# -*-Perl-*- Test Harness script for Bioperl
# $Id: SearchIO.t 14995 2008-11-16 06:20:00Z cjfields $
use strict;
BEGIN {
use lib '.';
use Bio::Root::Test;
test_begin(-tests => 391,
-requires_module => 'XML::SAX');
use_ok('Bio::SearchIO');
}
my ($searchio, $result,$iter,$hit,$hsp);
# XML encoding/decoding done within XML::SAX now, though some parsers
# do not work properly (XML::SAX::PurePerl, XML::LibXML::SAX)
eval {
# test with RPSBLAST data first
# this needs to be eval'd b/c the XML::SAX parser object is
# instantiated in the constructor
$searchio = Bio::SearchIO->new('-tempfile' => 1,
'-format' => 'blastxml',
'-file' => test_input_file('ecoli_domains.rps.xml'),
'-blasttype' => 'blast',
'-verbose' => -1);
# PurePerl works with these BLAST reports, so removed verbose promotion
$result = $searchio->next_result;
die if !defined $result;
};
SKIP: {
# this should be fixed with newer installations of XML::SAX::Expat, but as we
# don't require a certain version (multiple backends can be used) we catch
# and skip if needed
if ($@ && $@ =~ m{Handler could not resolve external entity}) {
skip("Older versions of XML::SAX::Expat may not work with XML tests; skipping",297);
} elsif ($@) {
skip("Problem with XML::SAX setup: $@. Check ParserDetails.ini; skipping XML tests",297);
}
is($searchio->result_count, 1);
# basic ResultI data
isa_ok($result, 'Bio::Search::Result::ResultI');
is($result->database_name, '/data_2/jason/db/cdd/cdd/Pfam', 'database_name()');
is($result->query_name,'gi|1786182|gb|AAC73112.1|','query_name()');
is($result->query_description, '(AE000111) thr operon leader peptide [Escherichia coli]');
is($result->query_accession, 'AAC73112.1');
is($result->query_gi, 1786182);
is($result->query_length, 21);
is($result->algorithm, 'BLASTP');
is($result->algorithm_version, 'blastp 2.1.3 [Apr-1-2001]');
# check parameters
is($result->available_parameters, 8);
is($result->get_parameter('matrix'), 'BLOSUM62');
float_is($result->get_parameter('expect'), '1e-05');
is($result->get_parameter('include'), 0);
is($result->get_parameter('match'), 0);
is($result->get_parameter('mismatch'), 0);
is($result->get_parameter('gapopen'), 11);
is($result->get_parameter('gapext'), 1);
is($result->get_parameter('filter'), 'F');
# check statistics
is($result->available_statistics, 5);
is($result->database_entries, 0);
is($result->database_letters, 0);
is($result->get_statistic('hsplength'), 0);
float_is($result->get_statistic('effectivespace'), 4.16497e+11);
is($result->get_statistic('lambda'), 0.267);
is($result->get_statistic('kappa'), 0.041);
is($result->get_statistic('entropy'), 0.14);
# this result actually has a hit
$result = $searchio->next_result;
