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blast.t
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blast.t
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# -*-Perl-*- Test Harness script for Bioperl
# $Id: SearchIO_blast.t 14995 2008-11-16 06:20:00Z cjfields $
use strict;
BEGIN {
use lib '.';
use Bio::Root::Test;
test_begin(-tests => 1348);
use_ok('Bio::SearchIO');
}
my ($searchio, $result,$iter,$hit,$hsp);
$searchio = Bio::SearchIO->new('-format' => 'blast',
'-file' => test_input_file('ecolitst.bls'));
$result = $searchio->next_result;
is($result->algorithm_reference, 'Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
');
is($result->database_name, 'ecoli.aa', 'database_name()');
is($result->database_entries, 4289);
is($result->database_letters, 1358990);
is($result->algorithm, 'BLASTP');
like($result->algorithm_version, qr/^2\.1\.3/);
like($result->query_name, qr/gi|1786183|gb|AAC73113.1| (AE000111) aspartokinase I,\s+homoserine dehydrogenase I [Escherichia coli]/);
is($result->query_accession, 'AAC73113.1');
is($result->query_gi, 1786183);
is($result->query_length, 820);
is($result->get_statistic('kappa'), '0.135');
is($result->get_statistic('kappa_gapped'), '0.0410');
is($result->get_statistic('lambda'), '0.319');
is($result->get_statistic('lambda_gapped'), '0.267');
is($result->get_statistic('entropy'), '0.383');
is($result->get_statistic('entropy_gapped'), '0.140');
is($result->get_statistic('dbletters'), 1358990);
is($result->get_statistic('dbentries'), 4289);
is($result->get_statistic('effective_hsplength'), 47);
is($result->get_statistic('effectivespace'), 894675611);
is($result->get_parameter('matrix'), 'BLOSUM62');
is($result->get_parameter('gapopen'), 11);
is($result->get_parameter('gapext'), 1);
is($result->get_statistic('S2'), '92');
is($result->get_statistic('S2_bits'), '40.0');
float_is($result->get_parameter('expect'), '1.0e-03');
is($result->get_statistic('num_extensions'), '82424');
is($result->get_statistic('querylength'), 773);
is($result->get_statistic('effectivedblength'), 1157407);
is($result->get_statistic('effectivespaceused'), 894675611);
my @valid = ( [ 'gb|AAC73113.1|', 820, 'AAC73113', '0', 1567, 4058],
[ 'gb|AAC76922.1|', 810, 'AAC76922', '1e-91', 332, 850],
[ 'gb|AAC76994.1|', 449, 'AAC76994', '3e-47', 184, 467]);
my $count = 0;
while( $hit = $result->next_hit ) {
my $d = shift @valid;
is($hit->name, shift @$d);
is($hit->length, shift @$d);
is($hit->accession, shift @$d);
float_is($hit->significance, shift @$d);
is($hit->bits, shift @$d );
is($hit->raw_score, shift @$d );
if( $count == 0 ) {
my $hsps_left = 1;
while( my $hsp = $hit->next_hsp ) {
is($hsp->query->start, 1);
is($hsp->query->end, 820);
is($hsp->hit->start, 1);
is($hsp->hit->end, 820);
is($hsp->length('total'), 820);
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, 0.0);
is($hsp->score, 4058);
is($hsp->bits,1567);
is(sprintf("%.2f",$hsp->percent_identity), 98.29);
is(sprintf("%.4f",$hsp->frac_identical('query')), 0.9829);
is(sprintf("%.4f",$hsp->frac_identical('hit')), 0.9829);
is($hsp->gaps, 0);
is($hsp->n, 1);
$hsps_left--;
}
is($hsps_left, 0);
}
last if( $count++ > @valid );
}
is(@valid, 0);
$searchio = Bio::SearchIO->new('-format' => 'blast',
'-file' => test_input_file('ecolitst.wublastp'));
$result = $searchio->next_result;
is($result->algorithm_reference, 'Gish, W. (1996-2000) http://blast.wustl.edu
');
is($result->database_name, 'ecoli.aa');
is($result->database_letters, 1358990);
is($result->database_entries, 4289);
is($result->algorithm, 'BLASTP');
like($result->algorithm_version, qr/^2\.0MP\-WashU/);
like($result->query_name, qr/gi|1786183|gb|AAC73113.1| (AE000111) aspartokinase I,\s+homoserine dehydrogenase I [Escherichia coli]/);
is($result->query_accession, 'AAC73113.1');
is($result->query_length, 820);
is($result->query_gi, 1786183);
is($result->get_statistic('kappa'), 0.136);
is($result->get_statistic('lambda'), 0.319);
is($result->get_statistic('entropy'), 0.384);
is($result->get_statistic('dbletters'), 1358990);
is($result->get_statistic('dbentries'), 4289);
is($result->get_parameter('matrix'), 'BLOSUM62');
is($result->get_statistic('Frame+0_lambda_used'), '0.319');
is($result->get_statistic('Frame+0_kappa_used'), '0.136');
is($result->get_statistic('Frame+0_entropy_used'), '0.384');
is($result->get_statistic('Frame+0_lambda_computed'), '0.319');
is($result->get_statistic('Frame+0_kappa_computed'), '0.136');
is($result->get_statistic('Frame+0_entropy_computed'), '0.384');
is($result->get_statistic('Frame+0_lambda_gapped'), '0.244');
is($result->get_statistic('Frame+0_kappa_gapped'), '0.0300');
is($result->get_statistic('Frame+0_entropy_gapped'), '0.180');
@valid = ( [ 'gb|AAC73113.1|', 820, 'AAC73113', '0', 4141],
[ 'gb|AAC76922.1|', 810, 'AAC76922', '3.1e-86', 844],
[ 'gb|AAC76994.1|', 449, 'AAC76994', '2.8e-47', 483]);
$count = 0;
while( $hit = $result->next_hit ) {
my $d = shift @valid;
