Changes

 Summary of important user-visible changes for Bio-Variation
 -----------------------------------------------------------
 
+1.7.5     2020-01-06 13:58:44-06:00 America/Chicago
+  * Remove Bio::DB::EMBL and Bio::DB::NCBIHelper dependencies, which cause a circular dependency (see issue #3)
+
 1.7.4     2019-12-07 16:56:21-06:00 America/Chicago
   * Add named module (very simple for now)
   * Minor release to address CPAN indexing and permissions issues

LICENSE

-This software is copyright (c) 2019 by See individual modules.
+This software is copyright (c) 2020 by See individual modules.
 
 This is free software; you can redistribute it and/or modify it under
 the same terms as the Perl 5 programming language system itself.
@@ -12,7 +12,7 @@ b) the "Artistic License"
 
 --- The GNU General Public License, Version 1, February 1989 ---
 
-This software is Copyright (c) 2019 by See individual modules.
+This software is Copyright (c) 2020 by See individual modules.
 
 This is free software, licensed under:
 
@@ -272,7 +272,7 @@ That's all there is to it!
 
 --- The Artistic License 1.0 ---
 
-This software is Copyright (c) 2019 by See individual modules.
+This software is Copyright (c) 2020 by See individual modules.
 
 This is free software, licensed under:
 

MANIFEST

@@ -15,7 +15,6 @@ lib/Bio/Variation/DNAMutation.pm
 lib/Bio/Variation/IO.pm
 lib/Bio/Variation/IO/flat.pm
 lib/Bio/Variation/IO/xml.pm
-lib/Bio/Variation/README
 lib/Bio/Variation/RNAChange.pm
 lib/Bio/Variation/SNP.pm
 lib/Bio/Variation/SeqDiff.pm

META.json

@@ -30,8 +30,6 @@
       },
       "runtime" : {
          "requires" : {
-            "Bio::DB::EMBL" : "0",
-            "Bio::DB::GenBank" : "0",
             "Bio::DBLinkContainerI" : "0",
             "Bio::PrimarySeq" : "0",
             "Bio::Root::IO" : "0",
@@ -77,7 +75,7 @@
          "web" : "https://github.com/bioperl/bio-variation"
       }
    },
-   "version" : "1.7.4",
+   "version" : "1.7.5",
    "x_Dist_Zilla" : {
       "perl" : {
          "version" : "5.028001"
@@ -297,7 +295,7 @@
                   "branch" : null,
                   "changelog" : "Changes",
                   "signed" : 0,
-                  "tag" : "Bio-Variation-v1.7.4",
+                  "tag" : "Bio-Variation-v1.7.5",
                   "tag_format" : "%N-v%v",
                   "tag_message" : "%N-v%v"
                },

META.yml

@@ -21,8 +21,6 @@ meta-spec:
   version: '1.4'
 name: Bio-Variation
 requires:
-  Bio::DB::EMBL: '0'
-  Bio::DB::GenBank: '0'
   Bio::DBLinkContainerI: '0'
   Bio::PrimarySeq: '0'
   Bio::Root::IO: '0'
@@ -45,7 +43,7 @@ resources:
   bugtracker: https://github.com/bioperl/bio-variation/issues
   homepage: https://metacpan.org/release/Bio-Variation
   repository: git://github.com/bioperl/bio-variation.git
-version: 1.7.4
+version: 1.7.5
 x_Dist_Zilla:
   perl:
     version: '5.028001'
@@ -218,7 +216,7 @@ x_Dist_Zilla:
           branch: ~
           changelog: Changes
           signed: 0
-          tag: Bio-Variation-v1.7.4
+          tag: Bio-Variation-v1.7.5
           tag_format: '%N-v%v'
           tag_message: '%N-v%v'
         Dist::Zilla::Role::Git::Repo:

