Changes

 Summary of important user-visible changes for BioPerl
 -----------------------------------------------------
 
+1.7.6     2019-08-28 12:37:01+01:00 Europe/London
+
+    * The program bp_classify_hits_kingdom has been removed and is
+      now part of the examples documentation instead.
+
+    * GD is now listed as a suggestion instead of a requirement.  The
+      bp_chaos_plot program will now work with the GD module.
+
+    * New method Bio::Tree::Statistics::transfer_bootstrap_expectation
+      to compute Transfer Bootstrap Expectation (TBE) for internal
+      nodes based on the methods outlined in Lemoine et al, Nature,
+      2018.
+
+    * New method Bio::SeqIO::fasta::next_seq_fast to retrieve next
+      sequence in the stream faster but not perfect.
+
+
 1.7.5     2019-02-11 14:57:45+00:00 Europe/London
 
     * The following modules have been removed from the BioPerl

MANIFEST

@@ -12,7 +12,6 @@ bin/bp_aacomp
 bin/bp_bioflat_index
 bin/bp_biogetseq
 bin/bp_chaos_plot
-bin/bp_classify_hits_kingdom
 bin/bp_dbsplit
 bin/bp_extract_feature_seq
 bin/bp_fastam9_to_table
@@ -56,6 +55,7 @@ examples/align/FastAlign.pl
 examples/align/align_on_codons.pl
 examples/align/aligntutorial.pl
 examples/align/simplealign.pl
+examples/classify_hits_kingdom
 examples/contributed/nmrpdb_parse.pl
 examples/contributed/prosite2perl.pl
 examples/contributed/rebase2list.pl

META.json

@@ -30,13 +30,11 @@
             "AnyDBM_File" : "0",
             "Carp" : "0",
             "Cwd" : "0",
-            "DBI" : "0",
             "DB_File" : "0",
             "Data::Dumper" : "0",
             "Data::Stag" : "0",
             "Digest::MD5" : "0",
             "Dumpvalue" : "0",
-            "Env" : "0",
             "Error" : "0",
             "Exporter" : "0",
             "Fcntl" : "0",
@@ -47,7 +45,6 @@
             "File::Spec::Functions" : "0",
             "File::Temp" : "0",
             "FileHandle" : "0",
-            "GD" : "0",
             "Getopt::Long" : "0",
             "Graph::Directed" : "0",
             "HTTP::Request::Common" : "0",
@@ -108,17 +105,20 @@
             "Bio::DB::EMBL" : "0",
             "Bio::DB::GenBank" : "0",
             "Bio::DB::GenPept" : "0",
-            "Bio::DB::SwissProt" : "0"
+            "Bio::DB::SwissProt" : "0",
+            "GD" : "0"
          }
       },
       "test" : {
          "requires" : {
             "File::Spec" : "0",
+            "FindBin" : "0",
             "IO::Handle" : "0",
             "IPC::Open3" : "0",
             "Test::Memory::Cycle" : "0",
             "Test::More" : "0",
             "Test::Weaken" : "0",
+            "lib" : "0",
             "perl" : "5.006"
          }
       }
@@ -136,7 +136,7 @@
          "web" : "https://github.com/bioperl/bioperl-live"
       }
    },
-   "version" : "1.7.5",
+   "version" : "1.7.6",
    "x_Dist_Zilla" : {
       "perl" : {
          "version" : "5.028001"
@@ -346,7 +346,7 @@
                   "branch" : null,
                   "changelog" : "Changes",
                   "signed" : 0,
-                  "tag" : "BioPerl-v1.7.5",
+                  "tag" : "BioPerl-v1.7.6",
                   "tag_format" : "%N-v%v",
                   "tag_message" : "%N-v%v"
                },
@@ -382,6 +382,17 @@
             "name" : "bin_bp_fetch_RuntimeSuggests",
             "version" : "6.012"
          },
+         {
+            "class" : "Dist::Zilla::Plugin::Prereqs",
+            "config" : {
+               "Dist::Zilla::Plugin::Prereqs" : {
+                  "phase" : "runtime",
+                  "type" : "suggests"
+               }
+            },
+            "name" : "bin_bp_chaos_plot_RuntimeSuggests",
+            "version" : "6.012"
+         },
          {
             "class" : "Dist::Zilla::Plugin::FileFinder::ByName",
             "name" : "PodWeaver-Ready",
@@ -589,6 +600,6 @@
       }
    },
    "x_generated_by_perl" : "v5.28.1",
-   "x_serialization_backend" : "Cpanel::JSON::XS version 4.08"
+   "x_serialization_backend" : "Cpanel::JSON::XS version 4.09"
 }
 