if ($count==1) {
# Test HSP contig data returned by SearchUtils::tile_hsps()
# Second hit has two hsps that overlap.
# compare with the contig made by hand for these two contigs
# in t/data/contig-by-hand.wublastp
# (in this made-up file, the hsps from ecolitst.wublastp
# were aligned and contiged, and Length, Identities, Positives
# were counted, by a human (maj) )
my $hand_hit = Bio::SearchIO->new(
-format=>'blast',
-file=>test_input_file('contig-by-hand.wublastp')
)->next_result->next_hit;
my $hand_hsp = $hand_hit->next_hsp;
my @hand_qrng = $hand_hsp->range('query');
my @hand_srng = $hand_hsp->range('hit');
my @hand_matches = $hand_hit->matches;
my($qcontigs, $scontigs) = Bio::Search::SearchUtils::tile_hsps($hit);
# Query contigs
is($qcontigs->[0]->{'start'}, $hand_qrng[0]);
is($qcontigs->[0]->{'stop'}, $hand_qrng[1]);
is($qcontigs->[0]->{'iden'}, $hand_matches[0]);
is($qcontigs->[0]->{'cons'}, $hand_matches[1]);
# Subject contigs
is($scontigs->[0]->{'start'}, $hand_srng[0]);
is($scontigs->[0]->{'stop'}, $hand_srng[1]);
is($scontigs->[0]->{'iden'}, $hand_matches[0]);
is($scontigs->[0]->{'cons'}, $hand_matches[1]);
}
is($hit->name, shift @$d);
is($hit->length, shift @$d);
is($hit->accession, shift @$d);
float_is($hit->significance, shift @$d);
is($hit->raw_score, shift @$d );
if( $count == 0 ) {
my $hsps_left = 1;
while( my $hsp = $hit->next_hsp ) {
is($hsp->query->start, 1);
is($hsp->query->end, 820);
is($hsp->hit->start, 1);
is($hsp->hit->end, 820);
is($hsp->length('total'), 820);
float_is($hsp->evalue, 0.0);
float_is($hsp->pvalue, '0.0');
is($hsp->score, 4141);
is($hsp->bits,1462.8);
is($hsp->percent_identity, 100);
is($hsp->frac_identical('query'), 1.00);
is($hsp->frac_identical('hit'), 1.00);
is($hsp->gaps, 0);
is($hsp->n, 1);
$hsps_left--;
}
is($hsps_left, 0);
}
last if( $count++ > @valid );
}
is(@valid, 0);
# test that add hit really works properly for BLAST objects
# bug 1611
my @hits = $result->hits;
$result->add_hit($hits[0]);
is($result->num_hits, @hits + 1);
# test WU-BLAST -noseqs option
$searchio = Bio::SearchIO->new('-format' => 'blast',
'-file' => test_input_file('ecolitst.noseqs.wublastp'));
$result = $searchio->next_result;
is($result->algorithm_reference, 'Gish, W. (1996-2004) http://blast.wustl.edu
');
is($result->database_name, 'ecoli.aa');
is($result->database_letters, 1358990);
is($result->database_entries, 4289);
is($result->algorithm, 'BLASTP');
like($result->algorithm_version, qr/^2\.0MP\-WashU/);
like($result->query_name, qr/gi|1786183|gb|AAC73113.1| (AE000111) aspartokinase I,\s+homoserine dehydrogenase I [Escherichia coli]/);
is($result->query_accession, 'AAC73113.1');
is($result->query_gi, 1786183);
is($result->query_length, 820);
is($result->get_statistic('kappa'), 0.135);
is($result->get_statistic('lambda'), 0.319);
is($result->get_statistic('entropy'), 0.384);
is($result->get_statistic('dbletters'), 1358990);
is($result->get_statistic('dbentries'), 4289);
is($result->get_parameter('matrix'), 'BLOSUM62');
is($result->get_statistic('Frame+0_lambda_used'), '0.319');
is($result->get_statistic('Frame+0_kappa_used'), '0.135');
is($result->get_statistic('Frame+0_entropy_used'), '0.384');
is($result->get_statistic('Frame+0_lambda_computed'), '0.319');
is($result->get_statistic('Frame+0_kappa_computed'), '0.135');
is($result->get_statistic('Frame+0_entropy_computed'), '0.384');
is($result->get_statistic('Frame+0_lambda_gapped'), '0.244');
is($result->get_statistic('Frame+0_kappa_gapped'), '0.0300');
is($result->get_statistic('Frame+0_entropy_gapped'), '0.180');
@valid = ( [ 'gb|AAC73113.1|', 820, 'AAC73113', '0', 4141],
[ 'gb|AAC76922.1|', 810, 'AAC76922', '6.6e-93', 907],
[ 'gb|AAC76994.1|', 449, 'AAC76994', '2.8e-47', 483]);
$count = 0;
while( $hit = $result->next_hit ) {
my $d = shift @valid;
is($hit->name, shift @$d);
is($hit->length, shift @$d);
is($hit->accession, shift @$d);
float_is($hit->significance, shift @$d);
is($hit->raw_score, shift @$d );
if( $count == 0 ) {
my $hsps_left = 1;
while( my $hsp = $hit->next_hsp ) {
is($hsp->query->start, 1);
is($hsp->query->end, 820);
is($hsp->hit->start, 1);
is($hsp->hit->end, 820);
is($hsp->length('total'), 820);
float_is($hsp->evalue, 0.);
float_is($hsp->pvalue , '0.');
is($hsp->score, 4141);
is($hsp->bits,1462.8);
is($hsp->percent_identity, 100);
is($hsp->frac_identical('query'), 1.00);
is($hsp->frac_identical('hit'), 1.00);
is($hsp->gaps, 0);
is($hsp->n, 1);
$hsps_left--;
}
is($hsps_left, 0);
}
last if( $count++ > @valid );
}
is(@valid, 0);
# test tblastx
$searchio = Bio::SearchIO->new('-format' => 'blast',
'-file' => test_input_file('HUMBETGLOA.tblastx'));
$result = $searchio->next_result;
is($result->algorithm_reference, 'Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
');
is($result->database_name, 'ecoli.nt');
is($result->database_letters, 4662239);
is($result->database_entries, 400);
is($result->algorithm, 'TBLASTX');
like($result->algorithm_version, qr/^2\.1\.2/);
is($result->query_name, 'HUMBETGLOA');
is($result->query_description, 'Human haplotype C4 beta-globin gene, complete cds.');
is($result->query_length, 3002);
is($result->get_statistic('kappa'), 0.135);
is($result->get_statistic('lambda'), 0.318);
is($result->get_statistic('entropy'), 0.401);
is($result->get_statistic('dbletters'), 4662239);
is($result->get_statistic('dbentries'), 400);
is($result->get_statistic('querylength'), 953);
is($result->get_statistic('effectivedblength'), 1535279);
is($result->get_statistic('effectivespace'), 1463120887);
is($result->get_statistic('effectivespaceused'), 1463120887);
is($result->get_statistic('T'), 13);
is($result->get_statistic('X1'), 16);
is($result->get_statistic('X1_bits'), 7.3);
is($result->get_statistic('X2'), 0);
is($result->get_statistic('X2_bits'), '0.0');
is($result->get_statistic('S1'), 41);
