[Bioperl-guts-l] bioperl-live/Bio/DB BiblioI.pm, 1.12, 1.13 BioFetch.pm, 1.33, 1.34 EMBL.pm, 1.22, 1.23 Expression.pm, 1.5, 1.6 Fasta.pm, 1.49, 1.50 GDB.pm, 1.22, 1.23 GFF.pm, 1.150, 1.151 GenBank.pm, 1.60, 1.61 GenPept.pm, 1.32, 1.33 MeSH.pm, 1.10, 1.11 NCBIHelper.pm, 1.56, 1.57 QueryI.pm, 1.6, 1.7 RefSeq.pm, 1.14, 1.15 Registry.pm, 1.41, 1.42 SeqHound.pm, 1.8, 1.9 SeqVersion.pm, 1.13, 1.14 SwissProt.pm, 1.31, 1.32 Taxonomy.pm, 1.17, 1.18 XEMBL.pm, 1.12, 1.13

Senduran Balasubramaniam sendu at dev.open-bio.org
Thu Jun 14 10:16:13 EDT 2007


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

Modified Files:
	BiblioI.pm BioFetch.pm EMBL.pm Expression.pm Fasta.pm GDB.pm 
	GFF.pm GenBank.pm GenPept.pm MeSH.pm NCBIHelper.pm QueryI.pm 
	RefSeq.pm Registry.pm SeqHound.pm SeqVersion.pm SwissProt.pm 
	Taxonomy.pm XEMBL.pm 
Log Message:
removed bad "new Bio::Module" syntax, replaced with "Bio::Module->new"

Index: BioFetch.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/DB/BioFetch.pm,v
retrieving revision 1.33
retrieving revision 1.34
diff -C2 -d -r1.33 -r1.34
*** BioFetch.pm	21 Dec 2006 17:56:16 -0000	1.33
--- BioFetch.pm	14 Jun 2007 14:16:10 -0000	1.34
***************
*** 24,33 ****
   use Bio::DB::BioFetch;
  
!  $bf = new Bio::DB::BioFetch;
  
   $seq = $bf->get_Seq_by_id('BUM');  # EMBL or SWALL ID
  
   # change formats, storage procedures
!  $bf = new Bio::DB::BioFetch(-format        => 'fasta',
   			     -retrievaltype => 'tempfile',
    			     -db            => 'EMBL');
--- 24,33 ----
   use Bio::DB::BioFetch;
  
!  $bf = Bio::DB::BioFetch->new();
  
   $seq = $bf->get_Seq_by_id('BUM');  # EMBL or SWALL ID
  
   # change formats, storage procedures
!  $bf = Bio::DB::BioFetch->new(-format        => 'fasta',
   			     -retrievaltype => 'tempfile',
    			     -db            => 'EMBL');

Index: XEMBL.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/DB/XEMBL.pm,v
retrieving revision 1.12
retrieving revision 1.13
diff -C2 -d -r1.12 -r1.13
*** XEMBL.pm	16 Feb 2007 01:45:27 -0000	1.12
--- XEMBL.pm	14 Jun 2007 14:16:11 -0000	1.13
***************
*** 20,24 ****
    use Bio::DB::XEMBL;
  
!   $embl = new Bio::DB::XEMBL;
  
    # remember that XEMBL_ID does not equal GenBank_ID!
--- 20,24 ----
    use Bio::DB::XEMBL;
  
!   $embl = Bio::DB::XEMBL->new();
  
    # remember that XEMBL_ID does not equal GenBank_ID!

Index: EMBL.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/DB/EMBL.pm,v
retrieving revision 1.22
retrieving revision 1.23
diff -C2 -d -r1.22 -r1.23
*** EMBL.pm	26 Sep 2006 22:03:06 -0000	1.22
--- EMBL.pm	14 Jun 2007 14:16:10 -0000	1.23
***************
*** 20,24 ****
    use Bio::DB::EMBL;
  
