistic('hsplength'), 82);
 466         float_is($result->get_statistic('effectivespace'), 1.88702e+08);
 467         is($result->get_statistic('lambda'), 0.267);
 468         is($result->get_statistic('kappa'), 0.0450367);
 469         is($result->get_statistic('entropy'), 0.14);
 470
 471         $iter_count = 0;
 472
 473         @valid_hit_data = ( [ 'gi|16409361|emb|CAC98217.1|', 381, 'CAC98217', 16409361, '5.57178e-119', 420.239],
 474                                    [ 'gi|16409959|emb|CAC98662.1|', 776, 'CAC98662', 16409959, '0.0242028', 32.7278],
 475                                    [ 'gi|16410942|emb|CAC99591.1|', 382, 'CAC99591', 16410942, '0.340848', 28.8758]);
 476         @valid_iter_data = ( [ 11, 11, 0, 1, 10, 0, 0, 0, 0],
 477                                 [ 19, 11, 8, 0, 11, 0, 1, 0, 7]);
 478
 479         while (my $iter = $result->next_iteration) {
 480                 $iter_count++;
 481                 my $di = shift @valid_iter_data;
 482                 is($iter->number, $iter_count);
 483                 is($iter->num_hits, shift @$di);
 484                 is($iter->num_hits_new, shift @$di);
 485                 is($iter->num_hits_old, shift @$di);
 486                 is(scalar($iter->newhits_below_threshold), shift @$di);
 487                 is(scalar($iter->newhits_not_below_threshold), shift @$di);
 488                 is(scalar($iter->newhits_unclassified), shift @$di);
 489                 is(scalar($iter->oldhits_below_threshold), shift @$di);
 490                 is(scalar($iter->oldhits_newly_below_threshold), shift @$di);
 491                 is(scalar($iter->oldhits_not_below_threshold), shift @$di);
 492                 my $hit_count = 0;
 493                 if ($iter_count == 1) {
 494                         while( my $hit = $result->next_hit ) {
 495                                 my $d = shift @valid_hit_data;
 496                                 is($hit->name, shift @$d);
 497                                 is($hit->length, shift @$d);
 498                                 is($hit->accession, shift @$d);
 499                                 is($hit->ncbi_gi, shift @$d);
 500                                 float_is($hit->significance, shift @$d);
 501                                 is($hit->bits, shift @$d );
 502                                 if( $hit_count == 1 ) {
 503                                         my $hsps_left = 1;
 504                                         while( my $hsp = $hit->next_hsp ){
 505                                                 is($hsp->query->start, 63);
 506                                                 is($hsp->query->end, 181);
 507                                                 is($hsp->hit->start, 304);
 508                                                 is($hsp->hit->end, 432);
 509                                                 is($hsp->length('total'), 129);
 510                                                 is($hsp->start('hit'), $hsp->hit->start);
 511                                                 is($hsp->end('query'), $hsp->query->end);
 512                                                 is($hsp->strand('sbjct'), $hsp->subject->strand);# alias for hit
 513                                                 float_is($hsp->evalue, 0.0242028);
 514                                                 is($hsp->score, 73);
 515                                                 is($hsp->bits, 32.7278);
 516                                                 is(sprintf("%.1f",$hsp->percent_identity), '24.0');
 517                                                 is(sprintf("%.4f",$hsp->frac_identical('query')), '0.2605');
 518                                                 is(sprintf("%.3f",$hsp->frac_identical('hit')), '0.240');
 519                                                 is($hsp->gaps, 10);
 520                                                 $hsps_left--;
 521                                         }
 522                                         is($hsps_left, 0);
 523                                 }
 524                                 last if( $hit_count++ > @valid_hit_data );
 525                         }
 526                 }
 527         }
 528         is(@valid_hit_data, 0);
 529         is(@valid_iter_data, 0);
 530         is($iter_count, 2);
 531 }