is($result->get_statistic('S1_bits'), 21.7);
is($result->get_statistic('S2'), 53);
is($result->get_statistic('S2_bits'), 27.2);
is($result->get_statistic('decayconst'), 0.1);
is($result->get_parameter('matrix'), 'BLOSUM62');
@valid = ( [ 'gb|AE000479.1|AE000479', 10934, 'AE000479', '0.13', 33.6, 67],
[ 'gb|AE000302.1|AE000302', 10264, 'AE000302', '0.61', 31.3, 62],
[ 'gb|AE000277.1|AE000277', 11653, 'AE000277', '0.84', 30.8, 61]);
$count = 0;
while( $hit = $result->next_hit ) {
my $d = shift @valid;
is($hit->name, shift @$d);
is($hit->length, shift @$d);
is($hit->accession, shift @$d);
float_is($hit->significance, shift @$d);
is($hit->bits, shift @$d );
is($hit->raw_score, shift @$d );
if( $count == 0 ) {
my $hsps_left = 1;
while( my $hsp = $hit->next_hsp ) {
is($hsp->query->start, 1057);
is($hsp->query->end, 1134);
is($hsp->query->strand, 1);
is($hsp->strand('query'), $hsp->query->strand);
is($hsp->hit->end, 5893);
is($hsp->hit->start, 5816);
is($hsp->hit->strand, -1);
is($hsp->strand('sbjct'), $hsp->subject->strand);
is($hsp->length('total'), 26);
float_is($hsp->evalue, 0.13);
is($hsp->score, 67);
is($hsp->bits,33.6);
is(sprintf("%.2f",$hsp->percent_identity), 42.31);
is(sprintf("%.4f",$hsp->frac_identical('query')), '0.4231');
is(sprintf("%.4f",$hsp->frac_identical('hit')), '0.4231');
is($hsp->query->frame(), 0);
is($hsp->hit->frame(), 1);
is($hsp->gaps, 0);
is($hsp->query_string, 'SAYWSIFPPLGCWWSTLGPRGSLSPL');
is($hsp->hit_string, 'AAVWALFPPVGSQWGCLASQWRTSPL');
is($hsp->homology_string, '+A W++FPP+G W L + SPL');
# changed to reflect positional ambiguities, note extra flag
is(join(' ', $hsp->seq_inds('query', 'nomatch',1)), '1063-1065 1090-1095 1099-1104 1108-1113 1117-1125');
is(join(' ', $hsp->seq_inds('hit', 'nomatch',1)), '5825-5833 5837-5842 5846-5851 5855-5860 5885-5887');
is($hsp->ambiguous_seq_inds, 'query/subject');
is($hsp->n, 1);
$hsps_left--;
}
is($hsps_left, 0);
}
last if( $count++ > @valid );
}
is(@valid, 0);
# test for MarkW bug in blastN
$searchio = Bio::SearchIO->new('-format' => 'blast',
'-file' => test_input_file('a_thaliana.blastn'));
$result = $searchio->next_result;
is($result->algorithm_reference, 'Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
');
is($result->rid, '1012577175-3730-28291');
is($result->database_name, 'All GenBank+EMBL+DDBJ+PDB sequences (but no EST, STS, GSS,or phase 0, 1 or 2 HTGS sequences) ');
is($result->database_letters, 4677375331);
is($result->database_entries, 1083200);
is($result->algorithm, 'BLASTN');
like($result->algorithm_version, qr/^2\.2\.1/);
is($result->query_name, '');
is($result->query_length, 60);
is($result->get_parameter('gapopen'), 5);
is($result->get_parameter('gapext'), 2);
is($result->get_parameter('ktup'), undef);
is($result->get_statistic('querylength'), 41);
is($result->get_statistic('effectivedblength'), 4656794531);
is($result->get_statistic('effectivespace'), 190928575771);
is($result->get_statistic('effectivespaceused'), 190928575771);
is($result->get_statistic('lambda'), 1.37);
is($result->get_statistic('kappa'), 0.711);
is($result->get_statistic('entropy'),1.31 );
is($result->get_statistic('T'), 0);
is($result->get_statistic('A'), 30);
is($result->get_statistic('X1'), '6');
is($result->get_statistic('X1_bits'), 11.9);
is($result->get_statistic('X2'), 15);
is($result->get_statistic('X2_bits'), 29.7);
is($result->get_statistic('S1'), 12);
is($result->get_statistic('S1_bits'), 24.3);
is($result->get_statistic('S2'), 17);
is($result->get_statistic('S2_bits'), 34.2);
is($result->get_statistic('dbentries'), 1083200);
@valid = ( [ 'gb|AY052359.1|', 2826, 'AY052359', '3e-18', 95.6, 48, 1, 60,
'1.0000'],
[ 'gb|AC002329.2|AC002329', 76170, 'AC002329', '3e-18', 95.6, 48, 1, 60,
'1.0000' ],
[ 'gb|AF132318.1|AF132318', 5383, 'AF132318', '0.04', 42.1, 21, 35, 55,
'0.3500']);
$count = 0;
while( my $hit = $result->next_hit ) {
my $d = shift @valid;
is($hit->name, shift @$d);
is($hit->length, shift @$d);
is($hit->accession, shift @$d);
float_is($hit->significance, shift @$d);
is($hit->bits, shift @$d );
is($hit->raw_score, shift @$d );
is($hit->start, shift @$d);
is($hit->end,shift @$d);
is(sprintf("%.4f",$hit->frac_aligned_query), shift @$d);
if( $count == 0 ) {
my $hsps_left = 1;
while( my $hsp = $hit->next_hsp ) {
is($hsp->query->start, 1);
is($hsp->query->end, 60);
is($hsp->query->strand, 1);
is($hsp->hit->start, 154);
is($hsp->hit->end, 212);
is($hsp->hit->strand, 1);
is($hsp->length('total'), 60);
float_is($hsp->evalue, 3e-18);
is($hsp->score, 48);
is($hsp->bits,95.6);
is(sprintf("%.2f",$hsp->percent_identity), 96.67);
is(sprintf("%.4f",$hsp->frac_identical('query')), 0.9667);
is(sprintf("%.4f",$hsp->frac_identical('hit')), 0.9831);
is($hsp->query->frame(), 0);
is($hsp->hit->frame(), 0);
is($hsp->query->seq_id, undef);
is($hsp->hit->seq_id, 'gb|AY052359.1|');
is($hsp->gaps('query'), 0);
is($hsp->gaps('hit'), 1);
is($hsp->gaps, 1);
is($hsp->query_string, 'aggaatgctgtttaattggaatcgtacaatggagaatttgacggaaatagaatcaacgat');
is($hsp->hit_string, 'aggaatgctgtttaattggaatca-acaatggagaatttgacggaaatagaatcaacgat');
is($hsp->homology_string, '||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||');
my $aln = $hsp->get_aln;
is(sprintf("%.2f", $aln->overall_percentage_identity), 96.67);
is(sprintf("%.2f",$aln->percentage_identity), 98.31);
is($hsp->n, 1);
$hsps_left--;
}
is($hsps_left, 0);
}
last if( $count++ > @valid );
}
is(@valid, 0);
#WU-BlastX test
$searchio = Bio::SearchIO->new('-format' => 'blast',
'-file' => test_input_file('dnaEbsub_ecoli.wublastx'));
$result = $searchio->next_result;
is($result->algorithm_reference, 'Gish, W. (1996-2000) http://blast.wustl.edu
Gish, Warren and David J. States (1993). Identification of protein coding
regions by database similarity search. Nat. Genet. 3:266-72.
