[Bioperl-guts-l] bioperl-live/Bio/LiveSeq Mutator.pm, 1.35, 1.36 Translation.pm, 1.16, 1.17

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


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

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

Index: Mutator.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/LiveSeq/Mutator.pm,v
retrieving revision 1.35
retrieving revision 1.36
diff -C2 -d -r1.35 -r1.36
*** Mutator.pm	26 Sep 2006 22:03:08 -0000	1.35
--- Mutator.pm	14 Jun 2007 14:16:11 -0000	1.36
***************
*** 594,598 ****
      if ($len == 1 and $refstring =~ /[^\.\-\*\?]/ and 
  	$varstring  =~ /[^\.\-\*\?]/ ) { #point
! 	$mutation = new Bio::LiveSeq::Mutation (-seq => $varstring,
  						-pos => $pos,
  						);
--- 594,598 ----
      if ($len == 1 and $refstring =~ /[^\.\-\*\?]/ and 
  	$varstring  =~ /[^\.\-\*\?]/ ) { #point
! 	$mutation = Bio::LiveSeq::Mutation->new(-seq => $varstring,
  						-pos => $pos,
  						);
***************
*** 600,604 ****
      elsif ( $refstring =~ /^[^\.\-\*\?]+$/ and 
  	    $varstring  !~ /^[^\.\-\*\?]+$/ ) { # deletion
! 	$mutation = new Bio::LiveSeq::Mutation (-pos => $pos,
  						-len => $len
  						);
--- 600,604 ----
      elsif ( $refstring =~ /^[^\.\-\*\?]+$/ and 
  	    $varstring  !~ /^[^\.\-\*\?]+$/ ) { # deletion
! 	$mutation = Bio::LiveSeq::Mutation->new(-pos => $pos,
  						-len => $len
  						);
***************
*** 606,615 ****
      elsif ( $refstring !~ /^[^\.\-\*\?]+$/ and 
  	    $varstring  =~ /^[^\.\-\*\?]+$/ ) { # insertion
! 	$mutation = new Bio::LiveSeq::Mutation (-seq => $varstring,
  						-pos => $pos,
  						-len => 0
  						);
      } else { # complex
! 	$mutation = new Bio::LiveSeq::Mutation (-seq => $varstring,
  						-pos => $pos,
  						-len => $len
--- 606,615 ----
      elsif ( $refstring !~ /^[^\.\-\*\?]+$/ and 
  	    $varstring  =~ /^[^\.\-\*\?]+$/ ) { # insertion
! 	$mutation = Bio::LiveSeq::Mutation->new(-seq => $varstring,
  						-pos => $pos,
  						-len => 0
  						);
      } else { # complex
! 	$mutation = Bio::LiveSeq::Mutation->new(-seq => $varstring,
  						-pos => $pos,
  						-len => $len

Index: Translation.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/LiveSeq/Translation.pm,v
retrieving revision 1.16
retrieving revision 1.17
diff -C2 -d -r1.16 -r1.17
*** Translation.pm	26 Sep 2006 22:03:08 -0000	1.16
--- Translation.pm	14 Jun 2007 14:16:11 -0000	1.17
***************
*** 147,151 ****
      #carp "the downstream is: $downstreamseq"; # debug
      my $cdnaseq=$transcript->seq();
!     my $extendedseq = new Bio::PrimarySeq(-seq => "$cdnaseq$downstreamseq",
  					  -alphabet => 'dna'
  					  );
--- 147,151 ----
      #carp "the downstream is: $downstreamseq"; # debug
      my $cdnaseq=$transcript->seq();
!     my $extendedseq = Bio::PrimarySeq->new(-seq => "$cdnaseq$downstreamseq",
  					  -alphabet => 'dna'
  					  );



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