!   $embl = new Bio::DB::EMBL;
  
    # remember that EMBL_ID does not equal GenBank_ID!
--- 20,24 ----
    use Bio::DB::EMBL;
  
!   $embl = Bio::DB::EMBL->new();
  
    # remember that EMBL_ID does not equal GenBank_ID!
***************
*** 43,47 ****
    # also don't want features, just sequence so let's save bandwith
    # and request Fasta sequence
!   $embl = new Bio::DB::EMBL(-retrievaltype => 'tempfile' ,
   			    -format => 'fasta');
    my $seqio = $embl->get_Stream_by_id(['AC013798', 'AC021953'] );
--- 43,47 ----
    # also don't want features, just sequence so let's save bandwith
    # and request Fasta sequence
!   $embl = Bio::DB::EMBL->new(-retrievaltype => 'tempfile' ,
   			    -format => 'fasta');
    my $seqio = $embl->get_Stream_by_id(['AC013798', 'AC021953'] );
***************
*** 201,205 ****
  		   " Redirecting the request.\n")
  	    if $self->verbose >= 0;
! 	return  new Bio::DB::RefSeq(-verbose => $self->verbose);
      }
  }
--- 201,205 ----
  		   " Redirecting the request.\n")
  	    if $self->verbose >= 0;
! 	return  Bio::DB::RefSeq->new(-verbose => $self->verbose);
      }
  }

Index: SeqVersion.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/DB/SeqVersion.pm,v
retrieving revision 1.13
retrieving revision 1.14
diff -C2 -d -r1.13 -r1.14
*** SeqVersion.pm	3 Oct 2006 03:42:29 -0000	1.13
--- SeqVersion.pm	14 Jun 2007 14:16:10 -0000	1.14
***************
*** 77,81 ****
  =head2 new()
  
!  Usage   : my $obj = new Bio::DB::SeqVersion();
   Function: Create a Bio::DB::SeqVersion object 
   Returns : An instance of Bio::DB::SeqVersion
--- 77,81 ----
  =head2 new()
  
!  Usage   : my $obj = Bio::DB::SeqVersion->new();
   Function: Create a Bio::DB::SeqVersion object 
   Returns : An instance of Bio::DB::SeqVersion

Index: BiblioI.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/DB/BiblioI.pm,v
retrieving revision 1.12
retrieving revision 1.13
diff -C2 -d -r1.12 -r1.13
*** BiblioI.pm	2 Oct 2006 04:34:52 -0000	1.12
--- BiblioI.pm	14 Jun 2007 14:16:10 -0000	1.13
***************
*** 19,23 ****
  
    use Bio::Biblio;
!   my $biblio = new Bio::Biblio (@args);
  
  =head1 DESCRIPTION
--- 19,23 ----
  
    use Bio::Biblio;
!   my $biblio = Bio::Biblio->new(@args);
  
  =head1 DESCRIPTION
***************
*** 331,335 ****
      use Bio::Biblio;
      print
!       new Bio::Biblio (-collection_id => '1014324148861')->exists;
  
  It throws an exception if this object does not represent any query
--- 331,335 ----
      use Bio::Biblio;
      print
!       Bio::Biblio->new(-collection_id => '1014324148861')->exists;
  
  It throws an exception if this object does not represent any query

Index: NCBIHelper.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/DB/NCBIHelper.pm,v
retrieving revision 1.56
retrieving revision 1.57
diff -C2 -d -r1.56 -r1.57
*** NCBIHelper.pm	10 Nov 2006 16:41:34 -0000	1.56
--- NCBIHelper.pm	14 Jun 2007 14:16:10 -0000	1.57
***************
*** 389,393 ****
  							" Redirecting the request.\n")
  			  if $self->verbose >= 0;
! 			return  new Bio::DB::RefSeq;
  		}
  	}
--- 389,393 ----
  							" Redirecting the request.\n")
  			  if $self->verbose >= 0;
! 			return  Bio::DB::RefSeq->new();
  		}
  	}

