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# -*-Perl-*- Test Harness script for Bioperl
# $Id: SearchIO_hmmer.t 14989 2008-11-11 19:52:02Z cjfields $
use strict;
BEGIN {
use lib '.';
use Bio::Root::Test;
test_begin(-tests => 300);
use_ok('Bio::SearchIO');
}
my $searchio = Bio::SearchIO->new(-format => 'hmmer',
-file => test_input_file('hmmpfam.out'));
my $result;
while( $result = $searchio->next_result ) {
is(ref($result),'Bio::Search::Result::HMMERResult', 'Check for the correct result reference type');
is($result->algorithm, 'HMMPFAM', 'Check algorithm');
is($result->algorithm_version, '2.1.1', 'Check algorithm version');
is($result->hmm_name, 'pfam', 'Check hmm_name');
is($result->sequence_file, '/home/birney/src/wise2/example/road.pep', 'Check sequence_file');
is($result->query_name, 'roa1_drome', 'Check query_name');
is($result->query_description, '', 'Check query_description');
is($result->num_hits(), 2, 'Check num_hits');
my ($hsp,$hit);
if( $hit = $result->next_model ) {
is($hit->name, 'SEED', 'Check hit name');
is($hit->raw_score, '146.1', 'Check hit raw_score');
float_is($hit->significance, 6.3e-40, 'Check hit significance');
is(ref($hit), 'Bio::Search::Hit::HMMERHit', 'Check for the correct hit reference type');
is($hit->num_hsps, 1, 'Check num_hsps');
if( defined( $hsp = $hit->next_domain ) ) {
is($hsp->hit->start, 1, 'Check for hit hmmfrom value');
is($hsp->hit->end, 77, 'Check for hit hmm to value');
is($hsp->query->start, 33, 'Check for query alifrom value');
is($hsp->query->end, 103, 'Check for query ali to value');
is($hsp->score, 71.2, 'Check for hsp score');
float_is($hsp->evalue, 2.2e-17, 'Check for hsp c-Evalue');
is($hsp->query_string, 'LFIGGLDYRTTDENLKAHFEKWGNIVDVVVMKD-----PRTKRSRGFGFITYSHSSMIDEAQK--SRpHKIDGRVVEP',
'Check for query string');
is($hsp->gaps('query'), 7, 'Check for number of gaps in query');
is($hsp->hit_string, 'lfVgNLppdvteedLkdlFskfGpivsikivrDiiekpketgkskGfaFVeFeseedAekAlealnG-kelggrklrv',
'Check for hit string');
is($hsp->homology_string, 'lf+g+L + +t+e Lk++F+k G iv++ +++D + t++s+Gf+F+++ ++ + A + +++++gr+++ ',
'Check for homology string');
is( length($hsp->homology_string), length($hsp->hit_string),
'Check if homology string and hit string have an equal lenght');
is( length($hsp->query_string), length($hsp->homology_string),
'Check if query string and homology string have an equal lenght');
}
}
if( defined ($hit = $result->next_model) ) {
if( defined($hsp = $hit->next_domain) ) {
is($hsp->hit->start, 1, 'Check for hit hmmfrom value');
is($hsp->hit->end, 77, 'Check for hit hmm to value');
is($hsp->query->start, 124, 'Check for query alifrom value');
is($hsp->query->end, 194, 'Check for query ali to value');
is($hsp->score, 75.5, 'Check for hsp score');
float_is($hsp->evalue, 1.1e-18, 'Check for hsp c-Evalue');
is($hsp->query_string, 'LFVGALKDDHDEQSIRDYFQHFGNIVDINIVID-----KETGKKRGFAFVEFDDYDPVDKVVL-QKQHQLNGKMVDV',
'Check for query string');
is($hsp->gaps('query'), 6, 'Check for number of gaps in query');
is($hsp->hit_string, 'lfVgNLppdvteedLkdlFskfGpivsikivrDiiekpketgkskGfaFVeFeseedAekAlealnGkelggrklrv',
'Check for hit string');
is($hsp->homology_string, 'lfVg L d +e+ ++d+F++fG iv+i+iv+D ketgk +GfaFVeF++++ ++k + ++l+g+ + v',
'Check for homology string');
is( length($hsp->homology_string), length($hsp->hit_string),