');
is($result->database_name, 'ecoli.aa');
is($result->database_letters, 1358990);
is($result->database_entries, 4289);
is($result->algorithm, 'BLASTX');
like($result->algorithm_version, qr/^2\.0MP\-WashU/);
is($result->query_name, 'gi|142864|gb|M10040.1|BACDNAE');
is($result->query_description, 'B.subtilis dnaE gene encoding DNA primase, complete cds');
is($result->query_accession, 'M10040.1');
is($result->query_gi, 142864);
is($result->query_length, 2001);
is($result->get_parameter('matrix'), 'blosum62');
is($result->get_statistic('lambda'), 0.318);
is($result->get_statistic('kappa'), 0.135);
is($result->get_statistic('entropy'),0.401 );
is($result->get_statistic('dbentries'), 4289);
@valid = ( [ 'gi|1789447|gb|AAC76102.1|', 581, 'AAC76102', '1.1e-74', 671]);
$count = 0;
while( my $hit = $result->next_hit ) {
my $d = shift @valid;
is($hit->name, shift @$d);
is($hit->length, shift @$d);
is($hit->accession, shift @$d);
float_is($hit->significance, shift @$d);
is($hit->raw_score, shift @$d );
is(sprintf("%.4f",$hit->frac_identical('query')), '0.3640');
is(sprintf("%.4f",$hit->frac_identical('hit')), '0.3660');
is(sprintf("%.4f",$hit->frac_conserved('query')), '0.5370');
is(sprintf("%.4f",$hit->frac_conserved('hit')), '0.5400');
is(sprintf("%.4f",$hit->frac_aligned_query), '0.6200');
is(sprintf("%.4f",$hit->frac_aligned_hit), '0.7100');
if( $count == 0 ) {
my $hsps_left = 1;
while( my $hsp = $hit->next_hsp ) {
is($hsp->query->start, 21);
is($hsp->query->end, 1265);
is($hsp->query->strand, 1);
is($hsp->hit->start, 1);
is($hsp->hit->end, 413);
is($hsp->hit->strand, 0);
is($hsp->length('total'), 421);
float_is($hsp->evalue, 1.1e-74);
float_is($hsp->pvalue, '1.1e-74');
is($hsp->score,671);
is($hsp->bits,265.8);
is(sprintf("%.2f",$hsp->percent_identity), 35.87);
is(sprintf("%.4f",$hsp->frac_identical('query')), 0.3639);
is(sprintf("%.4f",$hsp->frac_identical('hit')), 0.3656);
is(sprintf("%.4f",$hsp->frac_conserved('query')), 0.5373);
is(sprintf("%.2f",$hsp->frac_conserved('hit')), 0.54);
is(sprintf("%.4f",$hsp->frac_identical('hsp')), 0.3587);
is(sprintf("%.4f",$hsp->frac_conserved('hsp')), 0.5297);
is($hsp->query->frame(), 2);
is($hsp->hit->frame(), 0);
is($hsp->gaps('query'), 6);
is($hsp->gaps('hit'), 8);
is($hsp->gaps, 14);
is($hsp->query_string, 'MGNRIPDEIVDQVQKSADIVEVIGDYVQLKKQGRNYFGLCPFHGESTPSFSVSPDKQIFHCFGCGAGGNVFSFLRQMEGYSFAESVSHLADKYQIDFPDDITVHSGARP---ESSGEQKMAEAHELLKKFYHHLLINTKEGQEALDYLLSRGFTKELINEFQIGYALDSWDFITKFLVKRGFSEAQMEKAGLLIRREDGSGYFDRFRNRVMFPIHDHHGAVVAFSGRALGSQQPKYMNSPETPLFHKSKLLYNFYKARLHIRKQERAVLFEGFADVYTAVSSDVKESIATMGTSLTDDHVKILRRNVEEIILCYDSDKAGYEATLKASELL---QKKGCKVRVAMIPDGLDPDDYIKKFGGEKFKNDIIDASVTVMAFKMQYFRKGKNLSDEGDRLAYIKDVLKEISTLSGSLEQEVYVKQ');
is($hsp->hit_string, 'MAGRIPRVFINDLLARTDIVDLIDARVKLKKQGKNFHACCPFHNEKTPSFTVNGEKQFYHCFGCGAHGNAIDFLMNYDKLEFVETVEELAAMHNLEVPFE----AGSGPSQIERHQRQTLYQLMDGLNTFYQQSL-QQPVATSARQYLEKRGLSHEVIARFAIGFAPPGWDNVLKRFGGNPENRQSLIDAGMLVTNDQGRSY-DRFRERVMFPIRDKRGRVIGFGGRVLGNDTPKYLNSPETDIFHKGRQLYGLYEAQQDNAEPNRLLVVEGYMDVVALAQYGINYAVASLGTSTTADHIQLLFRATNNVICCYDGDRAGRDAAWRALETALPYMTDGRQLRFMFLPDGEDPDTLVRKEGKEAFEARM-EQAMPLSAFLFNSLMPQVDLSTPDGRARLSTLALPLISQVPGETLR-IYLRQ');
is($hsp->homology_string, 'M RIP ++ + DIV++I V+LKKQG+N+ CPFH E TPSF+V+ +KQ +HCFGCGA GN FL + F E+V LA + ++ P + +G+ P E Q + + + L FY L A YL RG + E+I F IG+A WD + K + + AG+L+ + G Y DRFR RVMFPI D G V+ F GR LG+ PKY+NSPET +FHK + LY Y+A+ + R ++ EG+ DV + ++A++GTS T DH+++L R +I CYD D+AG +A +A E G ++R +PDG DPD ++K G E F+ + + ++ + AF +LS R L IS + G + +Y++Q');
