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don't match strings that wrap lines, use fuzzy match instead
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Chris Fields committed Dec 2, 2011
1 parent 75d8f48 commit 9eb55a9
Showing 1 changed file with 15 additions and 94 deletions.
109 changes: 15 additions & 94 deletions t/SearchIO/blast.t
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Expand Up @@ -38,13 +38,8 @@ $searchio = Bio::SearchIO->new(

$result = $searchio->next_result;

is(
$result->algorithm_reference,
'Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
'
like($result->algorithm_reference,
qr/Gapped BLAST and PSI-BLAST: a new generation of protein database search/
);

is( $result->database_name, 'ecoli.aa', 'database_name()' );
Expand Down Expand Up @@ -131,10 +126,8 @@ $searchio = Bio::SearchIO->new(

$result = $searchio->next_result;

is(
$result->algorithm_reference, 'Gish, W. (1996-2000) http://blast.wustl.edu
'
);
like($result->algorithm_reference,
qr/Gish, W. \(1996-2000\)/);

is( $result->database_name, 'ecoli.aa' );
is( $result->database_letters, 1358990 );
Expand Down Expand Up @@ -337,14 +330,7 @@ $searchio = Bio::SearchIO->new(
);

$result = $searchio->next_result;
is(
$result->algorithm_reference,
'Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
'
);
like($result->algorithm_reference,qr/Gapped BLAST and PSI-BLAST/);
is( $result->database_name, 'ecoli.nt' );
is( $result->database_letters, 4662239 );
is( $result->database_entries, 400 );
Expand Down Expand Up @@ -446,14 +432,7 @@ $searchio = Bio::SearchIO->new(
);

$result = $searchio->next_result;
is(
$result->algorithm_reference,
'Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
'
);
like($result->algorithm_reference,qr/Gapped BLAST and PSI-BLAST/);
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) '
Expand Down Expand Up @@ -1034,14 +1013,7 @@ $searchio = Bio::SearchIO->new(
@expected = qw(CATH_RAT CATL_HUMAN CATL_RAT PAPA_CARPA);
my $results_left = 4;
while ( my $result = $searchio->next_result ) {
is(
$result->algorithm_reference,
'Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
'
);
like($result->algorithm_reference, qr/Gapped BLAST and PSI-BLAST/);
is( $result->query_name, shift @expected, "Multiblast query test" );
$results_left--;
}
Expand All @@ -1054,14 +1026,7 @@ $searchio = Bio::SearchIO->new(
'-file' => test_input_file('test.gcgblast')
);
$result = $searchio->next_result();
is(
$result->algorithm_reference,
'Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
'
);
like($result->algorithm_reference,qr/Gapped BLAST and PSI-BLAST/);
is( $result->query_name, '/v0/people/staji002/test.gcg' );
is( $result->algorithm, 'BLASTP' );
is( $result->algorithm_version, '2.2.1 [Apr-13-2001]' );
Expand Down Expand Up @@ -1113,14 +1078,7 @@ $searchio = Bio::SearchIO->new(
-file => test_input_file('testdbaccnums.out')
);
$result = $searchio->next_result;
is(
$result->algorithm_reference,
'Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
'
);
like($result->algorithm_reference,qr/Gapped BLAST and PSI-BLAST/);
is( $result->rid, '1036160600-011802-21377' );
is( $result->get_statistic('querylength'), 9 );
is( $result->get_statistic('effectivedblength'), 35444647 );
Expand Down Expand Up @@ -1208,13 +1166,7 @@ my @dcompare = (
]
);

is(
$r->algorithm_reference,
'Zheng Zhang, Scott Schwartz, Lukas Wagner, and Webb Miller (2000),
"A greedy algorithm for aligning DNA sequences",
J Comput Biol 2000; 7(1-2):203-14.
'
);
like($r->algorithm_reference,qr/A greedy algorithm for aligning DNA sequences/);
is( $r->algorithm, 'MEGABLAST' );
is( $r->query_name, '503384' );
is( $r->query_description, '11337 bp 2 contigs' );
Expand Down Expand Up @@ -1290,14 +1242,7 @@ $searchio = Bio::SearchIO->new(
);

$result = $searchio->next_result;
is(
$result->algorithm_reference,
'Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
'
);
like($result->algorithm_reference, qr/Gapped BLAST and PSI-BLAST/);
is( $result->database_name, '/home/peter/blast/data/swissprot.pr' );
is( $result->database_entries, 88780 );
is( $result->database_letters, 31984247 );
Expand Down Expand Up @@ -1679,14 +1624,7 @@ $searchio = Bio::SearchIO->new(
$result = $searchio->next_result;
isa_ok( $result, 'Bio::Search::Result::ResultI' );
is( $result->algorithm, 'TBLASTN' );
is(
$result->algorithm_reference,
'Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
'
);
like($result->algorithm_reference,qr/Gapped BLAST and PSI-BLAST/);
is( $result->get_statistic('querylength'), 102 );
is( $result->get_statistic('effectivedblength'), 4342 );
is( $result->get_statistic('effectivespace'), 442884 );
Expand All @@ -1700,10 +1638,7 @@ $searchio = Bio::SearchIO->new(
-format => 'blast'
);
$result = $searchio->next_result;
is(
$result->algorithm_reference, 'Gish, W. (1996-2003) http://blast.wustl.edu
'
);
like($result->algorithm_reference,qr/Gish, W. \(1996-2003\)/);
is( $result->query_name, 'mgri:MG00189.3' );
$hit = $result->next_hit;
is( $hit->name, 'mgri:MG00189.3' );
Expand Down Expand Up @@ -1804,14 +1739,7 @@ is( $result->database_entries, 3742891 );
is( $result->database_letters, 16670205594 );
is( $result->algorithm, 'BLASTN' );
is( $result->algorithm_version, '2.2.13 [Nov-27-2005]' );
is(
$result->algorithm_reference,
'Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schäffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman
(1997), "Gapped BLAST and PSI-BLAST: a new generation of
protein database search programs", Nucleic Acids Res. 25:3389-3402.
'
);
like($result->algorithm_reference, qr/Gapped BLAST and PSI-BLAST/);
is( $result->rid, '1141079027-8324-8848328247.BLASTQ4' );
is( $result->query_name, 'pyrR,' );
is( $result->query_length, 558 );
Expand Down Expand Up @@ -2132,13 +2060,7 @@ $result = $searchio->next_result;
# Parse BLAST header details
is( $result->algorithm, 'BLASTN' );
is( $result->algorithm_version, '2.2.20+' );
is(
$result->algorithm_reference,
'Zheng Zhang, Scott Schwartz, Lukas Wagner, and
Webb Miller (2000), "A greedy algorithm for aligning DNA
sequences", J Comput Biol 2000; 7(1-2):203-14.
'
);
like($result->algorithm_reference, qr/A greedy algorithm for aligning DNA\s+sequences/);
is( $result->database_name,
'human build 35 genome database (reference assembly only)' );
is( $result->database_entries, 378 );
Expand Down Expand Up @@ -2279,4 +2201,3 @@ is( $hsp->start('query'), 3255 );
is( $hsp->start('sbjct'), 128516 );
is( $hsp->end('query'), 5720 );
is( $hsp->end('sbjct'), 131000 );

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