'Check if homology string and hit string have an equal lenght');
is( length($hsp->query_string), length($hsp->homology_string),
'Check if query string and homology string have an equal lenght');
}
last;
}
}
$searchio = Bio::SearchIO->new(-format => 'hmmer',
-file => test_input_file('hmmsearch.out'));
while( $result = $searchio->next_result ) {
is(ref($result),'Bio::Search::Result::HMMERResult', 'Check for the correct result reference type');
is($result->algorithm, 'HMMSEARCH', 'Check algorithm');
is($result->algorithm_version, '2.0', 'Check algorithm version');
is($result->hmm_name, 'HMM [SEED]', 'Check hmm_name');
is($result->sequence_file, 'HMM.dbtemp.29591', 'Check sequence_file');
is($result->database_name, 'HMM.dbtemp.29591', 'Check database_name');
is($result->query_name, 'SEED', 'Check query_name');
is($result->query_description, '', 'Check query_description');
is($result->num_hits(), 1215, 'Check num_hits');
my $hit = $result->next_model;
is($hit->name, 'Q91581', 'Check hit name');
is($hit->description,'Q91581 POLYADENYLATION FACTOR 64 KDA SUBUN', 'Check for hit description');
float_is($hit->significance, 2e-31, 'Check hit significance');
is($hit->raw_score, 119.7, 'Check hit raw_score');
my $hsp = $hit->next_domain;
is($hsp->score,119.7, 'Check for hsp score');
float_is($hsp->evalue, 2e-31, 'Check for hsp c-Evalue');
is($hsp->query->start, 18, 'Check for query alifrom value');
is($hsp->query->end, 89, 'Check for query ali to value');
is($hsp->hit->start, 1, 'Check for hit hmmfrom value');
is($hsp->hit->end, 77, 'Check for hit hmm to value');
is($hsp->query->seq_id(), 'SEED', 'Check for query seq_id');
is($hsp->hit->seq_id(), 'Q91581', 'Check for hit seq_id');
}
$searchio = Bio::SearchIO->new(-format => 'hmmer',
-file => test_input_file('L77119.hmmer'));
while( $result = $searchio->next_result ) {
is(ref($result),'Bio::Search::Result::HMMERResult', 'Check for the correct result reference type');
is($result->algorithm, 'HMMPFAM', 'Check algorithm');
is($result->algorithm_version, '2.2g', 'Check algorithm version');
is($result->hmm_name, 'Pfam', 'Check hmm_name');
is($result->sequence_file, 'L77119.faa', 'Check sequence_file');
is($result->query_name, 'gi|1522636|gb|AAC37060.1|', 'Check query_name');
is($result->query_description, 'M. jannaschii predicted coding region MJECS02 [Methanococcus jannaschii]',
'Check query_description');
is($result->num_hits(), 1, 'Check num_hits');
my $hit = $result->next_hit;
is($hit->name, 'Methylase_M', 'Check hit name');
is($hit->description,'Type I restriction modification system, M', 'Check for hit description');
float_is($hit->significance, 0.0022, 'Check hit significance');
is($hit->raw_score, -105.2, 'Check hit raw_score');
my $hsp = $hit->next_hsp;
is($hsp->score,-105.2, 'Check for hsp score');
float_is($hsp->evalue, 0.0022, 'Check for hsp evalue');
is($hsp->query->start, 280, 'Check for query alifrom value');
is($hsp->query->end, 481, 'Check for query ali to value');
is($hsp->hit->start, 1, 'Check for hit hmmfrom value');
is($hsp->hit->end, 279, 'Check for hit hmm to value');
is($hsp->query->seq_id(), 'gi|1522636|gb|AAC37060.1|', 'Check for query seq_id');
is($hsp->hit->seq_id(), 'Methylase_M', 'Check for hit seq_id');