is(join(' ', $hsp->seq_inds('query', 'nomatch',1)), '24-29 39-47 54-56 60-71 90-98 129-137 150-152 156-158 180-182 192-194 219-221 228-236 243-251 255-263 267-269 279-284 291-296 300-302 309-311 315-317 321-332 342-344 351-362 366-368 372-374 378-383 387-389 393-398 405-413 417-440 444-449 456-461 468-470 474-476 486-491 495-497 510-518 525-527 531-533 537-557 561-569 573-578 594-599 603-605 609-614 618-620 633-635 654-656 660-665 669-671 678-680 684-686 693-695 705-710 738-740 753-755 759-761 768-773 786-797 801-806 810-812 819-821 831-833 840-860 864-869 894-896 900-902 921-923 927-938 945-947 957-959 972-974 981-986 993-995 999-1013 1017-1019 1029-1037 1050-1052 1062-1067 1077-1079 1083-1085 1089-1091 1098-1103 1107-1109 1113-1115 1122-1124 1128-1130 1137-1163 1173-1184 1188-1208 1212-1217 1224-1226 1230-1232 1236-1244 1248-1250');
is(join(' ', $hsp->seq_inds('query', 'mismatch',1)), '24-29 39-47 54-56 60-71 90-98 129-137 150-152 156-158 180-182 192-194 219-221 228-236 243-251 255-263 267-269 279-284 291-296 300-302 309-311 315-317 342-344 351-362 366-368 372-374 378-383 387-389 393-398 405-413 420-440 444-449 456-461 468-470 474-476 486-491 495-497 510-518 525-527 531-533 537-557 561-569 573-578 594-599 603-605 609-614 633-635 654-656 660-665 669-671 678-680 684-686 693-695 705-710 738-740 753-755 759-761 768-773 786-797 801-806 810-812 819-821 831-833 840-860 864-869 894-896 900-902 921-923 927-938 945-947 957-959 972-974 981-986 993-995 999-1013 1017-1019 1029-1037 1050-1052 1062-1067 1077-1079 1083-1085 1089-1091 1098-1103 1113-1115 1122-1124 1128-1130 1137-1163 1173-1184 1188-1208 1212-1217 1224-1226 1230-1232 1236-1244');
is(join(' ', $hsp->seq_inds('hit', 'nomatch',1)), '2 3 7-9 12 14-17 24-26 37-39 44 46 54 58 67 70-72 75-77 79-81 83 87 88 91 92 94 97 99 104 106-108 110-113 115 117 119 120 122 124 125 128-130 132-138 140 141 144 145 148 150 154 155 157 162-164 167 169 171-177 179-181 183 184 190 191 193 195 196 202 209 211 212 214 217 219 222 226 227 237 242 244 247 248 253-256 258 259 261 264 268 271-277 279 280 289 291 298 300-303 306 310 315 318 319 322 324-331 333 337-339 344 348 349 353 355 357 360 361 364 367 369 372-380 384-387 389-395 397 398 401 403 405-407');
is(join(' ', $hsp->seq_inds('hit', 'mismatch',1)), '2 3 7-9 12 14-17 24-26 37-39 44 46 54 58 67 70-72 75-77 79-81 83 87 88 91 92 94 97 99 104 110-113 115 117 119 120 122 124 125 128-130 132-138 140 141 144 145 148 150 154 155 157 162-164 167 169 171-177 179-181 183 184 190 191 193 195 196 202 209 211 212 214 217 219 222 226 227 237 242 244 247 248 253-256 258 259 261 264 268 271-277 279 280 289 291 298 300-303 306 310 315 318 319 322 324 325 329-331 333 337-339 344 348 349 353 355 357 360 361 364 367 369 372-380 384-387 389-395 397 398 401 403 405-407');
is(join(' ', $hsp->seq_inds('query', 'gaps',1)), '347 1004');
is(join(' ', $hsp->seq_inds('hit', 'gaps',1)), '100 131 197 362 408');
is($hsp->ambiguous_seq_inds, 'query');
is($hsp->n, 1);
$hsps_left--;
}
is($hsps_left, 0);
}
last if( $count++ > @valid );
}
is(@valid, 0);
#Trickier WU-Blast
$searchio = Bio::SearchIO->new('-format' => 'blast',
'-file' => test_input_file('tricky.wublast'));
$result = $searchio->next_result;
my $hits_left = 1;
while (my $hit = $result->next_hit) {
# frac_aligned_hit used to be over 1, frac_identical & frac_conserved are still too wrong
TODO: {
local $TODO = 'frac_identical & frac_conserved are still too wrong';
cmp_ok sprintf("%.3f",$hit->frac_identical), '>', 0.9;
cmp_ok sprintf("%.3f",$hit->frac_conserved), '<=', 1;
}
is(sprintf("%.2f",$hit->frac_aligned_query), '0.92');
is(sprintf("%.2f",$hit->frac_aligned_hit), '0.91');
$hits_left--;
}
is($hits_left, 0);
# More frac_ method testing, this time on ncbi blastn
$searchio = Bio::SearchIO->new('-format' => 'blast',
'-file' => test_input_file('frac_problems.blast'));
my @expected = ("1.000", "0.943");
while (my $result = $searchio->next_result) {
my $hit = $result->next_hit;
is($hit->frac_identical, shift @expected);
}
is(@expected, 0);
