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View file @ be360743
Summary of important user-visible changes for BioPerl
-----------------------------------------------------
1.7.7 2019-12-07 13:41:36-06:00 America/Chicago
* The program bp_chaos_plot has been removed.
* GD is now no longer a dependency, suggestion or requirement.
* #321 - GenBank format fix for un-quoted features, text wrapping
* Bio::DB::Query::WebQuery now includes methods for delay(), delay_policy(),
and a 'private' _sleep() function that mirror those from
Bio::DB::WebDBSeqI, primarily for compliance with potential website
restrictions for the number and frequency of queries (e.g. NCBI eUtils).
* Fix bug #329, related to Bio::Tree::Statistics::transfer_bootstrap_expectation
in last release.
1.7.6 2019-08-28 12:37:01+01:00 Europe/London
* The program bp_classify_hits_kingdom has been removed and is
......
HACKING.md
View file @ be360743
......@@ -26,6 +26,19 @@ The bioperl-live repository structure is organized as follows:
## `Bio::` namespace summary
The BioPerl project is split over multiple Perl module distributions.
The BioPerl distribution is the BioPerl core distribution, including a
selection of modules and namespaces but not all. For example, the
entire Bio::Biblio is not included in the BioPerl distribution.
Similarly, while many Bio::SearchIO modules in the BioPerl
distribution, there also Bio::SearchIO modules in other distributions
such as Bio-SearchIO-blastxml.
This section describes most of the Bio:: namespaces developed by the
BioPerl project, including those which are not part of the BioPerl
distribution. For example, the Bio::Biblio and Bio::Assembly are
documented here but are not part of the BioPerl distribution.
* `Bio::Seq` is for *Sequences* (protein and DNA).
* `Bio::PrimarySeq` is a plain sequence (sequence data +
identifiers)
......
MANIFEST
View file @ be360743
......@@ -11,7 +11,6 @@ README.md
bin/bp_aacomp
bin/bp_bioflat_index
bin/bp_biogetseq
bin/bp_chaos_plot
bin/bp_dbsplit
bin/bp_extract_feature_seq
bin/bp_fastam9_to_table
......
META.json
View file @ be360743
......@@ -105,8 +105,7 @@
"Bio::DB::EMBL" : "0",
"Bio::DB::GenBank" : "0",
"Bio::DB::GenPept" : "0",
"Bio::DB::SwissProt" : "0",
"GD" : "0"
"Bio::DB::SwissProt" : "0"
}
},
"test" : {
......@@ -136,7 +135,7 @@
"web" : "https://github.com/bioperl/bioperl-live"
}
},
"version" : "1.7.6",
"version" : "1.7.7",
"x_Dist_Zilla" : {
"perl" : {
"version" : "5.028001"
......@@ -346,7 +345,7 @@
"branch" : null,
"changelog" : "Changes",
"signed" : 0,
"tag" : "BioPerl-v1.7.6",
"tag" : "BioPerl-v1.7.7",
"tag_format" : "%N-v%v",
"tag_message" : "%N-v%v"
},
......@@ -382,17 +381,6 @@
"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",
......@@ -502,7 +490,7 @@
{
"class" : "Pod::Weaver::Section::Legal::Complicated",
"name" : "@BioPerl/Legal",
"version" : "1.22"
"version" : "1.23"
},
{
"class" : "Pod::Weaver::Section::Contributors",
......
META.yml
View file @ be360743
......@@ -98,7 +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: 1.7.6
version: 1.7.7
x_Dist_Zilla:
perl:
version: '5.028001'
......@@ -263,7 +263,7 @@ x_Dist_Zilla:
branch: ~
changelog: Changes
signed: 0
tag: BioPerl-v1.7.6
tag: BioPerl-v1.7.7
tag_format: '%N-v%v'
tag_message: '%N-v%v'
Dist::Zilla::Role::Git::Repo:
......@@ -288,14 +288,6 @@ 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
......@@ -384,7 +376,7 @@ x_Dist_Zilla:
-
class: Pod::Weaver::Section::Legal::Complicated
name: '@BioPerl/Legal'
version: '1.22'
version: '1.23'
-
class: Pod::Weaver::Section::Contributors
name: '@BioPerl/Contributors'
......
Makefile.PL
View file @ be360743
......@@ -17,7 +17,6 @@ my %WriteMakefileArgs = (
"bin/bp_aacomp",
"bin/bp_bioflat_index",
"bin/bp_biogetseq",
"bin/bp_chaos_plot",
"bin/bp_dbsplit",
"bin/bp_extract_feature_seq",
"bin/bp_fastam9_to_table",
......@@ -143,7 +142,7 @@ my %WriteMakefileArgs = (
"Test::Weaken" => 0,
"lib" => 0
},
"VERSION" => "1.7.6",
"VERSION" => "1.7.7",
"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"
}
......
bin/bp_chaos_plot deleted 100644 → 0
View file @ 9be3a5a7
#!/usr/bin/perl
use strict;
use warnings;
use Bio::SeqIO;
use Getopt::Long;
use GD;
use vars qw( $USAGE %VALIDFORMATS);
%VALIDFORMATS = ( 'png' => 1,
'jpeg' => 1,
'gd2' => 1,
'gd' => 1,
'gif' => 1,
'wbmp' => 1 );
$USAGE = "usage:\tchaos_plot -i/--input=INPUTFILE -f/--format=SEQFORMAT \n".
