Fixed some undefined warnings in SeqIO::embl

bioperl · Feb 28, 2012 · 65261c6 · 65261c6
1 parent 2bc6058
commit 65261c6
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Showing 2 changed files with 38 additions and 38 deletions.
diff --git a/Bio/SeqIO/embl.pm b/Bio/SeqIO/embl.pm
@@ -215,26 +215,26 @@ sub next_seq {
         # ID   DQ299383; SV 1; linear; mRNA; STD; MAM; 431 BP.
         # This regexp comes from the new2old.pl conversion script, from EBI
         if ($line =~ m/^ID   (\w+);\s+SV (\d+); (\w+); ([^;]+); (\w{3}); (\w{3}); (\d+) BP./) {
-        ($name, $sv, $topology, $mol, $div) = ($1, $2, $3, $4, $6);
+            ($name, $sv, $topology, $mol, $div) = ($1, $2, $3, $4, $6);
         }
-        if (defined($sv)) {
-        $params{'-seq_version'} = $sv;
-        $params{'-version'} = $sv;
+        if (defined $sv) {
+            $params{'-seq_version'} = $sv;
+            $params{'-version'} = $sv;
         }
 
-        if ($topology eq "circular") {
-        $params{'-is_circular'} = 1;
+        if (defined $topology && $topology eq 'circular') {
+            $params{'-is_circular'} = 1;
         }
 
-    if (defined $mol ) {
-        if ($mol =~ /DNA/) {
-        $alphabet='dna';
-        } elsif ($mol =~ /RNA/) {
-        $alphabet='rna';
-        } elsif ($mol =~ /AA/) {
-        $alphabet='protein';
+        if (defined $mol ) {
+            if ($mol =~ /DNA/) {
+                $alphabet = 'dna';
+            } elsif ($mol =~ /RNA/) {
+                $alphabet = 'rna';
+            } elsif ($mol =~ /AA/) {
+                $alphabet = 'protein';
+            }
         }
-    }
     } else {
 
         # Old style header (EMBL Release < 87, before June 2006)

diff --git a/t/SeqIO/embl.t b/t/SeqIO/embl.t
@@ -4,20 +4,20 @@
 use strict;
 
 BEGIN {
-	use lib '.';
-	use lib '../..';
-	use Bio::Root::Test;
-	
-	test_begin(-tests => 96);
-	
+    use lib '.';
+    use lib '../..';
+    use Bio::Root::Test;
+
+    test_begin(-tests => 96);
+
     use_ok('Bio::SeqIO::embl');
 }
 
 my $verbose = test_debug();
 
 my $ast = Bio::SeqIO->new( -format => 'embl',
-			   -verbose => $verbose,
-			   -file => test_input_file('roa1.dat'));
+                           -verbose => $verbose,
+                           -file => test_input_file('roa1.dat'));
 $ast->verbose($verbose);
 my $as = $ast->next_seq();
 ok defined $as->seq;
@@ -35,8 +35,8 @@ is($as->species->binomial(), 'Homo sapiens');
 # EMBL Release 87 changes (8-17-06)
 
 $ast = Bio::SeqIO->new( -format => 'embl',
-			   -verbose => $verbose,
-			   -file => test_input_file('roa1_v2.dat'));
+                        -verbose => $verbose,
+                        -file => test_input_file('roa1_v2.dat'));
 $ast->verbose($verbose);
 $as = $ast->next_seq();
 ok defined $as->seq;
@@ -54,7 +54,7 @@ is($as->length, 1198);
 is($as->species->binomial(), 'Homo sapiens');
 
 my $ent = Bio::SeqIO->new( -file => test_input_file('test.embl'),
-			   -format => 'embl');
+                           -format => 'embl');
 my $seq = $ent->next_seq();
 
 is(defined $seq->seq(), 1,
@@ -63,27 +63,27 @@ is(scalar $seq->annotation->get_Annotations('reference'), 3);
 
 my $out_file = test_output_file();
 my $out = Bio::SeqIO->new(-file=> ">$out_file",
-			  -format => 'embl');
+                          -format => 'embl');
 is($out->write_seq($seq),1,
    'success writing Embl format with ^ < and > locations');
 
 # embl with no FT
 $ent = Bio::SeqIO->new( -file => test_input_file('test.embl'),
-			-format => 'embl');
+                        -format => 'embl');
 $seq = $ent->next_seq();
 
 ok($seq);
 is(lc($seq->subseq(1,10)),'gatcagtaga');
 is($seq->length, 4870);
 
 # embl with no FH
-my $noFH = Bio::SeqIO->new(-file => test_input_file('no_FH.embl'),
-			-format => 'embl');
+my $noFH = Bio::SeqIO->new( -file => test_input_file('no_FH.embl'),
+                            -format => 'embl');
 is(scalar($noFH->next_seq->get_SeqFeatures), 4);
 
 # bug 1571
-$ent = Bio::SeqIO->new(-format => 'embl',
-		       -file   => test_input_file('test.embl2sq'));
+$ent = Bio::SeqIO->new( -format => 'embl',
+                        -file   => test_input_file('test.embl2sq'));
 is($ent->next_seq->length,4877);
 
 # embl repbase
@@ -92,8 +92,8 @@ $seq = $ent->next_seq;
 is($seq->display_id,'BEL16-LTR_AG');
 
 # test secondary accessions in EMBL (bug #1332)
-my $seqio = Bio::SeqIO->new(-format => 'embl',
-			   -file => test_input_file('ECAPAH02.embl'));
+my $seqio = Bio::SeqIO->new( -format => 'embl',
+                             -file => test_input_file('ECAPAH02.embl'));
 $seq = $seqio->next_seq;
 is($seq->accession_number, 'D10483');
 is($seq->seq_version, 2);
@@ -104,8 +104,8 @@ is($accs[-1], 'X56742');
 ### TPA TESTS - Thanks to Richard Adams ###
 # test Third Party Annotation entries in EMBL/Gb format 
 # to ensure compatability with parsers.
-my $str = Bio::SeqIO->new(-format =>'embl',
-			 -file => test_input_file('BN000066-tpa.embl'));
+my $str = Bio::SeqIO->new( -format =>'embl',
+                           -file => test_input_file('BN000066-tpa.embl'));
 $seq = $str->next_seq;
 ok(defined $seq);
 is($seq->accession_number, 'BN000066');
@@ -163,7 +163,7 @@ ok($embl->write_seq($primaryseq));
 # this should generate a warning
 my $scalar = "test";
 eval {
-	$embl->write_seq($scalar);
+    $embl->write_seq($scalar);
 };
 ok ($@);
 
@@ -192,8 +192,8 @@ is($cds_dblink->primary_id, '9606', 'CDS - OX primary_id');
 
 #bug 2982 - parsing contig descriptions sans sequence data
 
-ok( $embl = Bio::SeqIO->new(-file => test_input_file('bug2982.embl'),
-			    -format => 'embl') );
+ok( $embl = Bio::SeqIO->new( -file => test_input_file('bug2982.embl'),
+                             -format => 'embl') );
 my $i;
 for ($i=0; my $seq = $embl->next_seq; $i++) {
     ok !$seq->seq;