# And even more: frac_aligned_query should never be over 1!
$searchio = Bio::SearchIO->new('-format' => 'blast',
'-file' => test_input_file('frac_problems2.blast'));
$result = $searchio->next_result;
$hit = $result->next_hit;
is $hit->frac_aligned_query, 0.97;
# Also, start and end should be sane
$searchio = Bio::SearchIO->new('-format' => 'blast',
'-file' => test_input_file('frac_problems3.blast'));
$result = $searchio->next_result;
$hit = $result->next_hit;
is $hit->start('sbjct'), 207;
is $hit->end('sbjct'), 1051;
#WU-TBlastN test
$searchio = Bio::SearchIO->new('-format' => 'blast',
'-file' => test_input_file('dnaEbsub_ecoli.wutblastn'));
$result = $searchio->next_result;
is($result->algorithm_reference, 'Gish, W. (1996-2000) http://blast.wustl.edu
');
is($result->database_name, 'ecoli.nt');
is($result->database_letters, 4662239);
is($result->database_entries, 400);
is($result->algorithm, 'TBLASTN');
like($result->algorithm_version, qr/^2\.0MP\-WashU/);
is($result->query_name, 'gi|142865|gb|AAA22406.1|');
is($result->query_description, 'DNA primase');
is($result->query_accession, 'AAA22406.1');
is($result->query_gi, 142865);
is($result->query_length, 603);
is($result->get_parameter('matrix'), 'blosum62');
is($result->get_statistic('lambda'), '0.320');
is($result->get_statistic('kappa'), 0.136);
is($result->get_statistic('entropy'),0.387 );
is($result->get_statistic('dbentries'), 400);
@valid = ( [ 'gi|1789441|gb|AE000388.1|AE000388', 10334, 'AE000388', '1.4e-73', 671]);
$count = 0;
while( my $hit = $result->next_hit ) {
my $d = shift @valid;
is($hit->name, shift @$d);
is($hit->length, shift @$d);
is($hit->accession, shift @$d);
float_is($hit->significance, shift @$d);
is($hit->raw_score, shift @$d );
if( $count == 0 ) {
my $hsps_left = 1;
while( my $hsp = $hit->next_hsp ) {
is($hsp->query->start, 1);
is($hsp->query->end, 415);
is($hsp->query->strand, 0);
is($hsp->hit->start, 4778);
is($hsp->hit->end, 6016);
is($hsp->hit->strand, 1);
is($hsp->length('total'), 421);
float_is($hsp->evalue, 1.4e-73);
float_is($hsp->pvalue,1.4e-73);
is($hsp->score,671);
is($hsp->bits,265.8);
is(sprintf("%.2f",$hsp->percent_identity), 35.87);
is(sprintf("%.4f",$hsp->frac_identical('hit')), 0.3656);
is(sprintf("%.4f",$hsp->frac_identical('query')), 0.3639);
is(sprintf("%.4f",$hsp->frac_conserved('hsp')), 0.5297);
is($hsp->query->frame(), 0);
is($hsp->hit->frame(), 1);
is($hsp->gaps('query'), 6);
is($hsp->gaps('hit'), 8);
is($hsp->gaps, 14);
is($hsp->query_string, 'MGNRIPDEIVDQVQKSADIVEVIGDYVQLKKQGRNYFGLCPFHGESTPSFSVSPDKQIFHCFGCGAGGNVFSFLRQMEGYSFAESVSHLADKYQIDFPDDITVHSGARP---ESSGEQKMAEAHELLKKFYHHLLINTKEGQEALDYLLSRGFTKELINEFQIGYALDSWDFITKFLVKRGFSEAQMEKAGLLIRREDGSGYFDRFRNRVMFPIHDHHGAVVAFSGRALGSQQPKYMNSPETPLFHKSKLLYNFYKARLHIRKQERAVLFEGFADVYTAVSSDVKESIATMGTSLTDDHVKILRRNVEEIILCYDSDKAGYEATLKASELL---QKKGCKVRVAMIPDGLDPDDYIKKFGGEKFKNDIIDASVTVMAFKMQYFRKGKNLSDEGDRLAYIKDVLKEISTLSGSLEQEVYVKQ');
is($hsp->hit_string, 'MAGRIPRVFINDLLARTDIVDLIDARVKLKKQGKNFHACCPFHNEKTPSFTVNGEKQFYHCFGCGAHGNAIDFLMNYDKLEFVETVEELAAMHNLEVPFE----AGSGPSQIERHQRQTLYQLMDGLNTFYQQSL-QQPVATSARQYLEKRGLSHEVIARFAIGFAPPGWDNVLKRFGGNPENRQSLIDAGMLVTNDQGRSY-DRFRERVMFPIRDKRGRVIGFGGRVLGNDTPKYLNSPETDIFHKGRQLYGLYEAQQDNAEPNRLLVVEGYMDVVALAQYGINYAVASLGTSTTADHIQLLFRATNNVICCYDGDRAGRDAAWRALETALPYMTDGRQLRFMFLPDGEDPDTLVRKEGKEAFEARM-EQAMPLSAFLFNSLMPQVDLSTPDGRARLSTLALPLISQVPGETLR-IYLRQ');
is($hsp->homology_string, 'M RIP ++ + DIV++I V+LKKQG+N+ CPFH E TPSF+V+ +KQ +HCFGCGA GN FL + F E+V LA + ++ P + +G+ P E Q + + + L FY L A YL RG + E+I F IG+A WD + K + + AG+L+ + G Y DRFR RVMFPI D G V+ F GR LG+ PKY+NSPET +FHK + LY Y+A+ + R ++ EG+ DV + ++A++GTS T DH+++L R +I CYD D+AG +A +A E G ++R +PDG DPD ++K G E F+ + + ++ + AF +LS R L IS + G + +Y++Q');
is(join(' ', $hsp->seq_inds('query', 'nomatch',1)), '2 3 7-9 12 14-17 24-26 37-39 44 46 54 58 67 70-72 75-77 79-81 83 87 88 91 92 94 97 99 101-104 108 111-114 116 118 120 121 123 125 126 129-131 133-140 142 143 146 147 150 152 156 157 159 164-166 169 171 173-179 181-183 185 186 192 193 195 197 198 200 205 212 214 215 217 220 222 225 229 230 240 245 247 250 251 256-259 261 262 264 267 271 274-280 282 283 292 294 301 303-306 309 313 318 321 322 325 327-331 333 337-339 344 348 349 353 355 357 360 361 363 365 368 370 373-381 385-388 390-396 398 399 402 404 406-408 410');
is(join(' ', $hsp->seq_inds('hit', 'nomatch',1)), '4781-4786 4796-4804 4811-4813 4817-4828 4847-4855 4886-4894 4907-4909 4913-4915 4937-4939 4949-4951 4976-4978 4985-4993 5000-5008 5012-5020 5024-5026 5036-5041 5048-5053 5057-5059 5066-5068 5072-5074 5087-5089 5093-5101 5105-5116 5120-5122 5126-5128 5132-5137 5141-5143 5147-5152 5159-5167 5171-5191 5195-5200 5207-5212 5219-5221 5225-5227 5237-5242 5246-5248 5261-5269 5276-5278 5282-5284 5288-5308 5312-5320 5324-5329 5345-5350 5354-5356 5360-5365 5381-5383 5402-5404 5408-5413 5417-5419 5426-5428 5432-5434 5441-5443 5453-5458 5486-5488 5501-5503 5507-5509 5516-5521 5534-5545 5549-5554 5558-5560 5567-5569 5579-5581 5588-5608 5612-5617 5642-5644 5648-5650 5669-5671 5675-5686 5693-5695 5705-5707 5720-5722 5729-5734 5741-5743 5747-5770 5774-5776 5786-5794 5807-5809 5819-5824 5834-5836 5840-5842 5846-5848 5855-5860 5867-5869 5876-5878 5882-5884 5891-5917 5927-5938 5942-5962 5966-5971 5978-5980 5984-5986 5990-5998');