is($hsp->hit_string, 'lrnELentLWavADkLRGsmDaseYKdyVLGLlFlKYiSdkFlerrieieerktdtesepsldyakledqyeqlededlekedfyqkkGvFilPsqlFwdfikeaeknkldedigtdldkifseledqialgypaSeedfkGlfpdldfnsnkLgskaqarnetLtelidlfselelgtPmHNG-dfeelgikDlfGDaYEYLLgkFAeneGKsGGeFYTPqeVSkLiaeiLtigqpsegdfsIYDPAcGSGSLllqaskflgehdgkrnaisyYGQEsn',
'Check for hiy string');
is($hsp->query_string, 'NTSELDKKKFAVLLMNR--------------LIFIKFLEDK------GIV---------PRDLLRRTYEDY---KKSNVLI-NYYDAY-L----KPLFYEVLNTPEDER--KENIRT-NPYYKDIPYL---N-G-------GLFRSNNV--PNELSFTIKDNEIIGEVINFLERYKFTLSTSEGsEEVELNP-DILGYVYEKLINILAEKGQKGLGAYYTPDEITSYIAKNT-IEPIVVE----------------RFKEIIK--NWKINDINF----ST',
'Check for query string');
is($hsp->homology_string, ' ++EL+++ av+ R L+F K++ dk +i+ p + + +++y ++ ++ ++y ++ + lF++++ e ++ ++++ + + ++ + + Glf ++++ ++ +s+ +ne ++e+i+ +++ +++ G++ +el D++G +YE L+ Ae K+ G +YTP e++ ia+ + i+ ++ +++ ++ k+n+i + s+',
'Check for homology string');
is(join(' ', $hsp->seq_inds('query', 'nomatch',1)), '280 288 289 293-295 300 304 311 313-315 317 324-326 332 335 337 344-346 348 355 358-361 364-366 372 379 383-385 389 396 400 404-408 412 416 417 422 426 429-431 434-436 439 441 446 450 451 455 459 460 463 464 468 471 472 478',
'Check for nomatch indices in query');
is(join(' ', $hsp->seq_inds('hit', 'nomatch',1)), '1 9 10 14-16 18-31 35 39 42-47 51-59 61 63-65 67 72-74 77-79 82 86 89-94 96 103-105 107 110 111 116 118 120-123 126-131 133 135-141 145 150 151 154 158-160 164 171 175 179-183 187 191-193 198 202 205-207 210-212 215 217 222 226 227 231 233 236 237 240-257 261 264-267 273 275-278',
'Check for nomatch indices in hit');
is(join(' ', $hsp->seq_inds('query', 'gap',1)), '296 306 309 321 328 334 335 350 356 366-368 376 417 456 463 470 479',
'Check for gap indices in query');
is(join(' ', $hsp->seq_inds('hit', 'gap',1)), '', 'Check for gap indices in hit');
}
$searchio = Bio::SearchIO->new(-format => 'hmmer',
-file => test_input_file('cysprot1b.hmmsearch'));
while( $result = $searchio->next_result ) {
is(ref($result),'Bio::Search::Result::HMMERResult', 'Check for the correct result reference type');
is($result->algorithm, 'HMMSEARCH', 'Check algorithm');
is($result->algorithm_version, '2.2g', 'Check algorithm version');
is($result->hmm_name, 'Peptidase_C1.hmm [Peptidase_C1]', 'Check hmm_name');
is($result->database_name, 'cysprot1b.fa', 'Check database_name');
is($result->sequence_file, 'cysprot1b.fa', 'Check sequence_file');
is($result->query_name, 'Peptidase_C1', 'Check query_name');
is($result->query_accession, 'PF00112', 'Check query_accession');
is($result->query_description, 'Papain family cysteine protease', 'Check query_description');
is($result->num_hits(), 4, 'Check num_hits');
my $hit = $result->next_hit;
is($hit->name, 'CATL_RAT', 'Check hit name');
is($hit->description,'', 'Check for hit description');
float_is($hit->significance, 2e-135, 'Check hit significance');
is($hit->raw_score, 449.4, 'Check hit raw_score');
my $hsp = $hit->next_hsp;
is($hsp->score,449.4, 'Check for hsp score');
float_is($hsp->evalue, 2e-135, 'Check for hsp evalue');
is($hsp->query->start, 1, 'Check for query alifrom value');
is($hsp->query->end, 337, 'Check for query ali to value');
is($hsp->hit->start, 114, 'Check for hit hmmfrom value');
is($hsp->hit->end, 332, 'Check for hit hmm to value');
is($hsp->query->seq_id(), 'Peptidase_C1', 'Check for query seq_id');
is($hsp->hit->seq_id(), 'CATL_RAT', 'Check for hit seq_id');
