From f3c0f98444fa73312727d66b1b971fa41bf304a4 Mon Sep 17 00:00:00 2001 From: "Francisco J. Ossandon" Date: Thu, 7 Mar 2013 16:59:55 -0300 Subject: [PATCH] Revert "Fixed no-hit blast bug and faulty regexs, added tests" This reverts commit dc5696bd3ea191d8142a765fce81bc8f7560ba82. --- Bio/SearchIO/blast.pm | 43 ++++++++++++++++----------------- t/SearchIO/blast.t | 14 ++--------- t/data/rpsblast_no_hits.bls | 58 --------------------------------------------- 3 files changed, 23 insertions(+), 92 deletions(-) delete mode 100644 t/data/rpsblast_no_hits.bls diff --git a/Bio/SearchIO/blast.pm b/Bio/SearchIO/blast.pm index 1db03affd..03e8693dd 100644 --- a/Bio/SearchIO/blast.pm +++ b/Bio/SearchIO/blast.pm @@ -630,27 +630,6 @@ sub next_result { 'Data' => "$acc$version" } ) if $acc; - - # these elements are dropped with some multiquery reports; add - # back here - $self->element( - { - 'Name' => 'BlastOutput_db-len', - 'Data' => $self->{'_blsdb_length'} - } - ) if $self->{'_blsdb_length'}; - $self->element( - { - 'Name' => 'BlastOutput_db-let', - 'Data' => $self->{'_blsdb_letters'} - } - ) if $self->{'_blsdb_letters'}; - $self->element( - { - 'Name' => 'BlastOutput_db', - 'Data' => $self->{'_blsdb'} - } - ) if $self->{'_blsdb_letters'}; } # added check for WU-BLAST -echofilter option (bug 2388) elsif (/^>Unfiltered[+-]1$/) { @@ -676,6 +655,26 @@ sub next_result { if ( !$self->in_element('iteration') ) { $self->start_element( { 'Name' => 'Iteration' } ); } + # these elements are dropped with some multiquery reports; add + # back here + $self->element( + { + 'Name' => 'BlastOutput_db-len', + 'Data' => $self->{'_blsdb_length'} + } + ) if $self->{'_blsdb_length'}; + $self->element( + { + 'Name' => 'BlastOutput_db-let', + 'Data' => $self->{'_blsdb_letters'} + } + ) if $self->{'_blsdb_letters'}; + $self->element( + { + 'Name' => 'BlastOutput_db', + 'Data' => $self->{'_blsdb'} + } + ) if $self->{'_blsdb_letters'}; # changed 8/28/2008 to exit hit table if blank line is found after an # appropriate line @@ -758,7 +757,7 @@ sub next_result { } } - elsif (/^Database:\s*(.+?)\s*$/) { + elsif (/^Database:\s*(.+)$/) { $self->debug("blast.pm: Database: $1\n"); my $db = $1; diff --git a/t/SearchIO/blast.t b/t/SearchIO/blast.t index 23f62ed5e..861f08ed6 100644 --- a/t/SearchIO/blast.t +++ b/t/SearchIO/blast.t @@ -8,7 +8,7 @@ BEGIN { use lib '.'; use Bio::Root::Test; - test_begin(-tests => 1360); + test_begin(-tests => 1357); use_ok('Bio::SearchIO'); } @@ -1171,7 +1171,7 @@ is( $r->algorithm, 'MEGABLAST' ); is( $r->query_name, '503384' ); is( $r->query_description, '11337 bp 2 contigs' ); is( $r->query_length, 11337 ); -is( $r->database_name, 'cneoA.nt' ); +is( $r->database_name, 'cneoA.nt ' ); is( $r->database_letters, 17206226 ); is( $r->database_entries, 4935 ); is( $r->get_statistic('querylength'), 11318 ); @@ -2211,13 +2211,3 @@ $searchio = Bio::SearchIO->new( is ($searchio->next_result->algorithm_version, '2.2.25+', "testing Bug 3298"); is ($searchio->next_result->algorithm_version, '2.2.25+', "testing Bug 3298"); is ($searchio->next_result->algorithm_version, '2.2.25+', "testing Bug 3298"); - -# testing for Bug #3251 -$searchio = Bio::SearchIO->new( - '-format' => 'blast', - '-file' => test_input_file('rpsblast_no_hits.bls') -); - -is ($searchio->next_result->database_name, 'CDD.v.2.13', "testing Bug 3251"); -is ($searchio->next_result->database_name, 'CDD.v.2.13', "testing Bug 3251"); -is ($searchio->next_result->database_name, 'CDD.v.2.13', "testing Bug 3251"); diff --git a/t/data/rpsblast_no_hits.bls b/t/data/rpsblast_no_hits.bls deleted file mode 100644 index f750dec58..000000000 --- a/t/data/rpsblast_no_hits.bls +++ /dev/null @@ -1,58 +0,0 @@ -RPS-BLAST 2.2.18 [Mar-02-2008] - -Database: CDD.v.2.13 - 24,083 sequences; 5,982,884 total letters - -Searching..................................................done - -Query= lcl|YP_134044.1|Plus1 F 4437 4742 NC_006391 hypothetical -protein {Haloarcula marismortui ATCC 43049} - (101 letters) - - ***** No hits found ****** - - -Query= lcl|YP_134045.1|Plus1 F 4742 5065 NC_006391 transcription -regulator {Haloarcula marismortui ATCC 43049} - (107 letters) - - ***** No hits found ****** - - -Query= lcl|YP_134046.1|Plus1 F 5275 5808 NC_006391 hypothetical -protein {Haloarcula marismortui ATCC 43049} - (177 letters) - - ***** No hits found ****** - - - Database: CDD.v.2.13 - Posted date: Nov 8, 2007 6:30 PM - Number of letters in database: 5,982,884 - Number of sequences in database: 24,083 - -Lambda K H - 0.308 0.126 0.352 - -Gapped -Lambda K H - 0.267 0.0606 0.140 - - -Matrix: BLOSUM62 -Gap Penalties: Existence: 11, Extension: 1 -Number of Sequences: 24083 -Number of Hits to DB: 200,397,591 -Number of extensions: 14170162 -Number of successful extensions: 17150 -Number of sequences better than 1.0e-005: 6 -Number of HSP's gapped: 17124 -Number of HSP's successfully gapped: 29 -Length of database: 5,982,884 -Neighboring words threshold: 11 -Window for multiple hits: 40 -X1: 15 ( 6.7 bits) -X2: 38 (14.6 bits) -X3: 64 (24.7 bits) -S1: 40 (20.8 bits) -S2: 102 (43.3 bits) -- 2.11.4.GIT