is(join(' ', $hsp->seq_inds('query', 'gaps',1)), '109 328');
is(join(' ', $hsp->seq_inds('hit', 'gaps',1)), '5077 5170 5368 5863 6001');
is($hsp->ambiguous_seq_inds, 'subject');
is($hsp->n, 1);
$hsps_left--;
}
is($hsps_left, 0);
}
last if( $count++ > @valid );
}
is($count, 1);
# WU-BLAST TBLASTX
$searchio = Bio::SearchIO->new('-format' => 'blast',
'-file' => test_input_file('dnaEbsub_ecoli.wutblastx'));
$result = $searchio->next_result;
is($result->algorithm_reference, 'Gish, W. (1996-2000) http://blast.wustl.edu
');
is($result->database_name, 'ecoli.nt');
is($result->database_letters, 4662239);
is($result->database_entries, 400);
is($result->algorithm, 'TBLASTX');
like($result->algorithm_version, qr/^2\.0MP\-WashU/);
is($result->query_name, 'gi|142864|gb|M10040.1|BACDNAE');
is($result->query_description, 'B.subtilis dnaE gene encoding DNA primase, complete cds');
is($result->query_accession, 'M10040.1');
is($result->query_gi, 142864);
is($result->query_length, 2001);
is($result->get_parameter('matrix'), 'blosum62');
is($result->get_statistic('lambda'), 0.318);
is($result->get_statistic('kappa'), 0.135);
is($result->get_statistic('entropy'),0.401 );
is($result->get_statistic('dbentries'), 400);
@valid = ( [ 'gi|1789441|gb|AE000388.1|AE000388', 10334, 'AE000388', '6.4e-70', 318, 148.6],
[ 'gi|2367383|gb|AE000509.1|AE000509', 10589, 'AE000509', 1, 59, 29.9]
);
$count = 0;
while( my $hit = $result->next_hit ) {
my $d = shift @valid;
is($hit->name, shift @$d);
is($hit->length, shift @$d);
is($hit->accession, shift @$d);
# using e here to deal with 0.9992 coming out right here as well
float_is($hit->significance, shift @$d);
is($hit->raw_score, shift @$d );
is($hit->bits, shift @$d );
if( $count == 0 ) {
my $hspcounter = 0;
while( my $hsp = $hit->next_hsp ) {
$hspcounter++;
if( $hspcounter == 3 ) {
# let's actually look at the 3rd HSP
is($hsp->query->start, 441);
is($hsp->query->end, 617);
is($hsp->query->strand, 1);
is($hsp->hit->start, 5192);
is($hsp->hit->end, 5368);
is($hsp->hit->strand, 1);
is($hsp->length('total'), 59);
float_is($hsp->evalue, 6.4e-70);
float_is($hsp->pvalue,6.4e-70);
is($hsp->score,85);
is($hsp->bits,41.8);
is(sprintf("%.2f",$hsp->percent_identity), '32.20');
is(sprintf("%.3f",$hsp->frac_identical('hit')), 0.322);
is(sprintf("%.3f",$hsp->frac_identical('query')), 0.322);
is(sprintf("%.4f",$hsp->frac_conserved('hsp')), 0.4746);
is($hsp->query->frame(), 2);
is($hsp->hit->frame(), 1);
is($hsp->gaps('query'), 0);
is($hsp->gaps('hit'), 0);
is($hsp->gaps, 0);
is($hsp->n, 1);
is($hsp->query_string, 'ALDYLLSRGFTKELINEFQIGYALDSWDFITKFLVKRGFSEAQMEKAGLLIRREDGSGY');
is($hsp->hit_string, 'ARQYLEKRGLSHEVIARFAIGFAPPGWDNVLKRFGGNPENRQSLIDAGMLVTNDQGRSY');
is($hsp->homology_string, 'A YL RG + E+I F IG+A WD + K + + AG+L+ + G Y');
is(join(' ', $hsp->seq_inds('query', 'nomatch',1)), '444-449 456-461 468-470 474-476 486-491 495-497 510-518 525-527 531-533 537-557 561-569 573-578 594-599 603-605 609-614');
is(join(' ', $hsp->seq_inds('hit', 'nomatch',1)), '5195-5200 5207-5212 5219-5221 5225-5227 5237-5242 5246-5248 5261-5269 5276-5278 5282-5284 5288-5308 5312-5320 5324-5329 5345-5350 5354-5356 5360-5365');
is($hsp->ambiguous_seq_inds, 'query/subject');
last;
}
}
is($hspcounter, 3);
}
elsif( $count == 1 ) {
my $hsps_to_do = 1;
while( my $hsp = $hit->next_hsp ) {
is($hsp->query->start, 587);
is($hsp->query->end, 706);
is($hsp->query->strand, -1);
is($hsp->hit->start, 4108);
is($hsp->hit->end, 4227);
is($hsp->hit->strand, -1);
is($hsp->length('total'), 40);
float_is($hsp->evalue, 7.1);
float_is($hsp->pvalue , '1.00');
is($hsp->score,59);
is($hsp->bits,29.9);
is(sprintf("%.2f",$hsp->percent_identity), '37.50');
is(sprintf("%.4f",$hsp->frac_identical('hit')), '0.3750');
is(sprintf("%.4f",$hsp->frac_identical('query')), '0.3750');
is(sprintf("%.4f",$hsp->frac_conserved('hsp')), '0.4750');
is($hsp->query->frame(), 2);
is($hsp->hit->frame(), 2);
is($hsp->gaps('query'), 0);
is($hsp->gaps('hit'), 0);
is($hsp->gaps, 0);
is($hsp->n, 1);
is($hsp->query_string, 'WLPRALPEKATTAP**SWIGNMTRFLKRSKYPLPSSRLIR');
is($hsp->hit_string, 'WLSRTTVGSSTVSPRTFWITRMKVKLSSSKVTLPSTKSTR');
is($hsp->homology_string, 'WL R +T +P WI M L SK LPS++ R');
$hsps_to_do--;
last;
}
is($hsps_to_do, 0);
}
last if( $count++ > @valid );
}
is($count, 2);
# WU-BLAST -echofilter option test (Bug 2388)
$searchio = Bio::SearchIO->new('-format' => 'blast',
'-file' => test_input_file('echofilter.wublastn'));
$result = $searchio->next_result;
is($result->algorithm_reference, 'Gish, W. (1996-2006) http://blast.wustl.edu
');
is($result->database_name, 'NM_003201.fa');
is($result->database_letters, 1936);
is($result->database_entries, 1);
is($result->algorithm, 'BLASTN');
like($result->algorithm_version, qr/^2\.0MP\-WashU/);
like($result->query_name, qr/ref|NM_003201.1| Homo sapiens transcription factor A, mitochondrial \(TFAM\), mRNA/);
is($result->query_accession, 'NM_003201.1');
is($result->query_length, 1936);
is($result->get_statistic('lambda'), 0.192);
is($result->get_statistic('kappa'), 0.182);
is($result->get_statistic('entropy'), 0.357);
is($result->get_statistic('dbletters'), 1936);
is($result->get_statistic('dbentries'), 1);
is($result->get_parameter('matrix'), '+5,-4');