is($hsp->hit_string, 'IPKTVDWRE-KG-CVTPVKNQG-QCGSCWAFSASGCLEGQMFLKT------GKLISLSEQNLVDCSH-DQGNQ------GCNG-GLMDFAFQYIKE-----NGGLDSEESY-----PYE----AKD-------------------GSCKYR-AEYAV-----ANDTGFVDIPQQ-----EKALMKAVATVGPISVAMDASHPS---LQFYSSG-------IYYEP---NCSSK---DLDHGVLVVGYGYEG-T------------------------------------DSNKDKYWLVKNSWGKEWGMDGYIKIAKDRN----NHCGLATAASYPI',
'Check for hiy string');
is($hsp->homology_string, '+P+++DWRe kg VtpVK+QG qCGSCWAFSa g lEg+ ++kt gkl+sLSEQ+LvDC++ d gn+ GCnG Glmd Af+Yik+ NgGl++E++Y PY+ +kd g+Cky+ + ++ a+++g++d+p++ E+al+ka+a++GP+sVa+das+ s q+Y+sG +Y+++ C+++ +LdH+Vl+VGYG e+ ++++ +YW+VKNSWG++WG++GY++ia+++n n+CG+a+ asypi',
'Check for homology string');
is($hsp->query_string, 'lPesfDWReWkggaVtpVKdQGiqCGSCWAFSavgalEgryciktgtkawggklvsLSEQqLvDCdgedygnngesCGyGCnGGGlmdnAfeYikkeqIsnNgGlvtEsdYekgCkPYtdfPCgkdggndtyypCpgkaydpndTgtCkynckknskypktyakikgygdvpynvsTydEealqkalaknGPvsVaidasedskgDFqlYksGendvgyGvYkhtsageCggtpfteLdHAVliVGYGteneggtfdetssskksesgiqvssgsngssgSSgssgapiedkgkdYWIVKNSWGtdWGEnGYfriaRgknksgkneCGIaseasypi',
'Check for query string');
$hit = $result->next_hit;
is($hit->name, 'CATL_HUMAN', 'Check hit name');
is($hit->description,'', 'Check for hit description');
float_is($hit->significance, 6.1e-134, 'Check hit significance');
is($hit->raw_score, 444.5, 'Check hit raw_score');
}
# test for bug 2632 - CS lines should get ignored without breaking the parser
$searchio = Bio::SearchIO->new(-format => 'hmmer', -file => test_input_file('hmmpfam_cs.out'));
$result = $searchio->next_result;
my $hit = $result->next_hit;
my $hsp = $hit->next_hsp;
is($hsp->seq_str, 'CGV-GFIADVNNVANHKIVVQALEALTCMEHRGACSADRDSGDGAGITTAIPWNLFQKSLQNQNIKFEQnDSVGVGMLFLPAHKLKES--KLIIETVLKEENLEIIGWRLVPTVQEVLGKQAYLNKPHVEQVFCKSSNLSKDRLEQQLFLVRKKIEKYIGINGKDwaheFYICSLSCYTIVYKGMMRSAVLGQFYQDLYHSEYTSSFAIYHRRFSTNTMPKWPLAQPMR---------FVSHNGEINTLLGNLNWMQSREPLLQSKVWKDRIHELKPITNKDNSDSANLDAAVELLIASGRSPEEALMILVPEAFQNQPDFA-NNTEISDFYEYYSGLQEPWDGPALVVFTNGKV-IGATLDRNGL-RPARYVIT----KDNLVIVSSES',
'Check for hsp seq_str');
# Tests for hmmer3 output here
$searchio = Bio::SearchIO->new(-format => 'hmmer',
-file => test_input_file('hmmscan.out'),
-verbose => 1);
is(ref($searchio), 'Bio::SearchIO::hmmer3', 'Check if correct searchio object is returned');
while( $result = $searchio->next_result ) {
is(ref($result),'Bio::Search::Result::HMMERResult', 'Check for the correct result reference type');
is($result->algorithm, 'HMMSCAN', 'Check algorithm');
is($result->algorithm_version, '3.0', 'Check algorithm version');
is($result->hmm_name, '/data/biodata/HMMerDB/Pfam.hmm', 'Check hmm_name');
is($result->sequence_file, 'BA000019.orf1.fasta', 'Check sequence_file');
is($result->query_name, 'BA000019.orf1', 'Check query_name');
is($result->query_length, '198', 'Check query_length');
is($result->query_description, '', 'Check query_description');
is($result->num_hits(), 1, 'Check num_hits');
my ($hsp,$hit);
if( $hit = $result->next_model ) {
is(ref($hit), 'Bio::Search::Hit::HMMERHit', 'Check for the correct hit reference type');
is($hit->name, 'Peripla_BP_2', 'Check hit name');
is($hit->description, 'Periplasmic binding protein', 'Check for hit description');
is($hit->raw_score, '105.2', 'Check hit raw_score');
float_is($hit->significance, 6e-30, 'Check hit significance');
is($hit->num_hsps, 1, 'Check num_hsps');
if( defined( $hsp = $hit->next_domain ) ) {