Makefile.PL

@@ -20,8 +20,6 @@ my %WriteMakefileArgs = (
   "MIN_PERL_VERSION" => "5.006",
   "NAME" => "Bio::Variation",
   "PREREQ_PM" => {
-    "Bio::DB::EMBL" => 0,
-    "Bio::DB::GenBank" => 0,
     "Bio::DBLinkContainerI" => 0,
     "Bio::PrimarySeq" => 0,
     "Bio::Root::IO" => 0,
@@ -49,7 +47,7 @@ my %WriteMakefileArgs = (
     "Test::More" => 0,
     "lib" => 0
   },
-  "VERSION" => "1.7.4",
+  "VERSION" => "1.7.5",
   "test" => {
     "TESTS" => "t/*.t"
   }
@@ -57,8 +55,6 @@ my %WriteMakefileArgs = (
 
 
 my %FallbackPrereqs = (
-  "Bio::DB::EMBL" => 0,
-  "Bio::DB::GenBank" => 0,
   "Bio::DBLinkContainerI" => 0,
   "Bio::PrimarySeq" => 0,
   "Bio::Root::IO" => 0,

bin/bp_flanks

@@ -14,8 +14,6 @@
 
 use Bio::PrimarySeq;
 use Bio::SeqIO;
-use Bio::DB::EMBL;
-use Bio::DB::GenBank;
 use Getopt::Long;
 use strict;
 use warnings;
@@ -25,9 +23,11 @@ use constant VERSION => '3.0';
 my $help = '';
 my $flank = 100;              # flank length on both sides of the region
 my $in_format = 'EMBL';       # format of the file to read in
+# my $db_class = 'Bio::DB::EMBL';  # class of
 my @pos;                      # position(s) in the sequence
 
 
+
 GetOptions ("help" => \$help, "flanklength=i" => \$flank,
             "position=s" => \@pos );
 
@@ -61,15 +61,22 @@ sub get_seq {
     }
     elsif ($file =~ /\./) {	# sequence version from GenBank
         eval {
-	    my $gb = new Bio::DB::GenBank;
+            Bio::SeqIO->_load_module("Bio::DB::GenBank");
+            my $gb = Bio::DB::GenBank->new();
             $seq = $gb->get_Seq_by_version($file);
         };
+        if ($@) {
+            die "Encountered an error: $@";
+        }
     } else {			# plain accession mumber from more reliable EMBL
         eval {
-	    my $gb = new Bio::DB::EMBL;
+            Bio::SeqIO->_load_module("Bio::DB::EMBL");
+            my $gb = Bio::DB::EMBL->new();
             $seq = $gb->get_Seq_by_acc($file);
         };	
-	
+        if ($@) {
+            die "Encountered an error: $@";
+        }        
     }
     print STDERR "Could not find sequence [$file]" && return unless $seq;
     return $seq;
@@ -159,20 +166,20 @@ sub extract {
 
 	#build BioPerl sequence objects
 	if ($strand == -1) {
-	    my $five_prime_seq = new Bio::PrimarySeq(-alphabet=>'dna',-seq=>$five_prime);
-	    my $snp_seq = new Bio::PrimarySeq(-alphabet=>'dna',-seq=>$snp);
-	    my $three_prime_seq = new Bio::PrimarySeq(-alphabet=>'dna',-seq=>$three_prime);
+	    my $five_prime_seq = Bio::PrimarySeq->new(-alphabet=>'dna',-seq=>$five_prime);
+	    my $snp_seq = Bio::PrimarySeq->new(-alphabet=>'dna',-seq=>$snp);
+	    my $three_prime_seq = Bio::PrimarySeq->new(-alphabet=>'dna',-seq=>$three_prime);
 