META.yml

@@ -4,11 +4,13 @@ author:
   - 'See individual modules'
 build_requires:
   File::Spec: '0'
+  FindBin: '0'
   IO::Handle: '0'
   IPC::Open3: '0'
   Test::Memory::Cycle: '0'
   Test::More: '0'
   Test::Weaken: '0'
+  lib: '0'
   perl: '5.006'
 configure_requires:
   ExtUtils::MakeMaker: '0'
@@ -23,13 +25,11 @@ requires:
   AnyDBM_File: '0'
   Carp: '0'
   Cwd: '0'
-  DBI: '0'
   DB_File: '0'
   Data::Dumper: '0'
   Data::Stag: '0'
   Digest::MD5: '0'
   Dumpvalue: '0'
-  Env: '0'
   Error: '0'
   Exporter: '0'
   Fcntl: '0'
@@ -40,7 +40,6 @@ requires:
   File::Spec::Functions: '0'
   File::Temp: '0'
   FileHandle: '0'
-  GD: '0'
   Getopt::Long: '0'
   Graph::Directed: '0'
   HTTP::Request::Common: '0'
@@ -99,7 +98,7 @@ resources:
   bugtracker: https://github.com/bioperl/bioperl-live/issues
   homepage: https://metacpan.org/release/BioPerl
   repository: git://github.com/bioperl/bioperl-live.git
-version: 1.7.5
+version: 1.7.6
 x_Dist_Zilla:
   perl:
     version: '5.028001'
@@ -264,7 +263,7 @@ x_Dist_Zilla:
           branch: ~
           changelog: Changes
           signed: 0
-          tag: BioPerl-v1.7.5
+          tag: BioPerl-v1.7.6
           tag_format: '%N-v%v'
           tag_message: '%N-v%v'
         Dist::Zilla::Role::Git::Repo:
@@ -289,6 +288,14 @@ x_Dist_Zilla:
           type: suggests
       name: bin_bp_fetch_RuntimeSuggests
       version: '6.012'
+    -
+      class: Dist::Zilla::Plugin::Prereqs
+      config:
+        Dist::Zilla::Plugin::Prereqs:
+          phase: runtime
+          type: suggests
+      name: bin_bp_chaos_plot_RuntimeSuggests
+      version: '6.012'
     -
       class: Dist::Zilla::Plugin::FileFinder::ByName
       name: PodWeaver-Ready