# does the parser catch everything in the next result?
is($result->database_name, '/data_2/jason/db/cdd/cdd/Pfam', 'database_name()');
is($result->query_name,'gi|1786183|gb|AAC73113.1|');
is($result->query_description, '(AE000111) aspartokinase I, homoserine dehydrogenase I [Escherichia coli]');
is($result->query_accession, 'AAC73113.1');
is($result->query_gi, 1786183);
is($result->query_length, 820);
is($result->algorithm, 'BLASTP');
is($result->algorithm_version, 'blastp 2.1.3 [Apr-1-2001]');
is($searchio->result_count, 2);
# check parameters
is($result->available_parameters, 8);
is($result->get_parameter('matrix'), 'BLOSUM62');
float_is($result->get_parameter('expect'), '1e-05');
is($result->get_parameter('include'), 0);
is($result->get_parameter('match'), 0);
is($result->get_parameter('mismatch'), 0);
is($result->get_parameter('gapopen'), 11);
is($result->get_parameter('gapext'), 1);
is($result->get_parameter('filter'), 'F');
# check statistics
is($result->available_statistics, 5);
is($result->database_entries, 0);
is($result->database_letters, 0);
is($result->get_statistic('hsplength'), 0);
float_is($result->get_statistic('effectivespace'), 3.82682e+07);
is($result->get_statistic('lambda'), 0.267);
is($result->get_statistic('kappa'), 0.041);
is($result->get_statistic('entropy'), 0.14);
$hit = $result->next_hit;
is($hit->name, 'gnl|Pfam|pfam00742');
is($hit->description(), 'HomoS_dh, HomoS dehydrogenase');
is($hit->accession, 'pfam00742');
is($hit->ncbi_gi, ''); # not found
is($hit->length, 310);
$hsp = $hit->next_hsp;
is($hsp->query->seq_id, $result->query_name,'query name on HSP');
is($hsp->query->seqdesc, $result->query_description,'query desc on HSP');
is($hsp->hit->seq_id, $hit->name,'hitname');
is($hsp->hit->seqdesc, $hit->description,'hitdesc');
is($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'), $hsp->seq_inds('hit', 'gaps'));
is($hsp->gaps('query'), $hsp->seq_inds('query', 'gaps'));
is($hsp->length('total'), 326);
is($hsp->query_string, 'LRVCGVANSKALLTNVHGLNLENWQEELAQAKEPF-NLGRLIRLVKEYHLLN----PVIVDCTSSQAVAD-QYADFLREGFHVVTPNKKANTSSMDYYHQLRYAAEKSRRKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDE-GMSFSEATTLAREMGYTEPDPRDDLSGMDVARKLLILARET-GRELELADIEIEPVLPAEFNAEGDVAAFMANLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGENALAFYSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLS');
is($hsp->hit_string, 'GVVTGITDSREMLLSRIGLPLEIWKVALRDLEKPRKDLGKLDLTDDAFAVVDDPDIDVVVELTGGIEVARELYLDALEEGKHVVTANKALNASHGDEYLAL---AEKSGVDVLYEAAVAGGIPIIKTLRELLATGDRILKIEGIFNGTTNFILSEMDEKGLPFSDVLAEAQELGYTEADPRDDVEGIDAARKLAILARIAFGIELELDDVYVEGISPITAEDISSADEFGYTLKLLDEAMRQRVEDAESGGEVLRYPTLIPE-------------DHPLASVKGSDNAVAVEGEAYG--PLMFYGPGAGAEPTASAVVADIVRIAR');
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 ');
is(join(' ', $hsp->seq_inds('query', 'gap',1)), '532 548 562 649 690');
is($hsp->ambiguous_seq_inds, '');
# one more
$hit = $result->next_hit;
isa_ok($hit,'Bio::Search::Hit::HitI');
my $results_left = 8;
while( $result = $searchio->next_result ) { ok($result); $results_left--; }
is($results_left, 0);
$searchio = Bio::SearchIO->new(-format => 'blastxml',
-verbose => -1,
-file => test_input_file('plague_yeast.bls.xml'));
$result = $searchio->next_result;
is($searchio->result_count, 1);
is($result->database_name, 'yeast.aa');
is($result->query_name, 'gi|5763811|emb|CAB53164.1|');
is($result->query_description, 'putative transposase [Yersinia pestis]');
is($result->query_accession, 'CAB53164.1');
is($result->query_gi, 5763811);
is($result->query_length, 340);
$hit = $result->next_hit;
ok(! $hit);
$searchio = Bio::SearchIO->new(-format => 'blastxml',
-verbose => -1,
-file => test_input_file('mus.bls.xml'));
$result = $searchio->next_result;
is($searchio->result_count, 1);
is($result->database_name,'Hs15_up1000');
is($result->query_name,'NM_011441_up_1000_chr1_4505586_r');
is($result->query_description,'chr1:4505586-4506585');
is($result->query_accession,'NM_011441_up_1000_chr1_4505586_r');
is($result->query_gi, '');
is($result->query_length,'1000');
# check parameters
is($result->available_parameters, 6);
is($result->get_parameter('matrix'), undef); # not set
float_is($result->get_parameter('expect'), 10);
is($result->get_parameter('include'), undef); # not set
is($result->get_parameter('match'), 1);
is($result->get_parameter('mismatch'), -3);
is($result->get_parameter('gapopen'), 5);
is($result->get_parameter('gapext'), 2);
is($result->get_parameter('filter'), 'D');
# check statistics
is($result->available_statistics, 5);
