[med-svn] [Git][med-team/libbio-variation-perl][upstream] New upstream version 1.7.5
Michael R. Crusoe
gitlab at salsa.debian.org
Tue Jan 7 13:34:34 GMT 2020
Michael R. Crusoe pushed to branch upstream at Debian Med / libbio-variation-perl
Commits:
95dd8455 by Michael R. Crusoe at 2020-01-07T14:23:58+01:00
New upstream version 1.7.5
- - - - -
21 changed files:
- Changes
- LICENSE
- MANIFEST
- META.json
- META.yml
- Makefile.PL
- bin/bp_flanks
- dist.ini
- lib/Bio/Variation.pm
- lib/Bio/Variation/AAChange.pm
- lib/Bio/Variation/AAReverseMutate.pm
- lib/Bio/Variation/Allele.pm
- 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
- lib/Bio/Variation/VariantI.pm
Changes:
=====================================
Changes
=====================================
@@ -1,6 +1,9 @@
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
=====================================
@@ -1,4 +1,4 @@
-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 );
@@ -55,21 +55,28 @@ sub get_seq {
my $IN_FORMAT = 'EMBL'; # format of the local file on disk
if (-e $file ) { # local file
- my $in = Bio::SeqIO->new('-file' => $file,
- '-format' => $IN_FORMAT);
- $seq = $in->next_seq();
+ my $in = Bio::SeqIO->new('-file' => $file,
+ '-format' => $IN_FORMAT);
+ $seq = $in->next_seq();
}
elsif ($file =~ /\./) { # sequence version from GenBank
- eval {
- my $gb = new Bio::DB::GenBank;
- $seq = $gb->get_Seq_by_version($file);
- };
+ eval {
+ 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;
- $seq = $gb->get_Seq_by_acc($file);
- };
-
+ eval {
+ 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 => $str );
}
=====================================
dist.ini
=====================================
@@ -1,5 +1,5 @@
name = Bio-Variation
-version = 1.7.4
+version = 1.7.5
author = Allen Day <allenday at ucla.edu>
author = Heikki Lehvaslaiho <heikki at bioperl.org>
copyright_holder = See individual modules
=====================================
lib/Bio/Variation.pm
=====================================
@@ -1,5 +1,5 @@
package Bio::Variation;
-$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 $prevaaobj);
use strict;
=====================================
lib/Bio/Variation/README deleted
=====================================
@@ -1,30 +0,0 @@
-
- README for Bio::Variation classes
-
-
-These classes are part of "Computational Mutation Expression Toolkit"
-project at European Bioinformatics Institute
-<http://www.ebi.ac.uk/mutations/toolkit/>, but they are written to be
-as general as possinble.
-
-Bio::Variation name space contains modules to store sequence variation
-information as differences between the reference sequence and changes
-sequences. Also included are classes to write out and recrete objects
-from EMBL-like flat files and XML. Lastly, there are simple classes to
-calculate values for sequence change objects.
-
-See "Computational Mutation Expression Toolkit" web pages for more
-information:
-
- http://www.ebi.ac.uk/mutations/toolkit/
-
-
-Send bug reports using the bioperl bug-tracking system at
- https://github.com/bioperl/bioperl-live/issues.
-
-Send general comments, questions, and feature requests to the bioperl
-mailing list:
-
- bioperl-l at bioperl.org
-
-Heikki Lehväslaiho <heikki-at-bioperl-dot-org>
=====================================
lib/Bio/Variation/RNAChange.pm
=====================================
@@ -110,7 +110,7 @@ methods. Internal methods are usually preceded with a _
package Bio::Variation::RNAChange;
-$Bio::Variation::RNAChange::VERSION = '1.7.4';
+$Bio::Variation::RNAChange::VERSION = '1.7.5';
use strict;
# Object preamble - inheritance
=====================================
lib/Bio/Variation/SNP.pm
=====================================
@@ -61,7 +61,7 @@ methods. Internal methods are usually preceded with a _
# Let the code begin...
package Bio::Variation::SNP;
-$Bio::Variation::SNP::VERSION = '1.7.4';
+$Bio::Variation::SNP::VERSION = '1.7.5';
use strict;
use vars qw($AUTOLOAD);
use Bio::Root::Root;
=====================================
lib/Bio/Variation/SeqDiff.pm
=====================================
@@ -104,7 +104,7 @@ methods. Internal methods are usually preceded with a _
# Let the code begin...
package Bio::Variation::SeqDiff;
-$Bio::Variation::SeqDiff::VERSION = '1.7.4';
+$Bio::Variation::SeqDiff::VERSION = '1.7.5';
use strict;
use Bio::Tools::CodonTable;
use Bio::PrimarySeq;
=====================================
lib/Bio/Variation/VariantI.pm
=====================================
@@ -103,7 +103,7 @@ methods. Internal methods are usually preceded with a _
package Bio::Variation::VariantI;
-$Bio::Variation::VariantI::VERSION = '1.7.4';
+$Bio::Variation::VariantI::VERSION = '1.7.5';
use strict;
# Object preamble - inheritance
View it on GitLab: https://salsa.debian.org/med-team/libbio-variation-perl/commit/95dd84550fed6915bba79cf09d448dde3a8ed8d0
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View it on GitLab: https://salsa.debian.org/med-team/libbio-variation-perl/commit/95dd84550fed6915bba79cf09d448dde3a8ed8d0
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