Makefile.PL

@@ -18,7 +18,6 @@ my %WriteMakefileArgs = (
     "bin/bp_bioflat_index",
     "bin/bp_biogetseq",
     "bin/bp_chaos_plot",
-    "bin/bp_classify_hits_kingdom",
     "bin/bp_dbsplit",
     "bin/bp_extract_feature_seq",
     "bin/bp_fastam9_to_table",
@@ -64,13 +63,11 @@ my %WriteMakefileArgs = (
     "AnyDBM_File" => 0,
     "Carp" => 0,
     "Cwd" => 0,
-    "DBI" => 0,
     "DB_File" => 0,
     "Data::Dumper" => 0,
     "Data::Stag" => 0,
     "Digest::MD5" => 0,
     "Dumpvalue" => 0,
-    "Env" => 0,
     "Error" => 0,
     "Exporter" => 0,
     "Fcntl" => 0,
@@ -81,7 +78,6 @@ my %WriteMakefileArgs = (
     "File::Spec::Functions" => 0,
     "File::Temp" => 0,
     "FileHandle" => 0,
-    "GD" => 0,
     "Getopt::Long" => 0,
     "Graph::Directed" => 0,
     "HTTP::Request::Common" => 0,
@@ -139,13 +135,15 @@ my %WriteMakefileArgs = (
   },
   "TEST_REQUIRES" => {
     "File::Spec" => 0,
+    "FindBin" => 0,
     "IO::Handle" => 0,
     "IPC::Open3" => 0,
     "Test::Memory::Cycle" => 0,
     "Test::More" => 0,
-    "Test::Weaken" => 0
+    "Test::Weaken" => 0,
+    "lib" => 0
   },
-  "VERSION" => "1.7.5",
+  "VERSION" => "1.7.6",
   "test" => {
     "TESTS" => "t/*.t t/Align/*.t t/AlignIO/*.t t/Annotation/*.t t/LocalDB/*.t t/LocalDB/Index/*.t t/LocalDB/Taxonomy/*.t t/Matrix/*.t t/Matrix/IO/*.t t/Ontology/*.t t/Ontology/IO/*.t t/RemoteDB/*.t t/Root/*.t t/SearchIO/*.t t/SearchIO/Writer/*.t t/Seq/*.t t/SeqFeature/*.t t/SeqIO/*.t t/SeqTools/*.t t/Tools/*.t t/Tools/Alignment/*.t t/Tools/EMBOSS/*.t t/Tools/Phylo/*.t t/Tools/Phylo/Phylip/*.t t/Tools/Signalp/*.t t/Tools/Spidey/*.t t/Tree/*.t t/Tree/TreeIO/*.t"
   }
@@ -156,13 +154,11 @@ my %FallbackPrereqs = (
   "AnyDBM_File" => 0,
   "Carp" => 0,
   "Cwd" => 0,
-  "DBI" => 0,
   "DB_File" => 0,
   "Data::Dumper" => 0,
   "Data::Stag" => 0,
   "Digest::MD5" => 0,
   "Dumpvalue" => 0,
-  "Env" => 0,
   "Error" => 0,
   "Exporter" => 0,
   "Fcntl" => 0,
@@ -173,7 +169,7 @@ my %FallbackPrereqs = (
   "File::Spec::Functions" => 0,
   "File::Temp" => 0,
   "FileHandle" => 0,
-  "GD" => 0,
+  "FindBin" => 0,
   "Getopt::Long" => 0,
   "Graph::Directed" => 0,
   "HTTP::Request::Common" => 0,
@@ -225,6 +221,7 @@ my %FallbackPrereqs = (
   "base" => 0,
   "constant" => 0,
   "integer" => 0,
+  "lib" => 0,
   "overload" => 0,
   "parent" => 0,
   "strict" => 0,

README.md

 [![DOI](https://zenodo.org/badge/doi/10.5281/zenodo.16344.svg)](http://dx.doi.org/10.5281/zenodo.16344)
 [![Build Status](https://travis-ci.org/bioperl/bioperl-live.svg?branch=master)](https://travis-ci.org/bioperl/bioperl-live)
-[![Coverage Status](https://coveralls.io/repos/bioperl/bioperl-live/badge.png?branch=master)](https://coveralls.io/r/bioperl/bioperl-live?branch=master)
+[![Coverage Status](https://coveralls.io/repos/bioperl/bioperl-live/badge.svg?branch=master)](https://coveralls.io/r/bioperl/bioperl-live?branch=master)
 [![Documentation Status](https://readthedocs.org/projects/bioperl/badge/?version=latest)](https://readthedocs.org/projects/bioperl/?badge=latest)
 
 # About BioPerl

bin/bp_seqpart

@@ -22,7 +22,7 @@ Script wrapping SeqIO that allows partitioning of multiple sequence files into n
 
 =head1 AUTHOR
 
-B<Matt Oates> - I<Matt.Oates@bristol.ac.uk>
+B<Matt Oates> - I<mattoates+support@gmail.com>
 
 =head1 FEEDBACK
 

debian/changelog

-bioperl (1.7.5-2) UNRELEASED; urgency=medium
+bioperl (1.7.6-1) unstable; urgency=medium
 
   * Team upload.
   * Fix autopkgtests:
       Don't run the `use.t` autopkgtest, there is no longer a Bio::Perl module
       scripts/ → bin/
       No Build.PL anymore, skip it
+  * Add missing colon in closes line.
+  * Set fields Upstream-Name, Upstream-Contact in debian/copyright.
+  * Set upstream metadata fields: Repository-Browse.
+  * Remove obsolete fields Name, Contact from debian/upstream/metadata.
+  * New upstream release.
+  * No longer conflicts with libbio-perl-run-perl (Closes: #921495)
+  * Fixed some spelling typos
 