is($result->database_entries, 17516);
is($result->database_letters, 17516000);
is($result->get_statistic('hsplength'), 0);
float_is($result->get_statistic('effectivespace'), 1.69255e+10);
is($result->get_statistic('lambda'), 1.37407);
is($result->get_statistic('kappa'), 0.710605);
is($result->get_statistic('entropy'), 1.30725);
$hit = $result->next_hit;
is($hit->name,'NM_001938_up_1000_chr1_93161154_f');
is($hit->description,'chr1:93161154-93162153');
is($hit->ncbi_gi, ''); # none reported
is($hit->accession,'3153');
is($hit->length,'1000');
# deal with new BLAST XML changes
$searchio = Bio::SearchIO->new(-format => 'blastxml',
-verbose => -1,
-file => test_input_file('newblast.xml'));
$result = $searchio->next_result;
is($searchio->result_count, 1);
is($result->database_name,'nr');
is($result->algorithm,'BLASTP');
is($result->algorithm_version,'BLASTP 2.2.15 [Oct-15-2006]');
# some XML::SAX parsers (PurePerl, XML::SAX::LibXML) don't decode entities
# properly, not fixable using decode_entities()
like($result->algorithm_reference, qr{Nucleic Acids Res} );
is($result->query_name,'gi|15600734|ref|NP_254228.1|');
is($result->query_description,'dihydroorotase [Pseudomonas aeruginosa PAO1]');
is($result->query_accession,'NP_254228.1');
is($result->query_gi, 15600734);
is($result->query_length,'445');
# check parameters
is($result->available_parameters, 4);
is($result->get_parameter('matrix'), 'BLOSUM62');
float_is($result->get_parameter('expect'), 10);
is($result->get_parameter('include'), undef); # not set
is($result->get_parameter('match'), undef); # not set
is($result->get_parameter('mismatch'), undef);# not set
is($result->get_parameter('gapopen'), 11);
is($result->get_parameter('gapext'), 1);
is($result->get_parameter('filter'), undef); # not set
# check statistics
is($result->available_statistics, 5);
is($result->database_entries, 4299737);
is($result->database_letters, 1479795817);
is($result->get_statistic('hsplength'), 0);
float_is($result->get_statistic('effectivespace'), 0);
is($result->get_statistic('lambda'), 0.267);
is($result->get_statistic('kappa'), 0.041);
is($result->get_statistic('entropy'), 0.14);
$hit = $result->next_hit;
is($hit->name,'gi|15600734|ref|NP_254228.1|');
is($hit->description,'dihydroorotase [Pseudomonas aeruginosa PAO1] '.
'>gi|107104643|ref|ZP_01368561.1| hypothetical protein PaerPA_01005722 '.
'[Pseudomonas aeruginosa PACS2] >gi|9951880|gb|AAG08926.1|AE004966_8 '.
'dihydroorotase [Pseudomonas aeruginosa PAO1]');
is($hit->accession,'NP_254228');
is($hit->length,'445');
$hsp = $hit->next_hsp;
is($hsp->query->seq_id, $result->query_name,'query name on HSP');
is($hsp->query->seqdesc, $result->query_description,'query desc on HSP');
is($hsp->hit->seq_id, $hit->name,'hitname');
is($hsp->hit->seqdesc, $hit->description,'hitdesc');
is($hsp->pvalue, undef);
float_is($hsp->evalue, 0);
is($hsp->score, 2251);
is($hsp->bits,871.692);
is($hsp->query->start, 1);
is($hsp->query->end,445);
is($hsp->hit->start, 1);
is($hsp->hit->end, 445);
is($hsp->query->frame,0);
is($hsp->hit->frame,0);
$result = $searchio->next_result;
is($searchio->result_count, 2);
is($result->database_name,'nr');
is($result->algorithm,'BLASTP');
is($result->algorithm_version,'BLASTP 2.2.15 [Oct-15-2006]');
like($result->algorithm_reference, qr{Nucleic Acids Res} );
is($result->query_name,'gi|15598723|ref|NP_252217.1|');
is($result->query_description,'dihydroorotase [Pseudomonas aeruginosa PAO1]');
is($result->query_accession,'NP_252217.1');
is($result->query_gi, 15598723);
is($result->query_length,'348');
# check parameters
is($result->available_parameters, 4);
is($result->get_parameter('matrix'), 'BLOSUM62');
float_is($result->get_parameter('expect'), 10);
is($result->get_parameter('include'), undef); # not set
is($result->get_parameter('match'), undef); # not set
is($result->get_parameter('mismatch'), undef);# not set
is($result->get_parameter('gapopen'), 11);
is($result->get_parameter('gapext'), 1);
is($result->get_parameter('filter'), undef); # not set
# check statistics
is($result->available_statistics, 5);
is($result->database_entries, 4299737);
is($result->database_letters, 1479795817);
is($result->get_statistic('hsplength'), 0);
float_is($result->get_statistic('effectivespace'), 0);
is($result->get_statistic('lambda'), 0.267);
is($result->get_statistic('kappa'), 0.041);
is($result->get_statistic('entropy'), 0.14);
$hit = $result->next_hit;
is($hit->name,'gi|15598723|ref|NP_252217.1|');
is($hit->description,'dihydroorotase [Pseudomonas aeruginosa PAO1] '.