is(ref($hsp), 'Bio::Search::HSP::HMMERHSP', 'Check for correct hsp reference type');
is($hsp->hit->start, 59, 'Check for hit hmmfrom value');
is($hsp->hit->end, 236, 'Check for hit hmm to value');
is($hsp->query->start, 2, 'Check for query alifrom value');
is($hsp->query->end, 173, 'Check for query ali to value');
is($hsp->score, '105.0', 'Check for hsp score');
float_is($hsp->evalue, 1.5e-33, 'Check for hsp c-Evalue');
is($hsp->query_string, 'LKPDLIIGREYQ---KNIYNQLSNFAPTVLVDWGSF-TSFQDNFRYIAQVLNEEEQGKLVLQQYQKRIRDLQDRMGERlQKIEVSVIGFSGQSIKSLNR-DAVFNQVLDDAGIKRIsIQKNQQERYLEISIENLNKYDADVLFVINE---SKEQLYPDLKNPLWHHLRAVKKQQVYVVNQ', 'Check for query string');
is($hsp->hit_string, 'lkPDlvivsafgalvseieellelgipvvavessstaeslleqirllgellgeedeaeelvaelesridavkaridsl-kpktvlvfgyadegikvvfgsgswvgdlldaaggeni-iaeakgseseeisaEqilaadpdviivsgrgedtktgveelkenplwaelpAvkngrvyllds', 'Check for hit string');
is($hsp->homology_string, 'lkPDl+i+ +++ ++i+++l++ +p+v v+ s+ s+++ +r ++++l+ee++++ + +++++ri+++++r + ++ +v+v+g+++ +ik+++ + ++++ld+ag++ i i++++++ + eis+E+++++d+dv++v k+ + ++nplw +l+Avk+++vy++++', 'Check for homology string');
}
}
}
$searchio = Bio::SearchIO->new(-format => 'hmmer',
-file => test_input_file('hmmsearch3.out'),
-verbose => 1);
while( $result = $searchio->next_result ) {
is(ref($result),'Bio::Search::Result::HMMERResult', 'Check for the correct result reference type');
is($result->algorithm, 'HMMSEARCH', 'Check algorithm');
is($result->algorithm_version, '3.0', 'Check algorithm version');
is($result->hmm_name, 'Kv9.hmm', 'Check hmm_name');
is($result->sequence_file, '/home/pboutet/Desktop/databases/nr_May26', 'Check sequence_file');
is($result->query_name, 'Kv9', 'Check query_name');
is($result->query_length, '481', 'Check query_length');
is($result->query_description, '', 'Check query_description');
is($result->num_hits(), 2, 'Check num_hits');
while( my $hit = $result->next_model ) {
}
}
$searchio = Bio::SearchIO->new(-format => 'hmmer',
-file => test_input_file('hmmscan_multi_domain.out'),
-verbose => 1);
my @multi_hits = (
['PPC', 'Bacterial pre-peptidase C-terminal domain', '111.0', 3.1e-32, 6,
[[4, 59, 117, 183, 0.5, 0.16], [12, 58, 347, 388, -0.6, 0.36],
[1, 69, 470, 549, 71.3, 1.3e-23], [15, 25, 582, 603, -3.2, 2],
[13, 36, 987, 1019, -1.1, 0.5], [1, 69, 1087, 1168, 54.4, 2.4e-18]]],
['HemolysinCabind', 'Hemolysin-type calcium-binding repeat (2 cop', '47.9', 4.7e-13, 3,
[[2, 13, 1214, 1225, 5.9, 0.0026], [1, 18, 1231, 1248, 10.8, 6.8e-5],
[4, 18, 1243, 1257, 11.4, 4.3e-05]]]
);
while( $result = $searchio->next_result ) {
is(ref($result),'Bio::Search::Result::HMMERResult', 'Check for the correct result reference type');
is($result->algorithm, 'HMMSCAN', 'Check algorithm');
is($result->algorithm_version, '3.0', 'Check algorithm version');
is($result->hmm_name, '/data/biodata/HMMerDB/Pfam-A.hmm', 'Check hmm_name');
is($result->sequence_file, 'BA000019.orf37.fasta', 'Check sequence_file');
is($result->query_name, 'BA000019.orf37', 'Check query_name');
is($result->query_length, '1418', 'Check query_length');
is($result->query_description, '', 'Check query_description');
is($result->num_hits(), 2, 'Check num_hits');
my ($hsp,$hit);
while( $hit = $result->next_model ) {
my @expected = @{shift @multi_hits};
is(ref($hit), 'Bio::Search::Hit::HMMERHit', 'Check for the correct hit reference type');
