[Bioperl-guts-l] bioperl-live/Bio/Tools/Run RemoteBlast.pm, 1.43, 1.44 WrapperBase.pm, 1.35, 1.36

Senduran Balasubramaniam sendu at dev.open-bio.org
Thu Jun 14 10:16:20 EDT 2007


Update of /home/repository/bioperl/bioperl-live/Bio/Tools/Run
In directory dev.open-bio.org:/tmp/cvs-serv22328/Bio/Tools/Run

Modified Files:
	RemoteBlast.pm WrapperBase.pm 
Log Message:
removed bad "new Bio::Module" syntax, replaced with "Bio::Module->new"

Index: RemoteBlast.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/Run/RemoteBlast.pm,v
retrieving revision 1.43
retrieving revision 1.44
diff -C2 -d -r1.43 -r1.44
*** RemoteBlast.pm	14 Mar 2007 19:13:49 -0000	1.43
--- RemoteBlast.pm	14 Jun 2007 14:16:18 -0000	1.44
***************
*** 623,633 ****
              } 
              close($fh2);
!             $blastobj = new Bio::SearchIO( -file => $tempfile2,
                                 -format => 'blasttable');
              } elsif( $mthd =~ /xml/ ) {
!             $blastobj = new Bio::SearchIO( -file => $tempfile,
                                 -format => 'blastxml');
              } else {
!             $blastobj = new Bio::SearchIO( -file => $tempfile,
                                 -format => 'blast');
              } 
--- 623,633 ----
              } 
              close($fh2);
!             $blastobj = Bio::SearchIO->new( -file => $tempfile2,
                                 -format => 'blasttable');
              } elsif( $mthd =~ /xml/ ) {
!             $blastobj = Bio::SearchIO->new( -file => $tempfile,
                                 -format => 'blastxml');
              } else {
!             $blastobj = Bio::SearchIO->new( -file => $tempfile,
                                 -format => 'blast');
              } 
***************
*** 696,700 ****
  	if( ! ref $input ) {
  		if( -e $input ) {
! 			my $seqio = new Bio::SeqIO(-format => 'fasta',
  												-file => $input);
  			while( my $seq = $seqio->next_seq ) {
--- 696,700 ----
  	if( ! ref $input ) {
  		if( -e $input ) {
! 			my $seqio = Bio::SeqIO->new(-format => 'fasta',
  												-file => $input);
  			while( my $seq = $seqio->next_seq ) {

Index: WrapperBase.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/Run/WrapperBase.pm,v
retrieving revision 1.35
retrieving revision 1.36
diff -C2 -d -r1.35 -r1.36
*** WrapperBase.pm	16 May 2007 13:25:20 -0000	1.35
--- WrapperBase.pm	14 Jun 2007 14:16:18 -0000	1.36
***************
*** 263,267 ****
     my ($self) = @_;
     unless( defined $self->{'io'} ) {
!        $self->{'io'} = new Bio::Root::IO(-verbose => $self->verbose);
     }
      return $self->{'io'};
--- 263,267 ----
     my ($self) = @_;
     unless( defined $self->{'io'} ) {
!        $self->{'io'} = Bio::Root::IO->new(-verbose => $self->verbose);
     }
      return $self->{'io'};



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