'>gi|6226683|sp|P72170|PYRC_PSEAE Dihydroorotase (DHOase) '.
'>gi|9949676|gb|AAG06915.1|AE004773_4 dihydroorotase [Pseudomonas aeruginosa PAO1] '.
'>gi|3868712|gb|AAC73109.1| dihydroorotase [Pseudomonas aeruginosa]');
is($hit->ncbi_gi, 15598723);
is($hit->accession,'NP_252217');
is($hit->length,'348');
$hsp = $hit->next_hsp;
is($hsp->query->seq_id, $result->query_name,'query name on HSP');
is($hsp->query->seqdesc, $result->query_description,'query desc on HSP');
is($hsp->hit->seq_id, $hit->name,'hitname');
is($hsp->hit->seqdesc, $hit->description,'hitdesc');
is($hsp->pvalue, undef);
float_is($hsp->evalue, 0);
is($hsp->score, 1780);
is($hsp->bits,690.263);
is($hsp->query->start, 1);
is($hsp->query->end,348);
is($hsp->hit->start, 1);
is($hsp->hit->end, 348);
is($hsp->query->frame,0);
is($hsp->hit->frame,0);
# PSIBLAST XML parsing
$searchio = Bio::SearchIO->new('-tempfile' => 1,
'-format' => 'blastxml',
'-file' => test_input_file('psiblast.xml'),
'-blasttype' => 'psiblast');
$result = $searchio->next_result;
is($searchio->result_count, 1);
is($result->database_name, 'AL591824.faa');
is($result->algorithm, 'BLASTP');
like($result->algorithm_version, qr/2\.2\.16/);
is($result->query_name, 'gi|1373160|gb|AAB57770.1|');
is($result->query_accession, 'AAB57770.1');
is($result->query_gi, '1373160');
is($result->query_length, 173);
# check parameters
is($result->available_parameters, 6);
is($result->get_parameter('matrix'), 'BLOSUM62');
float_is($result->get_parameter('expect'), 10);
is($result->get_parameter('include'), 0.002);
is($result->get_parameter('match'), undef); # not set
is($result->get_parameter('mismatch'), undef);# not set
is($result->get_parameter('gapopen'), 11);
is($result->get_parameter('gapext'), 1);
is($result->get_parameter('filter'), 'F');
# check statistics
is($result->available_statistics, 5);
is($result->database_entries, 2846);
is($result->database_letters, 870878);
is($result->get_statistic('hsplength'), 75);
float_is($result->get_statistic('effectivespace'), 6.44279e+07);
is($result->get_statistic('lambda'), 0.267);
is($result->get_statistic('kappa'), 0.0475563);
is($result->get_statistic('entropy'), 0.14);
my $iter_count = 0;
my @valid_hit_data = ( [ 'gi|16411294|emb|CAC99918.1|', 183, 'CAC99918', 16411294, '4.5377e-56', 209.92],
[ 'gi|16409584|emb|CAD00746.1|', 648, 'CAD00746', 16409584, '0.000286309', 37.7354],
[ 'gi|16411285|emb|CAC99909.1|', 209, 'CAC99909', 16411285, '0.107059', 29.261]);
my @valid_iter_data = ( [ 16, 16, 0, 2, 14, 0, 0, 0, 0],
[ 16, 8, 8, 0, 8, 0, 2, 0, 6]);
while (my $iter = $result->next_iteration) {
$iter_count++;
my $di = shift @valid_iter_data;
is($iter->number, $iter_count);
is($iter->num_hits, shift @$di);
is($iter->num_hits_new, shift @$di);
is($iter->num_hits_old, shift @$di);
is(scalar($iter->newhits_below_threshold), shift @$di);
is(scalar($iter->newhits_not_below_threshold), shift @$di);
is(scalar($iter->newhits_unclassified), shift @$di);
is(scalar($iter->oldhits_below_threshold), shift @$di);
is(scalar($iter->oldhits_newly_below_threshold), shift @$di);
is(scalar($iter->oldhits_not_below_threshold), shift @$di);
my $hit_count = 0;
if ($iter_count == 1) {
while( my $hit = $result->next_hit ) {