Index: Fasta.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/DB/Fasta.pm,v
retrieving revision 1.49
retrieving revision 1.50
diff -C2 -d -r1.49 -r1.50
*** Fasta.pm	29 May 2007 04:28:50 -0000	1.49
--- Fasta.pm	14 Jun 2007 14:16:10 -0000	1.50
***************
*** 431,435 ****
  
   Title   : new
!  Usage   : my $db = new Bio::DB::Fasta( $path, @options);
   Function: initialize a new Bio::DB::Fasta object
   Returns : new Bio::DB::Fasta object
--- 431,435 ----
  
   Title   : new
!  Usage   : my $db = Bio::DB::Fasta->new( $path, @options);
   Function: initialize a new Bio::DB::Fasta object
   Returns : new Bio::DB::Fasta object

Index: GDB.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/DB/GDB.pm,v
retrieving revision 1.22
retrieving revision 1.23
diff -C2 -d -r1.22 -r1.23
*** GDB.pm	26 Sep 2006 22:03:06 -0000	1.22
--- GDB.pm	14 Jun 2007 14:16:10 -0000	1.23
***************
*** 20,24 ****
      use Bio::DB::GDB;
  
!     $gdb = new Bio::DB::GDB;
  
      $info = $gdb->get_info(-type => 'marker',
--- 20,24 ----
      use Bio::DB::GDB;
  
!     $gdb = Bio::DB::GDB->new();
  
      $info = $gdb->get_info(-type => 'marker',

Index: GFF.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/DB/GFF.pm,v
retrieving revision 1.150
retrieving revision 1.151
diff -C2 -d -r1.150 -r1.151
*** GFF.pm	20 Apr 2007 19:17:40 -0000	1.150
--- GFF.pm	14 Jun 2007 14:16:10 -0000	1.151
***************
*** 579,583 ****
  
   Title   : new
!  Usage   : my $db = new Bio::DB::GFF(@args);
   Function: create a new Bio::DB::GFF object
   Returns : new Bio::DB::GFF object
--- 579,583 ----
  
   Title   : new
!  Usage   : my $db = Bio::DB::GFF->new(@args);
   Function: create a new Bio::DB::GFF object
   Returns : new Bio::DB::GFF object

Index: SwissProt.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/DB/SwissProt.pm,v
retrieving revision 1.31
retrieving revision 1.32
diff -C2 -d -r1.31 -r1.32
*** SwissProt.pm	26 Sep 2006 22:03:06 -0000	1.31
--- SwissProt.pm	14 Jun 2007 14:16:10 -0000	1.32
***************
*** 21,25 ****
      use Bio::DB::SwissProt;
  
!     $sp = new Bio::DB::SwissProt;
  
      $seq = $sp->get_Seq_by_id('KPY1_ECOLI'); # SwissProt ID
--- 21,25 ----
      use Bio::DB::SwissProt;
  
!     $sp = Bio::DB::SwissProt->new();
  
      $seq = $sp->get_Seq_by_id('KPY1_ECOLI'); # SwissProt ID
***************
*** 35,39 ****
  
      # choose a different server to query
!     $sp = new Bio::DB::SwissProt('-servertype' => 'expasy',
  				 '-hostlocation' => 'us');
  
--- 35,39 ----
  
      # choose a different server to query
!     $sp = Bio::DB::SwissProt->new('-servertype' => 'expasy',
  				 '-hostlocation' => 'us');
  

Index: Taxonomy.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/DB/Taxonomy.pm,v
retrieving revision 1.17
retrieving revision 1.18
diff -C2 -d -r1.17 -r1.18
*** Taxonomy.pm	29 Mar 2007 15:50:51 -0000	1.17
--- Taxonomy.pm	14 Jun 2007 14:16:10 -0000	1.18
***************
*** 18,22 ****
  
    use Bio::DB::Taxonomy;
!   my $db = new Bio::DB::Taxonomy(-source => 'entrez');
    # use NCBI Entrez over HTTP
    my $taxonid = $db->get_taxonid('Homo sapiens');
--- 18,22 ----
  
    use Bio::DB::Taxonomy;
!   my $db = Bio::DB::Taxonomy->new(-source => 'entrez');
    # use NCBI Entrez over HTTP
    my $taxonid = $db->get_taxonid('Homo sapiens');
***************
*** 78,82 ****
  