@valid = ( [ 'ref|NM_003201.1|', 1936, 'NM_003201', '0', 9680],);
$count = 0;
while( $hit = $result->next_hit ) {
my $d = shift @valid;
is($hit->name, shift @$d);
is($hit->length, shift @$d);
is($hit->accession, shift @$d);
float_is($hit->significance, shift @$d);
is($hit->raw_score, shift @$d );
if( $count == 0 ) {
my $hsps_left = 1;
while( my $hsp = $hit->next_hsp ) {
is($hsp->query->start, 1);
is($hsp->query->end, 1936);
is($hsp->hit->start, 1);
is($hsp->hit->end, 1936);
is($hsp->length('total'), 1936);
float_is($hsp->evalue, 0.);
float_is($hsp->pvalue , '0.');
is($hsp->score, 9680);
is($hsp->bits,1458.4);
is($hsp->percent_identity, 100);
is($hsp->frac_identical('query'), 1.00);
is($hsp->frac_identical('hit'), 1.00);
is($hsp->gaps, 0);
is($hsp->n, 1);
$hsps_left--;
}
is($hsps_left, 0);
}
last if( $count++ > @valid );
}
is(@valid, 0);
# Do a multiblast report test
$searchio = Bio::SearchIO->new('-format' => 'blast',
'-file' => test_input_file('multi_blast.bls'));
@expected = qw(CATH_RAT CATL_HUMAN CATL_RAT PAPA_CARPA);
my $results_left = 4;
while( my $result = $searchio->next_result ) {
is($result->algorithm_reference, 'Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
');
is($result->query_name, shift @expected, "Multiblast query test");
$results_left--;
}
is($results_left, 0);
# Test GCGBlast parsing
$searchio = Bio::SearchIO->new('-format' => 'blast',
'-file' => test_input_file('test.gcgblast'));
$result = $searchio->next_result();
is($result->algorithm_reference, 'Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
');
is($result->query_name, '/v0/people/staji002/test.gcg');
is($result->algorithm, 'BLASTP');
is($result->algorithm_version, '2.2.1 [Apr-13-2001]');
is($result->database_name, 'pir');
is($result->database_entries, 274514);
is($result->database_letters, 93460074);
is($result->get_statistic('querylength'), 44);
is($result->get_statistic('effectivedblength'), 65459646);
is($result->get_statistic('effectivespace'), 2880224424);
is($result->get_statistic('effectivespaceused'), 2880224424);
$hit = $result->next_hit;
is($hit->description, 'F22B7.10 protein - Caenorhabditis elegans');
is($hit->name, 'PIR2:S44629');
is($hit->length, 628);
is($hit->accession, 'PIR2:S44629');
float_is($hit->significance, 2e-08);
is($hit->raw_score, 136 );
is($hit->bits, '57.0' );
$hsp = $hit->next_hsp;
float_is($hsp->evalue, 2e-08);
is($hsp->bits, '57.0');
is($hsp->score, 136);
is(int($hsp->percent_identity), 28);
is(sprintf("%.2f",$hsp->frac_identical('query')), 0.29);
is($hsp->frac_conserved('total'), 69/135);
is($hsp->gaps('total'), 8);
is($hsp->gaps('hit'), 6);
is($hsp->gaps('query'), 2);
is($hsp->hit->start, 342);
is($hsp->hit->end, 470);
is($hsp->query->start, 3);
is($hsp->query->end, 135);
is($hsp->query_string, 'CAAEFDFMEKETPLRYTKTXXXXXXXXXXXXXXRKIISDMWGVLAKQQTHVRKHQFDHGELVYHALQLLAYTALGILIMRLKLFLTPYMCVMASLICSRQLFGW--LFCKVHPGAIVFVILAAMSIQGSANLQTQ');
is($hsp->hit_string, 'CSAEFDFIQYSTIEKLCGTLLIPLALISLVTFVFNFVKNT-NLLWRNSEEIG----ENGEILYNVVQLCCSTVMAFLIMRLKLFMTPHLCIVAALFANSKLLGGDRISKTIRVSALVGVI-AILFYRGIPNIRQQ');
is($hsp->homology_string, 'C+AEFDF++ T + T + + +L + + ++GE++Y+ +QL T + LIMRLKLF+TP++C++A+L + +L G + + A+V VI A + +G N++ Q');
#test all the database accession number formats
$searchio = Bio::SearchIO->new(-format => 'blast',
-file => test_input_file('testdbaccnums.out'));
$result = $searchio->next_result;
is($result->algorithm_reference, 'Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
');
is($result->rid, '1036160600-011802-21377');
is($result->get_statistic('querylength'), 9);
is($result->get_statistic('effectivedblength'), 35444647);
is($result->get_statistic('effectivespace'), 319001823);
is($result->get_statistic('effectivespaceused'), 319001823);
@valid = ( ['pir||T14789','T14789','T14789','CAB53709','AAH01726'],
['gb|NP_065733.1|CYT19', 'NP_065733','CYT19'],
['emb|XP_053690.4|Cyt19','XP_053690'],
['dbj|NP_056277.2|DKFZP586L0724','NP_056277'],
['prf||XP_064862.2','XP_064862'],
['pdb|BAB13968.1|1','BAB13968'],
['sp|Q16478|GLK5_HUMAN','Q16478'],
['pat|US|NP_002079.2','NP_002079'],
['bbs|NP_079463.2|','NP_079463'],
['gnl|db1|NP_002444.1','NP_002444'],
['ref|XP_051877.1|','XP_051877'],
['lcl|AAH16829.1|','AAH16829'],
['gi|1|gb|NP_065733.1|CYT19','NP_065733'],
['gi|2|emb|XP_053690.4|Cyt19','XP_053690'],
['gi|3|dbj|NP_056277.2|DKFZP586L0724','NP_056277'],
['gi|4|pir||T14789','T14789'],
['gi|5|prf||XP_064862.2','XP_064862'],
['gi|6|pdb|BAB13968.1|1','BAB13968'],
['gi|7|sp|Q16478|GLK5_HUMAN','Q16478'],
['gi|8|pat|US|NP_002079.2','NP_002079'],
['gi|9|bbs|NP_079463.2|','NP_079463'],
['gi|10|gnl|db1|NP_002444.1','NP_002444'],
['gi|11|ref|XP_051877.1|','XP_051877'],
['gi|12|lcl|AAH16829.1|','AAH16829'],
['MY_test_ID','MY_test_ID']
);
$hit = $result->next_hit;
my $d = shift @valid;
is($hit->name, shift @$d);
is($hit->accession, shift @$d);
my @accnums = $hit->each_accession_number;
foreach my $a (@accnums) {
is($a, shift @$d);
}
$d = shift @valid;
$hit = $result->next_hit;
is($hit->name, shift @$d);
is($hit->accession, shift @$d);
is($hit->locus, shift @$d);
$hits_left = 23;
while( $hit = $result->next_hit ) {
my $d = shift @valid;
is($hit->name, shift @$d);
is($hit->accession, shift @$d);
$hits_left--;
}
is($hits_left, 0);
# Parse MEGABLAST