- -- Michael R. Crusoe <michael.crusoe@gmail.com>  Sat, 14 Sep 2019 12:56:58 +0200
+ -- Michael R. Crusoe <michael.crusoe@gmail.com>  Tue, 26 Nov 2019 11:22:39 +0100
 
 bioperl (1.7.5-1) unstable; urgency=medium
 
@@ -466,7 +473,7 @@ bioperl (0.05.1-2) unstable; urgency=low
 
 bioperl (0.05.1-1) unstable; urgency=low
 
-  * Complies with the new Perl policy. Closes #40564
+  * Complies with the new Perl policy. Closes: #40564
   * New upstream release
 
  -- Stephane Bortzmeyer <bortzmeyer@debian.org>  Wed,  7 Jul 1999 14:49:16 +0200

debian/control

@@ -146,6 +146,7 @@ Depends: libio-string-perl,
          ${misc:Depends},
          ${perl:Depends}
 # Temporary workaround as bioperl-run has not been split
+Breaks: libio-perl-run-perl (<= 1.7.3-1 )
 Recommends: bioperl-run | libbio-perl-run-perl,
 # Recommended in Build.PL
             libace-perl,

debian/copyright

 Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Source: https://metacpan.org/release/BioPerl
+Upstream-Name: BioPerl
+Upstream-Contact: Bioperl developers <bioperl-l@bioperl.org>
 
 Files: *
 Copyright: The Bioperl developers.