"\t-o/--output=OUTPUTFILE -g/--graphics=GRAPHIC TYPE\n".
"\t-w/--width=600 -h/--height=400\n";
$USAGE .= "\tValid graphics formats: (" . join(",", ( keys %VALIDFORMATS )) .")\n";
$USAGE .= "\tImage size defaults to 600x400, SEQFORMAT to fasta\n";
$USAGE .= "\tINPUTFILE can also be read from STDIN\n";
my ($format,$graph,$width,$height,$seqfile,$output) = ('fasta', 'png', 600, 400);
GetOptions( "i|input:s" => \$seqfile,
"f|format:s" => \$format,
"o|output:s" => \$output,
"g|graph|graphics:s" => \$graph,
"width:i" => \$width,
"height:i" => \$height
);
if( ! $output || ! $VALIDFORMATS{$graph} ) {
die $USAGE ;
}
my $seqin;
$seqfile = shift unless $seqfile;
if( defined $seqfile ) {
print "Could not open file [$seqfile]\n$USAGE" and exit unless -e $seqfile;
$seqin = new Bio::SeqIO(-format => $format,
-file => $seqfile);
} else {
$seqin = new Bio::SeqIO(-format => $format,
-fh => \*STDIN);
}
my $img = new GD::Image($width,$height);
my $white = $img->colorAllocate(255,255,255);
my $black = $img->colorAllocate(0,0,0);
my $seq = $seqin->next_seq;
die("Sequence type must be DNA not " . $seq->alphabet())
unless $seq->alphabet ne 'dna' or $seq->alphabet ne 'rna';
my %nmerdata;
my $len = $seq->length();
my $max = 0;
my ($x,$y) = ( 0.5, 0.5);
$img->string(gdGiantFont, 1,1, 'A', $black);
$img->string(gdGiantFont, 0,$height - 15, 'C', $black);
$img->string(gdGiantFont, $width - 15,1, 'T', $black);
$img->string(gdGiantFont, $width - 15,$height -20, 'G', $black);
for( my $i = 1; $i <= $len; $i++ ) {
my $base = lc $seq->subseq($i,$i);
if( $base eq 'a' ) {
$x *= 0.5;
$y *= 0.5;
} elsif ( $base eq 'g' ) {
$x = ( $x + 1.0 ) * 0.5;
$y = ( $y + 1.0 ) * 0.5;
} elsif ( $base eq 'c' ) {
$x *= 0.5;
$y = ( $y + 1.0 ) * 0.5;
} elsif ( $base eq 't' or $base eq 'u' ) {
$x = ( $x + 1.0 ) * 0.5;
$y *= 0.5;
}
$img->setPixel($x * $width,$y * $height, $black);
}
open my $OUT, '>', $output or die "Could not write file '$output': $!\n";
binmode $OUT;
$graph =~ s/jpg/jpeg/;
print $OUT $img->$graph();
close $OUT;
__END__
=head1 NAME
bp_chaos_plot - a chaos plot from DNA and RNA sequences
=head1 SYNOPSIS
bp_chaos_plot.pl -i/--input=INPUTFILE -f/--format=SEQFORMAT
-o/--output=OUTPUTFILE -g/--graphics=GRAPHIC FORMAT
-w/--width=WIGHT -h/--height=HEIGHT
=head1 DESCRIPTION
This scripts generates image files using GD image library to visualize
nucleotide sequences using chaos plot.
=head1 OPTIONS
Valid graphics formats are currently gd, gd2, png, wbmp, jpeg and gif.
The default size of the image file is 600x400.
The sequence input can be provided using any of the three methods:
=over 3
=item unnamed argument
bp_chaos_plot filename
=item named argument
bp_chaos_plot -i filename
=item standard input
bp_chaos_plot < filename
=back
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via the
web:
https://github.com/bioperl/bioperl-live/issues
=head1 AUTHOR - Jason Stajich
Email jason@bioperl.org
=head1 HISTORY
This code is based on EMBOSS C code for chaos.c by Ian Longden.
Included are documentation from EMBOSS code:
Chaos produces a chaos plot. The original application is part of the
ACEDB genome database package, written by ** Richard Durbin (MRC LMB,
UK) rd@mrc-lmba.cam.ac.uk, and Jean Thierry-Mieg (CRBM du CNRS,
France) mieg@crbm1.cnusc.fr
=cut
debian/changelog
View file @ be360743
bioperl (1.7.7-1) unstable; urgency=medium
* Team upload.