 	    my $str = $three_prime_seq->revcom->seq. " ".
 		$snp_seq->revcom->seq. " ". $five_prime_seq->revcom->seq;
 	    $str =~ s/ //g;
-	    $out_seq = new Bio::PrimarySeq (-id => $fastaid,
+	    $out_seq = Bio::PrimarySeq->new(-id => $fastaid,
 					    -alphabet=>'dna',
 					    -seq => $str );
 	} else {
 	    my $str = $five_prime. " ". $snp. " ". $three_prime;
 	    $str =~ s/ //g;
-	    $out_seq = new Bio::PrimarySeq (-id => $fastaid,
+	    $out_seq = Bio::PrimarySeq->new(-id => $fastaid,
 					    -alphabet=>'dna',
 					    -seq => $str );
 	}

debian/changelog

+libbio-variation-perl (1.7.5-1) unstable; urgency=medium
+
+  * New upstream version
+
+ -- Michael R. Crusoe <michael.crusoe@gmail.com>  Tue, 07 Jan 2020 14:27:05 +0100
+
 libbio-variation-perl (1.7.4-1) unstable; urgency=low
 
   * Initial release. (Closes: #946468)

debian/control

@@ -12,7 +12,7 @@ Build-Depends-Indep: perl,
                      libbio-db-embl-perl,
                      libio-string-perl,
                      libxml-twig-perl,
-                     libxml-writer-perl (>= 0.4),
+                     libxml-writer-perl
 Standards-Version: 4.4.1
 Vcs-Browser: https://salsa.debian.org/med-team/libbio-variation-perl
 Vcs-Git: https://salsa.debian.org/med-team/libbio-variation-perl.git
@@ -20,12 +20,13 @@ Homepage: https://metacpan.org/release/Bio-Variation
 
 Package: libbio-variation-perl
 Architecture: all
-Depends: ${misc:Depends}, ${perl:Depends},
+Depends: ${misc:Depends},
+         ${perl:Depends},
          libbio-perl-perl,
          libbio-db-ncbihelper-perl,
          libio-string-perl,
          libxml-twig-perl,
- libxml-writer-perl (>= 0.4)
+         libxml-writer-perl
 Breaks: libbio-perl-perl (<= 1.7.2)
 Replaces: libbio-perl-perl (<= 1.7.2)
 Description: BioPerl variation-related functionality

debian/libbio-variation-perl.docs

-lib/Bio/Variation/README

dist.ini

 name = Bio-Variation
-version = 1.7.4
+version = 1.7.5
 author = Allen Day <allenday@ucla.edu>
 author = Heikki Lehvaslaiho <heikki@bioperl.org>
 copyright_holder = See individual modules

lib/Bio/Variation.pm

 package Bio::Variation;
-$Bio::Variation::VERSION = '1.7.4';
+$Bio::Variation::VERSION = '1.7.5';
 use utf8;
 use strict;
 use warnings;
@@ -7,7 +7,7 @@ use warnings;
 1;
 
 # ABSTRACT: BioPerl variation-related functionality
-# AUTHOR: See the individual modules for their authors.
+# AUTHOR: Heikki Lehväslaiho <heikki-at-bioperl-dot-org>
 # OWNER: See the individual modules for their copyright holders
 # LICENSE: Perl_5
 
@@ -17,8 +17,21 @@ See L<Bio::Perl> for examples.
 
 =head1 DESCRIPTION
 
-The code in this distribution focuses on simple low-dependency variant-related
-functionality for BioPerl. See the specific modules for details.
+These classes are part of "Computational Mutation Expression Toolkit"
+project at European Bioinformatics Institute
+<http://www.ebi.ac.uk/mutations/toolkit/>, but they are written to be
+as general as possinble.
+
+Bio::Variation name space contains modules to store sequence variation
+information as differences between the reference sequence and changes
+sequences. Also included are classes to write out and recrete objects
+from EMBL-like flat files and XML. Lastly, there are simple classes to
+calculate values for sequence change objects.
+
+See "Computational Mutation Expression Toolkit" web pages for more
+information:
+
+	http://www.ebi.ac.uk/mutations/toolkit/
 