debian/patches/series

+spelling

debian/patches/spelling

+From: Michael R. Crusoe <michael.crusoe@gmail.com>
+Subject: Debian "lintian" inspired spelling fixes
+--- bioperl.orig/lib/Bio/AlignIO/Handler/GenericAlignHandler.pm
++++ bioperl/lib/Bio/AlignIO/Handler/GenericAlignHandler.pm
+@@ -469,7 +469,7 @@
+ boolean flag: it must be present and set to 0 for the data to be tagged for
+ Bio::LocatableSeq or similar (in all other cases it is assumed to be for the
+ alignment). In some cases this will not matter (the actual sequence data, for
+-instance) but it is highly recommmended adding this tag in to prevent possible
++instance) but it is highly recommended adding this tag in to prevent possible
+ ambiguities.
+ 
+ This is the current Annotation data chunk (via Data::Dumper):
+--- bioperl.orig/lib/Bio/Index/EMBL.pm
++++ bioperl/lib/Bio/Index/EMBL.pm
+@@ -48,7 +48,7 @@
+ =head1 DESCRIPTION
+ 
+ Inherits functions for managing dbm files from Bio::Index::Abstract.pm,
+-and provides the basic funtionallity for indexing EMBL files, and
++and provides the basic funtionality for indexing EMBL files, and
+ retrieving the sequence from them. Heavily snaffled from James Gilbert
+ and his Fasta system. Note: for best results 'use strict'.
+ 
+--- bioperl.orig/lib/Bio/Index/Fasta.pm
++++ bioperl/lib/Bio/Index/Fasta.pm
+@@ -48,7 +48,7 @@
+ =head1 DESCRIPTION
+ 
+ Inherits functions for managing dbm files from Bio::Index::Abstract.pm,
+-and provides the basic funtionallity for indexing fasta files, and
++and provides the basic funtionality for indexing fasta files, and
+ retrieving the sequence from them. For best results 'use strict'.
+ 
+ Bio::Index::Fasta supports the Bio::DB::BioSeqI interface, meaning
+--- bioperl.orig/lib/Bio/Index/Fastq.pm
++++ bioperl/lib/Bio/Index/Fastq.pm
+@@ -46,7 +46,7 @@
+ =head1 DESCRIPTION
+ 
+ Inherits functions for managing dbm files from Bio::Index::Abstract.pm,
+-and provides the basic funtionallity for indexing fastq files, and
++and provides the basic funtionality for indexing fastq files, and
+ retrieving the sequence from them. Note: for best results 'use strict'.
+ 
+ Bio::Index::Fastq supports the Bio::DB::BioSeqI interface, meaning
+--- bioperl.orig/lib/Bio/Index/Qual.pm
++++ bioperl/lib/Bio/Index/Qual.pm
+@@ -46,7 +46,7 @@
+ =head1 DESCRIPTION
+ 
+ Inherits functions for managing dbm files from Bio::Index::Abstract.pm,
+-and provides the basic funtionallity for indexing qual files, and
++and provides the basic funtionality for indexing qual files, and
+ retrieving the sequence from them. For best results 'use strict'.
+ 
+ Bio::Index::Qual supports the Bio::DB::BioSeqI interface, meaning
+--- bioperl.orig/lib/Bio/Index/SwissPfam.pm
++++ bioperl/lib/Bio/Index/SwissPfam.pm
+@@ -45,7 +45,7 @@
+ provides a way of indexing this module.
+ 
+ Inherits functions for managing dbm files from Bio::Index::Abstract.pm, and 
+-provides the basic funtionallity for indexing SwissPfam files.  Only 
++provides the basic funtionality for indexing SwissPfam files.  Only 
+ retrieves FileStreams at the moment. Once we have something better 
+ (ie, an object!), will use that. Heavily snaffled from Index::Fasta system of 
+ James Gilbert. Note: for best results 'use strict'.
+--- bioperl.orig/lib/Bio/Tools/Run/Analysis.pm
++++ bioperl/lib/Bio/Tools/Run/Analysis.pm
+@@ -776,7 +776,7 @@
+ 
+ It makes an expert guess what kind of access/transport protocol should
+ be used to access the underlying analysis. The guess is based on the
+-parameters in I<rh_params>. Rememeber that this method is called only
++parameters in I<rh_params>. Remember that this method is called only
+ if there was no I<-access> parameter which could tell directly what
+ access method to use.
+ 
+--- bioperl.orig/lib/Bio/Tools/Run/AnalysisFactory.pm
++++ bioperl/lib/Bio/Tools/Run/AnalysisFactory.pm
+@@ -336,7 +336,7 @@
+ 
+ It makes an expert guess what kind of access/transport protocol should
+ be used to access the underlying analysis. The guess is based on the
+-parameters in I<rh_params>. Rememeber that this method is called only
++parameters in I<rh_params>. Remember that this method is called only
+ if there was no I<-access> parameter which could tell directly what
+ access method to use.
+ 
+--- bioperl.orig/lib/Bio/Tools/TandemRepeatsFinder.pm
++++ bioperl/lib/Bio/Tools/TandemRepeatsFinder.pm
+@@ -26,7 +26,7 @@
+ Written and tested for version 4.00
+ 
+ Location, seq_id, and score are stored in Bio::SeqFeature::Generic feature.
+-All other data is stored in tags.  The availabale tags are
++All other data is stored in tags.  The available tags are
+ 
+         period_size
+         copy_number
+--- bioperl.orig/lib/Bio/Tree/Statistics.pm
++++ bioperl/lib/Bio/Tree/Statistics.pm
+@@ -673,7 +673,7 @@
+ 
+   Example    : phylotype_length($tree, $node);
+   Description: Sums up the branch lengths within phylotype
+-               exluding the subclusters where the trait values
++               excluding the subclusters where the trait values
+                are different
+   Returns    : float, length
+   Exceptions : all the  nodes need to have the trait defined
+@@ -723,7 +723,7 @@
+ 
+   Example    : sum_of_leaf_distances($tree, $node);
+   Description: Sums up the branch lengths from root to leaf
+-               exluding the subclusters where the trait values
++               excluding the subclusters where the trait values
+                are different
+   Returns    : float, length
+   Exceptions : all the  nodes need to have the trait defined

