Initialize Bio::SeqIO object throught the seqio() method instead of n…

…ext_read() and not no initialize Bio::SeqIO before we have reached the ##FASTA section of the GFF stream
bioperl · Oct 10, 2011 · bab00a6 · bab00a6
1 parent 3d9043a
commit bab00a6
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Showing 2 changed files with 21 additions and 14 deletions.
diff --git a/Bio/FeatureIO/gff.pm b/Bio/FeatureIO/gff.pm
@@ -241,7 +241,7 @@ sub next_feature_group {
 
  Usage   : $featureio->next_seq( );
  Function: access the FASTA section (if any) at the end of the GFF stream. Note
-           that this method will return undef until all the features in the GFF
+           that this method will return undef before all the features in the GFF
            stream have been handled.
  Returns : a Bio::SeqI object or undef
  Args    : none
@@ -250,12 +250,7 @@ sub next_feature_group {
 
 sub next_seq() {
   my $self = shift;
-  return unless $self->fasta_mode();
-
-  #first time next_seq has been called.  initialize Bio::SeqIO instance
-  if(!$self->seqio){
-    $self->seqio( Bio::SeqIO->new(-format => 'fasta', -fh => $self->_fh()) );
-  }
+  return undef unless $self->fasta_mode();
   return $self->seqio->next_seq();
 }
 
@@ -326,20 +321,28 @@ sub fasta_mode {
 =head2 seqio()
 
  Usage   : $obj->seqio($newval)
- Function: get/set a Bio::SeqIO instance for handling the GFF3 ##FASTA section.
-           Note that this method will return undef until all the features in the 
-           GFF stream have been handled.
- Returns : value of seqio (a scalar) or undef
+ Function: get/set a Bio::SeqIO instance to handle the GFF3 ##FASTA section.
+ Returns : a Bio::SeqIO object or undef
  Args    : on set, new value (a scalar or undef, optional)
 
 =cut
 
 sub seqio {
   my($self,$val) = @_;
-  $self->{'seqio'} = $val if defined($val);
+ if (defined $val) {
+    $self->{'seqio'} = $val;
+  } else {
+    # Cannot get seqio before we've reached the ##FASTA section
+    return undef unless $self->fasta_mode();
+    if (not defined $self->{'seqio'}) {
+      # Initialize Bio::SeqIO instance
+      $self->{'seqio'} = Bio::SeqIO->new(-format => 'fasta', -fh => $self->_fh());
+    }
+  }
   return $self->{'seqio'};
 }
 
+
 =head2 sequence_region()
 
  Usage   :

diff --git a/t/SeqFeature/FeatureIO.t b/t/SeqFeature/FeatureIO.t
@@ -7,8 +7,8 @@ BEGIN {
     use lib '.';
     use Bio::Root::Test;
 
-    test_begin(-tests => 47,
-	       -requires_module => 'Graph');
+    test_begin(-tests => 50,
+               -requires_module => 'Graph');
 
     use_ok('Bio::FeatureIO');
 }
@@ -35,6 +35,7 @@ while($f = $io->next_feature()){
 }
 is($fcount, 0);
 
+
 #then try to read sequences again.  should get seqs now
 while($s = $io->next_seq()){
     $scount++;
@@ -84,6 +85,7 @@ $scount = 0;
 ok( $io = Bio::FeatureIO->new( -file => test_input_file('hybrid1.gff3') ) );
 
 #try to read sequences first.  should be undef
+is $io->seqio, undef;
 while($s = $io->next_seq()){
     $scount++;
 }
@@ -96,8 +98,10 @@ while($f = $io->next_feature()){
 is($fcount , 6);
 
 #then try to read sequences again.
+isa_ok $io->seqio, 'Bio::SeqIO';
 while($s = $io->next_seq()){
     $scount++;
+    isa_ok $s, 'Bio::Seq';
     TODO: {
 	local $TODO = 'How did this ever work?!?';
 	if ($scount == 1) {