 =cut
 

lib/Bio/Variation/AAChange.pm

@@ -100,7 +100,7 @@ methods. Internal methods are usually preceded with a _
 
 
 package Bio::Variation::AAChange;
-$Bio::Variation::AAChange::VERSION = '1.7.4';
+$Bio::Variation::AAChange::VERSION = '1.7.5';
 use vars qw($MATRIX);
 use strict;
 

lib/Bio/Variation/AAReverseMutate.pm

@@ -93,7 +93,7 @@ methods. Internal methods are usually preceded with a _
 # Let the code begin...
 
 package Bio::Variation::AAReverseMutate;
-$Bio::Variation::AAReverseMutate::VERSION = '1.7.4';
+$Bio::Variation::AAReverseMutate::VERSION = '1.7.5';
 use strict;
 
 # Object preamble - inheritance

lib/Bio/Variation/Allele.pm

@@ -85,7 +85,7 @@ methods. Internal methods are usually preceded with a _
 # Let the code begin...
 
 package Bio::Variation::Allele;
-$Bio::Variation::Allele::VERSION = '1.7.4';
+$Bio::Variation::Allele::VERSION = '1.7.5';
 use strict;
 
 # Object preamble - inheritance

lib/Bio/Variation/DNAMutation.pm

@@ -97,7 +97,7 @@ methods. Internal methods are usually preceded with a _
 
 
 package Bio::Variation::DNAMutation;
-$Bio::Variation::DNAMutation::VERSION = '1.7.4';
+$Bio::Variation::DNAMutation::VERSION = '1.7.5';
 use strict;
 
 # Object preamble - inheritance

lib/Bio/Variation/IO.pm

@@ -236,7 +236,7 @@ methods. Internal methods are usually preceded with a _
 # Let the code begin...
 
 package Bio::Variation::IO;
-$Bio::Variation::IO::VERSION = '1.7.4';
+$Bio::Variation::IO::VERSION = '1.7.5';
 use strict;
 
 

lib/Bio/Variation/IO/flat.pm

@@ -68,7 +68,7 @@ methods. Internal methods are usually preceded with a _
 # Let the code begin...
 
 package Bio::Variation::IO::flat;
-$Bio::Variation::IO::flat::VERSION = '1.7.4';
+$Bio::Variation::IO::flat::VERSION = '1.7.5';
 use strict;
 
 use Text::Wrap;

lib/Bio/Variation/IO/xml.pm

@@ -77,7 +77,7 @@ methods. Internal methods are usually preceded with a _
 # Let the code begin...
 
 package Bio::Variation::IO::xml;
-$Bio::Variation::IO::xml::VERSION = '1.7.4';
+$Bio::Variation::IO::xml::VERSION = '1.7.5';
 use vars qw($seqdiff $var $prevdnaobj $prevrnaobj $prevaaobj);
 use strict;
 

lib/Bio/Variation/README

-
-                       README for Bio::Variation classes
-
-
-These classes are part of "Computational Mutation Expression Toolkit"
-project at European Bioinformatics Institute
-<http://www.ebi.ac.uk/mutations/toolkit/>, but they are written to be
-as general as possinble.
-
-Bio::Variation name space contains modules to store sequence variation
-information as differences between the reference sequence and changes
-sequences. Also included are classes to write out and recrete objects
-from EMBL-like flat files and XML. Lastly, there are simple classes to
-calculate values for sequence change objects.
-
-See "Computational Mutation Expression Toolkit" web pages for more
-information:
-
-	http://www.ebi.ac.uk/mutations/toolkit/
-
-
-Send bug reports using the bioperl bug-tracking system at
-  https://github.com/bioperl/bioperl-live/issues.
- 
-Send general comments, questions, and feature requests to the bioperl
-mailing list:
-
-	bioperl-l@bioperl.org
-
-Heikki Lehväslaiho <heikki-at-bioperl-dot-org>