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Revert "buglet (bad test count), reported by George Hartzell".
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Stripping eol markers seems to be breaking tests

This reverts commit 26ecb04.
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Chris Fields committed Aug 1, 2011
1 parent 256d5d2 commit b31561a
Showing 1 changed file with 23 additions and 22 deletions.
45 changes: 23 additions & 22 deletions t/SearchIO/blast.t
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Expand Up @@ -14,7 +14,7 @@ BEGIN {
}

SKIP: {
test_skip(-tests => 4, -requires_module => 'Path::Class');
test_skip(-tests => 2, -requires_module => 'Path::Class');


my $file = Path::Class::file(test_input_file('ecolitst.bls'));
Expand All @@ -40,8 +40,8 @@ $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),
'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.
'
Expand Down Expand Up @@ -339,8 +339,8 @@ $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),
'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.
'
Expand Down Expand Up @@ -448,8 +448,8 @@ $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),
'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.
'
Expand Down Expand Up @@ -1036,8 +1036,8 @@ 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),
'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.
'
Expand All @@ -1056,8 +1056,8 @@ $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),
'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.
'
Expand Down Expand Up @@ -1115,8 +1115,8 @@ $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),
'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.
'
Expand Down Expand Up @@ -1210,8 +1210,8 @@ my @dcompare = (

is(
$r->algorithm_reference,
'Zheng Zhang, Scott Schwartz, Lukas Wagner, and Webb Miller (2000),
"A greedy algorithm for aligning DNA sequences",
'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.
'
);
Expand Down Expand Up @@ -1292,8 +1292,8 @@ $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),
'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.
'
Expand Down Expand Up @@ -1681,8 +1681,8 @@ 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),
'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.
'
Expand Down Expand Up @@ -1806,9 +1806,9 @@ 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
'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.
'
);
Expand Down Expand Up @@ -2279,3 +2279,4 @@ is( $hsp->start('query'), 3255 );
is( $hsp->start('sbjct'), 128516 );
is( $hsp->end('query'), 5720 );
is( $hsp->end('sbjct'), 131000 );

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