is($hit->name, shift @expected, 'Check hit name');
is($hit->description, shift @expected, 'Check for hit description');
is($hit->raw_score, shift @expected, 'Check hit raw_score');
float_is($hit->significance, shift @expected, 'Check hit significance');
is($hit->num_hsps, shift @expected, 'Check num_hsps');
my @hsp_list = @{shift @expected};
while( defined( $hsp = $hit->next_domain ) ) {
my @hsp_exp = @{shift @hsp_list};
is(ref($hsp), 'Bio::Search::HSP::HMMERHSP', 'Check for correct hsp reference type');
is($hsp->hit->start, shift @hsp_exp, 'Check for hit envfrom value');
is($hsp->hit->end, shift @hsp_exp, 'Check for hit env to value');
is($hsp->query->start, shift @hsp_exp, 'Check for query hmmfrom value');
is($hsp->query->end, shift @hsp_exp, 'Check for query hmm to value');
is($hsp->score, shift @hsp_exp, 'Check for hsp score');
float_is($hsp->evalue, shift @hsp_exp, 'Check for hsp c-Evalue');
}
}
}
$searchio = Bio::SearchIO->new(-format => 'hmmer',
-file => test_input_file('hmmscan_sec_struct.out'),
-verbose => 1);
@multi_hits = (
['HTH_AraC', 'Bacterial regulatory helix-turn-helix proteins, Ara', '41.3', 6.7e-11, 2,
[['siadiAeevgfSpsyfsrlFkkytGvt', 'SLMELSRQVGLNDCTLKRGFRLVFDTT'],
['nwsiadiAeevgf-SpsyfsrlFkkytGvtPsqyr', 'EINISQAARRVGFsSRSYFATAFRKKFGINPKEFL']]],
['PKSI-KS_m3', '', '38.2', 3.8e-12, 2,
[['GPSvtVDTACSSSLvA', 'GPSVTVDTLCSSSLVA'],
['GPSvtVDTACSSSLv', 'GPNLVIDSACSSALV']]],
['DUF746', 'Domain of Unknown Function (DUF746)', '13.9', 0.023, 2,
[['rllIrlLsqplslaeaadqlgtdegiiak', 'EILIRNLENPPSLMELSRQVGLNDCTLKR'],
['plslaeaadqlgtdeg', 'EINISQAARRVGFSSR']]]
);
while( $result = $searchio->next_result ) {
is(ref($result),'Bio::Search::Result::HMMERResult', 'Check for the correct result reference type');
is($result->algorithm, 'HMMSCAN', 'Check algorithm');
is($result->algorithm_version, '3.0', 'Check algorithm version');
is($result->hmm_name, 'Pfam-A.hmm', 'Check hmm_name');
is($result->sequence_file, 'BA000019.orf8.fasta', 'Check sequence_file');
is($result->query_name, 'BA000019.orf8', 'Check query_name');
is($result->query_length, '348', 'Check query_length');
is($result->query_description, '', 'Check query_description');
is($result->num_hits(), 3, 'Check num_hits');
my ($hsp,$hit);
while( $hit = $result->next_model ) {
my @expected = @{shift @multi_hits};
is(ref($hit), 'Bio::Search::Hit::HMMERHit', 'Check for the correct hit reference type');
is($hit->name, shift @expected, 'Check hit name');
is($hit->description, shift @expected, 'Check for hit description');
is($hit->raw_score, shift @expected, 'Check hit raw_score');
float_is($hit->significance, shift @expected, 'Check hit significance');
is($hit->num_hsps, shift @expected, 'Check num_hsps');
my @hsp_list = @{shift @expected};
while( defined( $hsp = $hit->next_domain ) ) {
my @hsp_exp = @{shift @hsp_list};
is(ref($hsp), 'Bio::Search::HSP::HMMERHSP', 'Check for correct hsp reference type');
is($hsp->hit_string, shift @hsp_exp, 'Check hit sequence');
is($hsp->query_string, shift @hsp_exp, 'Check query sequence');
}
}
}
# Make sure that you can also directly call the hmmer2 and hmmer3 subclasses
$searchio = Bio::SearchIO->new(-format => 'hmmer2',
-file => test_input_file('hmmpfam.out'));
is(ref($searchio), 'Bio::SearchIO::hmmer2', 'Check if loading hmmpfam output via the hmm2 parser directly works');