my $d = shift @valid_hit_data;
is($hit->name, shift @$d);
is($hit->length, shift @$d);
is($hit->accession, shift @$d);
is($hit->ncbi_gi, shift @$d);
float_is($hit->significance, shift @$d);
is($hit->bits, shift @$d );
if( $hit_count == 1 ) {
my $hsps_left = 1;
while( my $hsp = $hit->next_hsp ){
is($hsp->query->start, 4);
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( $hit_count++ > @valid_hit_data );
}
}
}
is(@valid_hit_data, 0);
is(@valid_iter_data, 0);
is($iter_count, 2);
$result = $searchio->next_result;
is($searchio->result_count, 2);
is($result->database_name, 'AL591824.faa');
is($result->algorithm, 'BLASTP');
like($result->algorithm_version, qr/2\.2\.16/);
is($result->query_name, 'gi|154350371|gb|ABS72450.1|');
is($result->query_accession, 'ABS72450.1');
is($result->query_gi, '154350371');
is($result->query_length, 378);
# check parameters
is($result->available_parameters, 6);
is($result->get_parameter('matrix'), 'BLOSUM62');
float_is($result->get_parameter('expect'), 10);
is($result->get_parameter('include'), 0.002);
is($result->get_parameter('match'), undef); # not set
is($result->get_parameter('mismatch'), undef);# not set
is($result->get_parameter('gapopen'), 11);
is($result->get_parameter('gapext'), 1);
is($result->get_parameter('filter'), 'F');
# check statistics
is($result->available_statistics, 5);
is($result->database_entries, 2846);
is($result->database_letters, 870878);
is($result->get_statistic('hsplength'), 82);
float_is($result->get_statistic('effectivespace'), 1.88702e+08);
is($result->get_statistic('lambda'), 0.267);
is($result->get_statistic('kappa'), 0.0450367);
is($result->get_statistic('entropy'), 0.14);
$iter_count = 0;
@valid_hit_data = ( [ 'gi|16409361|emb|CAC98217.1|', 381, 'CAC98217', 16409361, '5.57178e-119', 420.239],
[ 'gi|16409959|emb|CAC98662.1|', 776, 'CAC98662', 16409959, '0.0242028', 32.7278],
[ 'gi|16410942|emb|CAC99591.1|', 382, 'CAC99591', 16410942, '0.340848', 28.8758]);
@valid_iter_data = ( [ 11, 11, 0, 1, 10, 0, 0, 0, 0],
[ 19, 11, 8, 0, 11, 0, 1, 0, 7]);
while (my $iter = $result->next_iteration) {
$iter_count++;
my $di = shift @valid_iter_data;
is($iter->number, $iter_count);
is($iter->num_hits, shift @$di);
is($iter->num_hits_new, shift @$di);
is($iter->num_hits_old, shift @$di);
is(scalar($iter->newhits_below_threshold), shift @$di);
is(scalar($iter->newhits_not_below_threshold), shift @$di);
is(scalar($iter->newhits_unclassified), shift @$di);
is(scalar($iter->oldhits_below_threshold), shift @$di);
is(scalar($iter->oldhits_newly_below_threshold), shift @$di);
is(scalar($iter->oldhits_not_below_threshold), shift @$di);
my $hit_count = 0;
if ($iter_count == 1) {
while( my $hit = $result->next_hit ) {
my $d = shift @valid_hit_data;
is($hit->name, shift @$d);
is($hit->length, shift @$d);
is($hit->accession, shift @$d);
is($hit->ncbi_gi, shift @$d);
float_is($hit->significance, shift @$d);
is($hit->bits, shift @$d );
if( $hit_count == 1 ) {
my $hsps_left = 1;
while( my $hsp = $hit->next_hsp ){
is($hsp->query->start, 63);
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( $hit_count++ > @valid_hit_data );
}
}
}
is(@valid_hit_data, 0);
is(@valid_iter_data, 0);
is($iter_count, 2);
}