   Title   : new
!  Usage   : my $obj = new Bio::DB::Taxonomy(-source => 'entrez');
   Function: Builds a new Bio::DB::Taxonomy object.
   Returns : an instance of Bio::DB::Taxonomy
--- 78,82 ----
  
   Title   : new
!  Usage   : my $obj = Bio::DB::Taxonomy->new(-source => 'entrez');
   Function: Builds a new Bio::DB::Taxonomy object.
   Returns : an instance of Bio::DB::Taxonomy

Index: GenPept.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/DB/GenPept.pm,v
retrieving revision 1.32
retrieving revision 1.33
diff -C2 -d -r1.32 -r1.33
*** GenPept.pm	26 Sep 2006 22:03:06 -0000	1.32
--- GenPept.pm	14 Jun 2007 14:16:10 -0000	1.33
***************
*** 19,23 ****
  =head1 SYNOPSIS
  
!     $gb = new Bio::DB::GenPept;
  
      $seq = $gb->get_Seq_by_id('195055'); # Unique ID
--- 19,23 ----
  =head1 SYNOPSIS
  
!     $gb = Bio::DB::GenPept->new();
  
      $seq = $gb->get_Seq_by_id('195055'); # Unique ID

Index: QueryI.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/DB/QueryI.pm,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** QueryI.pm	26 Sep 2006 22:03:06 -0000	1.6
--- QueryI.pm	14 Jun 2007 14:16:10 -0000	1.7
***************
*** 26,30 ****
  
     # get a genbank database handle
!    $gb = new Bio::DB::GenBank;
     my $stream = $db->get_Stream_by_query($query);
     while (my $seq = $stream->next_seq) {
--- 26,30 ----
  
     # get a genbank database handle
!    $gb = Bio::DB::GenBank->new();
     my $stream = $db->get_Stream_by_query($query);
     while (my $seq = $stream->next_seq) {

Index: Registry.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/DB/Registry.pm,v
retrieving revision 1.41
retrieving revision 1.42
diff -C2 -d -r1.41 -r1.42
*** Registry.pm	29 Nov 2006 11:26:00 -0000	1.41
--- Registry.pm	14 Jun 2007 14:16:10 -0000	1.42
***************
*** 11,15 ****
      use Bio::DB::Registry();
  
!     $registry = new Bio::DB::Registry();
  
      @available_services = $registry->services;
--- 11,15 ----
      use Bio::DB::Registry();
  
!     $registry = Bio::DB::Registry->new();
  
      @available_services = $registry->services;

Index: MeSH.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/DB/MeSH.pm,v
retrieving revision 1.10
retrieving revision 1.11
diff -C2 -d -r1.10 -r1.11
*** MeSH.pm	2 Oct 2006 03:09:27 -0000	1.10
--- MeSH.pm	14 Jun 2007 14:16:10 -0000	1.11
***************
*** 15,19 ****
  =head1 SYNOPSIS
  
!  my $mesh = new Bio::DB::MeSH();
   my $term = $mesh->get_exact_term('Butter');
   print $term->description;
--- 15,19 ----
  =head1 SYNOPSIS
  
!  my $mesh = Bio::DB::MeSH->new();
   my $term = $mesh->get_exact_term('Butter');
   print $term->description;

Index: SeqHound.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/DB/SeqHound.pm,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** SeqHound.pm	16 Oct 2006 14:18:27 -0000	1.8
--- SeqHound.pm	14 Jun 2007 14:16:10 -0000	1.9
***************
*** 12,16 ****
  
      use Bio::DB::SeqHound;
!     $sh = new Bio::DB::SeqHound();
  