is(ref($searchio->next_result), 'Bio::Search::Result::HMMERResult', 'Check for the correct result reference type');
$searchio = Bio::SearchIO->new(-format => 'hmmer2',
-file => test_input_file('hmmsearch.out'));
is(ref($searchio), 'Bio::SearchIO::hmmer2', 'Check if loading hmmsearch2 output via the hmm2 parser directly works');
is(ref($searchio->next_result), 'Bio::Search::Result::HMMERResult', 'Check for the correct result reference type');
$searchio = Bio::SearchIO->new(-format => 'hmmer3',
-file => test_input_file('hmmscan.out'));
is(ref($searchio), 'Bio::SearchIO::hmmer3', 'Check if loading hmmscan output via the hmm3 parser directly works');
is(ref($searchio->next_result), 'Bio::Search::Result::HMMERResult', 'Check for the correct result reference type');
$searchio = Bio::SearchIO->new(-format => 'hmmer',
-file => test_input_file('hmmsearch3.out'));
is(ref($searchio), 'Bio::SearchIO::hmmer3', 'Check if loading hmmsearch3 output via the hmm3 parser directly works');
is(ref($searchio->next_result), 'Bio::Search::Result::HMMERResult', 'Check for the correct result reference type');
# Make sure that you can also specify the -version parameter directly
$searchio = Bio::SearchIO->new(-format => 'hmmer',
-file => test_input_file('hmmpfam.out'),
-version => 2);
is(ref($searchio), 'Bio::SearchIO::hmmer2', 'Check if selecting the correct hmmpfam parser using -version works');
is(ref($searchio->next_result), 'Bio::Search::Result::HMMERResult', 'Check for the correct result reference type');
$searchio = Bio::SearchIO->new(-format => 'hmmer',
-file => test_input_file('hmmsearch.out'),
-version => 2);
is(ref($searchio), 'Bio::SearchIO::hmmer2', 'Check if selecting the correct hmmsearch2 parser using -version works');
is(ref($searchio->next_result), 'Bio::Search::Result::HMMERResult', 'Check for the correct result reference type');
$searchio = Bio::SearchIO->new(-format => 'hmmer3',
-file => test_input_file('hmmscan.out'),
-version => 3);
is(ref($searchio), 'Bio::SearchIO::hmmer3', 'Check if selecting the correct hmmscan parser using -version works');
is(ref($searchio->next_result), 'Bio::Search::Result::HMMERResult', 'Check for the correct result reference type');
$searchio = Bio::SearchIO->new(-format => 'hmmer',
-file => test_input_file('hmmsearch3.out'),
-version => 3);
is(ref($searchio), 'Bio::SearchIO::hmmer3', 'Check if selecting the correct hmmsearch3 parser using -version works');
is(ref($searchio->next_result), 'Bio::Search::Result::HMMERResult', 'Check for the correct result reference type');
my $pipestr = "cat " . test_input_file('hmmpfam.out') . " |";
open(my $pipefh, $pipestr);
$searchio = Bio::SearchIO->new(-format => 'hmmer',
-fh => $pipefh);
is(ref($searchio), 'Bio::SearchIO::hmmer2', 'Check if reading from a pipe works');
$result = $searchio->next_result;
is(ref($result), 'Bio::Search::Result::HMMERResult', 'Check for the correct result reference type');
is($result->num_hits(), 2, 'Check num_hits');
# bug 3376
{
my $in = Bio::SearchIO->new(-format => 'hmmer',
-file => test_input_file('pfamOutput-bug3376.out')
);
my $result = $in->next_result;
my $hit = $result->next_hit;
my $hsp = $hit->next_hsp;
is($hsp->hit_string,"svfqqqqssksttgstvtAiAiAigYRYRYRAvtWnsGsLssGvnDnDnDqqsdgLYtiYYsvtvpssslpsqtviHHHaHkasstkiiikiePr","bug3376");
}
# end bug 3376
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