[Bioperl-guts-l] bioperl-live/Bio/SeqIO scf.pm,1.40,1.41

Christopher John Fields cjfields at dev.open-bio.org
Mon Jan 29 09:40:32 EST 2007


Update of /home/repository/bioperl/bioperl-live/Bio/SeqIO
In directory dev.open-bio.org:/tmp/cvs-serv30448/Bio/SeqIO

Modified Files:
	scf.pm 
Log Message:
Bug 2197

Index: scf.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/SeqIO/scf.pm,v
retrieving revision 1.40
retrieving revision 1.41
diff -C2 -d -r1.40 -r1.41
*** scf.pm	4 Nov 2006 04:41:54 -0000	1.40
--- scf.pm	29 Jan 2007 14:40:30 -0000	1.41
***************
*** 115,119 ****
  		 %names);
  	# set up a filehandle to read in the scf
! 	$fh = $self->_filehandle();
  	unless ($fh) {		# simulate the <> function
  		if ( !fileno(ARGV) or eof(ARGV) ) {
--- 115,120 ----
  		 %names);
  	# set up a filehandle to read in the scf
! 	return if $self->{_readfile};
! 	$fh = $self->_fh();
  	unless ($fh) {		# simulate the <> function
  		if ( !fileno(ARGV) or eof(ARGV) ) {
***************
*** 222,229 ****
  	$buffer = $self->read_from_buffer($fh,$buffer,$length);
  	$creator->{comments} = $self->_get_comments($buffer);
!         my @name_comments = grep {$_->tagname() eq 'NAME'}
!                           $creator->{comments}->get_Annotations('comment');
!         my $name_comment = $name_comments[0]->as_text();
!         $name_comment =~ s/^Comment:\s+//;
  
  	my $swq = Bio::Seq::Quality->new(
--- 223,233 ----
  	$buffer = $self->read_from_buffer($fh,$buffer,$length);
  	$creator->{comments} = $self->_get_comments($buffer);
! 	my @name_comments = grep {$_->tagname() eq 'NAME'}
! 				$creator->{comments}->get_Annotations('comment');
! 	my $name_comment;
! 	if (@name_comments){
! 		 $name_comment = $name_comments[0]->as_text();
! 		 $name_comment =~ s/^Comment:\s+//;
! 	}
  
  	my $swq = Bio::Seq::Quality->new(
***************
*** 246,249 ****
--- 250,254 ----
  
          $returner->annotation($creator->{'comments'}); # add SCF comments
+ 	$self->{'_readfile'} = 1;
  	return $returner;
  }



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