Permalink
Browse files

squash warning

  • Loading branch information...
1 parent 7fc3bd3 commit c7e345450455b4833abc1c3b5353ab3a04127e57 Chris Fields committed Feb 19, 2013
Showing with 15 additions and 15 deletions.
  1. +15 −15 t/SeqIO/genbank.t
View
@@ -6,9 +6,9 @@ use strict;
BEGIN {
use lib '.';
use Bio::Root::Test;
-
+
test_begin(-tests => 281 );
-
+
use_ok('Bio::SeqIO::genbank');
}
@@ -392,24 +392,24 @@ my $outfile = test_output_file();
foreach my $in ('BK000016-tpa.gbk', 'ay116458.gb', 'ay149291.gb', 'NC_006346.gb', 'ay007676.gb', 'dq519393.gb') {
my $infile = test_input_file($in);
-
+
$str = Bio::SeqIO->new(-format =>'genbank',
-verbose => $verbose,
-file => $infile);
$seq = $str->next_seq;
-
+
$out = Bio::SeqIO->new(-file => ">$outfile", -format => 'genbank');
$out->write_seq($seq);
$out->close();
-
+
open (IN, $infile);
my @in = <IN>;
close(IN);
open (RESULT, $outfile);
my $line = 0;
my $check = 0;
my $is = 1;
-
+
FILECHECK:
while (my $result = <RESULT>) {
if ($result =~ /^KEYWORDS/) {
@@ -422,19 +422,19 @@ foreach my $in ('BK000016-tpa.gbk', 'ay116458.gb', 'ay149291.gb', 'NC_006346.gb'
}
if ($check) {
-
+
# end periods don't count (not all input files have them)
$result =~ s{\.$}{};
$in[$line] =~ s{\.$}{};
-
+
if ($result ne $in[$line]) {
$is = 0;
last;
}
}
} continue { $line++ }
close(RESULT);
-
+
ok $is, $in;
}
@@ -481,15 +481,15 @@ foreach my $in ('P35527.gb') {
}
ok ( $parts[1], "$parts[0]" );
}
-
+
}
}
}
is($ct, 46);
# bug 2195
-
+
$str = Bio::SeqIO->new(-format =>'genbank',
-verbose => $verbose,
-file => test_input_file('AF305198.gb')
@@ -504,7 +504,7 @@ is(join(', ',$species->classification), 'Virginia creeper phytoplasma, '.
'Firmicutes, Bacteria', 'Bug 2195');
# bug 2569, PROJECT line support, read and write, round-tripping
-
+
$str = Bio::SeqIO->new(-format =>'genbank',
-verbose => $verbose,
-file => test_input_file('NC_008536.gb'));
@@ -573,7 +573,7 @@ is($dblinks[0]->display_text, 'UniProtKB:PYRR_BACSU','operator overloading in An
#bug 2982 embl/genbank contig handling
-$ast = Bio::SeqIO->new( -file => test_input_file('bug2982.gb'),
+$ast = Bio::SeqIO->new( -file => test_input_file('bug2982.gb'),
-format => 'genbank' );
$seq = $ast->next_seq;
@@ -606,8 +606,8 @@ is(scalar @notes, 2);
#bug 3375
my $in = Bio::SeqIO->new(-format => 'genbank',
-file => test_input_file('NC_002058_multDBLINK_bug3375.gb'));
-my $seq = $in->next_seq(); # should not throw a warning now
-my @dblinks = $seq->annotation->get_Annotations('dblink'); # contains 5 dblink references
+$seq = $in->next_seq(); # should not throw a warning now
+@dblinks = $seq->annotation->get_Annotations('dblink'); # contains 5 dblink references
# testing DBLINK BioProject: PRJNA15288
is($dblinks[0]->database, 'BioProject', 'bug3375 database is BioProject');
is($dblinks[0]->primary_id, 'PRJNA15288', 'bug3375 primary_id is PRJNA15288');

0 comments on commit c7e3454

Please sign in to comment.