      $seq = $sh->get_Seq_by_acc("CAA28783"); # Accession Number
--- 12,16 ----
  
      use Bio::DB::SeqHound;
!     $sh = Bio::DB::SeqHound->new();
  
      $seq = $sh->get_Seq_by_acc("CAA28783"); # Accession Number

Index: Expression.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/DB/Expression.pm,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** Expression.pm	20 Sep 2006 05:53:50 -0000	1.5
--- Expression.pm	14 Jun 2007 14:16:10 -0000	1.6
***************
*** 76,80 ****
  =head2 new()
  
!  Usage   : my $obj = new Bio::DB::Expression();
   Function: Builds a new Bio::DB::Expression object 
   Returns : an instance of Bio::DB::Expression
--- 76,80 ----
  =head2 new()
  
!  Usage   : my $obj = Bio::DB::Expression->new();
   Function: Builds a new Bio::DB::Expression object 
   Returns : an instance of Bio::DB::Expression

Index: RefSeq.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/DB/RefSeq.pm,v
retrieving revision 1.14
retrieving revision 1.15
diff -C2 -d -r1.14 -r1.15
*** RefSeq.pm	26 Sep 2006 22:03:06 -0000	1.14
--- RefSeq.pm	14 Jun 2007 14:16:10 -0000	1.15
***************
*** 20,24 ****
    use Bio::DB::RefSeq;
  
!   $db = new Bio::DB::RefSeq;
  
    # most of the time RefSeq_ID eq RefSeq acc
--- 20,24 ----
    use Bio::DB::RefSeq;
  
!   $db = Bio::DB::RefSeq->new();
  
    # most of the time RefSeq_ID eq RefSeq acc
***************
*** 43,47 ****
    # also don't want features, just sequence so let's save bandwith
    # and request Fasta sequence
!   $db = new Bio::DB::RefSeq(-retrievaltype => 'tempfile' ,
   			       -format => 'fasta');
    my $seqio = $db->get_Stream_by_id(['NM_006732', 'NM_005252'] );
--- 43,47 ----
    # also don't want features, just sequence so let's save bandwith
    # and request Fasta sequence
!   $db = Bio::DB::RefSeq->new(-retrievaltype => 'tempfile' ,
   			       -format => 'fasta');
    my $seqio = $db->get_Stream_by_id(['NM_006732', 'NM_005252'] );

Index: GenBank.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/DB/GenBank.pm,v
retrieving revision 1.60
retrieving revision 1.61
diff -C2 -d -r1.60 -r1.61
*** GenBank.pm	26 Sep 2006 22:03:06 -0000	1.60
--- GenBank.pm	14 Jun 2007 14:16:10 -0000	1.61
***************
*** 30,34 ****
  
      use Bio::DB::GenBank;
!     $gb = new Bio::DB::GenBank;
  
      $seq = $gb->get_Seq_by_id('MUSIGHBA1'); # Unique ID
--- 30,34 ----
  
      use Bio::DB::GenBank;
!     $gb = Bio::DB::GenBank->new();
  
      $seq = $gb->get_Seq_by_id('MUSIGHBA1'); # Unique ID
***************
*** 56,60 ****
      # also don't want features, just sequence so let's save bandwith
      # and request Fasta sequence
!     $gb = new Bio::DB::GenBank(-retrievaltype => 'tempfile' , 
  			                      -format => 'Fasta');
      my $seqio = $gb->get_Stream_by_acc(['AC013798', 'AC021953'] );
--- 56,60 ----
      # also don't want features, just sequence so let's save bandwith
      # and request Fasta sequence
!     $gb = Bio::DB::GenBank->new(-retrievaltype => 'tempfile' , 
  			                      -format => 'Fasta');
      my $seqio = $gb->get_Stream_by_acc(['AC013798', 'AC021953'] );



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