debian/upstream/metadata

 Bug-Database: https://redmine.open-bio.org/projects/bioperl
-Contact: Bioperl developers <bioperl-l@bioperl.org>
-Name: BioPerl
 Reference:
- Author: >
-  Jason E Stajich and David Block and Kris Boulez and Steven E Brenner
-  and Stephen A Chervitz and Chris Dagdigian and Georg Fuellen
-  and James G R Gilbert and Ian Korf and Hilmar Lapp and Heikki Lehvaslaiho
-  and Chad Matsalla and Chris J Mungall and Brian I Osborne
-  and Matthew R Pocock and Peter Schattner and Martin Senger
-  and Lincoln D Stein and Elia Stupka and Mark D Wilkinson and Ewan Birney
+  Author: "Jason E Stajich and David Block and Kris Boulez and Steven E Brenner and\
+    \ Stephen A Chervitz and Chris Dagdigian and Georg Fuellen and James G R Gilbert\
+    \ and Ian Korf and Hilmar Lapp and Heikki Lehvaslaiho and Chad Matsalla and Chris\
+    \ J Mungall and Brian I Osborne and Matthew R Pocock and Peter Schattner and Martin\
+    \ Senger and Lincoln D Stein and Elia Stupka and Mark D Wilkinson and Ewan Birney\n"
   Title: "The Bioperl toolkit: Perl modules for the life sciences"
   Journal: Genome Res.
   Year: 2002
@@ -29,3 +25,4 @@ Registry:
   Entry: SCR_002989
 - Name: conda:bioconda
   Entry: perl-bioperl-core
+Repository-Browse: https://github.com/bioperl/bioperl-live

dist.ini

 name = BioPerl
-version = 1.7.5
+version = 1.7.6
 author = See individual modules
 copyright_holder = See individual modules
 license = Perl_5
@@ -25,6 +25,11 @@ AutoPrereqs.skips[3] = ^Bio::DB::GenBank$
 AutoPrereqs.skips[4] = ^Bio::DB::GenPept$
 AutoPrereqs.skips[5] = ^Bio::DB::SwissProt$
 
+;; The program bp_chaos_plot uses GD but for users without a package
+;; manager that can be tricky to install.  Make it a suggestion.
+AutoPrereqs.skips[6] = ^GD$
+
+
 [OSPrereqs / MSWin32]
 Win32 = 0
 
@@ -36,6 +41,9 @@ Bio::DB::GenBank = 0
 Bio::DB::GenPept = 0
 Bio::DB::SwissProt = 0
 
+[Prereqs / bin_bp_chaos_plot_RuntimeSuggests]
+-relationship = suggests
+GD = 0
 
 ;; PodWeaver has some minimum requirements on the files before it can
 ;; be used.  To allow a migration overtime, we can list the files that

lib/Bio/Align/AlignI.pm

@@ -93,7 +93,7 @@ Internal methods are usually preceded with a _
 
 
 package Bio::Align::AlignI;
-$Bio::Align::AlignI::VERSION = '1.7.5';
+$Bio::Align::AlignI::VERSION = '1.7.6';
 use strict;
 
 use base qw(Bio::Root::RootI);

lib/Bio/Align/DNAStatistics.pm

@@ -335,7 +335,7 @@ Internal methods are usually preceded with a _
 
 
 package Bio::Align::DNAStatistics;
-$Bio::Align::DNAStatistics::VERSION = '1.7.5';
+$Bio::Align::DNAStatistics::VERSION = '1.7.6';
 use vars qw(%DNAChanges @Nucleotides %NucleotideIndexes
 	    $GapChars $SeqCount $DefaultGapPenalty %DistanceMethods
             $CODONS %synchanges $synsites $Precision $GCChhars);

lib/Bio/Align/PairwiseStatistics.pm

@@ -76,7 +76,7 @@ Internal methods are usually preceded with a _
 
 
 package Bio::Align::PairwiseStatistics;
-$Bio::Align::PairwiseStatistics::VERSION = '1.7.5';
+$Bio::Align::PairwiseStatistics::VERSION = '1.7.6';
 use vars qw($GapChars);
 use strict;
 

lib/Bio/Align/ProteinStatistics.pm

@@ -86,7 +86,7 @@ Internal methods are usually preceded with a _
 
 
 package Bio::Align::ProteinStatistics;
-$Bio::Align::ProteinStatistics::VERSION = '1.7.5';
+$Bio::Align::ProteinStatistics::VERSION = '1.7.6';
 use vars qw(%DistanceMethods $Precision $DefaultGapPenalty);
 use strict;
 

lib/Bio/Align/StatisticsI.pm

@@ -69,7 +69,7 @@ Internal methods are usually preceded with a _
 
 
 package Bio::Align::StatisticsI;
-$Bio::Align::StatisticsI::VERSION = '1.7.5';
+$Bio::Align::StatisticsI::VERSION = '1.7.6';
 use strict;