* New upstream release.
-- Michael R. Crusoe <michael.crusoe@gmail.com> Sat, 14 Dec 2019 22:48:17 +0100
bioperl (1.7.6-3) unstable; urgency=medium
* Team upload.
......
debian/control
View file @ be360743
......@@ -62,7 +62,7 @@ Build-Depends-Indep: perl,
libtest-requiresinternet-perl,
# Needed to avoid downloading DTDs during the tests and therefore fail when network is not available:
libxml-sax-expatxs-perl
Standards-Version: 4.4.0
Standards-Version: 4.4.1
Vcs-Browser: https://salsa.debian.org/med-team/bioperl
Vcs-Git: https://salsa.debian.org/med-team/bioperl.git
Homepage: http://www.bioperl.org/
......
debian/patches/spelling deleted 100644 → 0
View file @ 9be3a5a7
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, $node);
Description: Sums up the branch lengths from root to leaf
- exluding the subclusters where the trait values
+ excluding the subclusters where the trait values
are different
Returns : float, length
Exceptions : all the nodes need to have the trait defined
dist.ini
View file @ be360743
name = BioPerl
version = 1.7.6
version = 1.7.7
author = See individual modules
copyright_holder = See individual modules
license = Perl_5
......@@ -25,10 +25,6 @@ AutoPrereqs.skips[3] = ^Bio::DB::GenBank$
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
......@@ -41,10 +37,6 @@ 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
;; are ready here.
......
lib/Bio/Align/AlignI.pm
View file @ be360743
......@@ -93,7 +93,7 @@ Internal methods are usually preceded with a _
package Bio::Align::AlignI;
$Bio::Align::AlignI::VERSION = '1.7.6';
$Bio::Align::AlignI::VERSION = '1.7.7';
use strict;
use base qw(Bio::Root::RootI);
......
lib/Bio/Align/DNAStatistics.pm
View file @ be360743
......@@ -335,7 +335,7 @@ Internal methods are usually preceded with a _
package Bio::Align::DNAStatistics;
$Bio::Align::DNAStatistics::VERSION = '1.7.6';
$Bio::Align::DNAStatistics::VERSION = '1.7.7';
use vars qw(%DNAChanges @Nucleotides %NucleotideIndexes
$GapChars $SeqCount $DefaultGapPenalty %DistanceMethods
$CODONS %synchanges $synsites $Precision $GCChhars);
......
lib/Bio/Align/PairwiseStatistics.pm
View file @ be360743
......@@ -76,7 +76,7 @@ Internal methods are usually preceded with a _
package Bio::Align::PairwiseStatistics;
$Bio::Align::PairwiseStatistics::VERSION = '1.7.6';
$Bio::Align::PairwiseStatistics::VERSION = '1.7.7';
use vars qw($GapChars);
use strict;
......
lib/Bio/Align/ProteinStatistics.pm
View file @ be360743
......@@ -86,7 +86,7 @@ Internal methods are usually preceded with a _
package Bio::Align::ProteinStatistics;
$Bio::Align::ProteinStatistics::VERSION = '1.7.6';
$Bio::Align::ProteinStatistics::VERSION = '1.7.7';
use vars qw(%DistanceMethods $Precision $DefaultGapPenalty);
use strict;
......
lib/Bio/Align/StatisticsI.pm
View file @ be360743
......@@ -69,7 +69,7 @@ Internal methods are usually preceded with a _
package Bio::Align::StatisticsI;
$Bio::Align::StatisticsI::VERSION = '1.7.6';
$Bio::Align::StatisticsI::VERSION = '1.7.7';
use strict;
......
lib/Bio/Align/Utilities.pm
View file @ be360743
package Bio::Align::Utilities;
$Bio::Align::Utilities::VERSION = '1.7.6';
$Bio::Align::Utilities::VERSION = '1.7.7';
use strict;
use warnings;
use Carp;
......
lib/Bio/AlignIO.pm
View file @ be360743
......@@ -274,7 +274,7 @@ methods. Internal methods are usually preceded with a _
# 'Let the code begin...
package Bio::AlignIO;
$Bio::AlignIO::VERSION = '1.7.6';
$Bio::AlignIO::VERSION = '1.7.7';
use strict;
use Bio::Seq;
......
lib/Bio/AlignIO/Handler/GenericAlignHandler.pm
View file @ be360743
# Let the code begin...
package Bio::AlignIO::Handler::GenericAlignHandler;
$Bio::AlignIO::Handler::GenericAlignHandler::VERSION = '1.7.6';
$Bio::AlignIO::Handler::GenericAlignHandler::VERSION = '1.7.7';
use strict;
use warnings;
......@@ -469,7 +469,7 @@ to disambiguate between the two in some cases. Here I use the ALIGNMENT tag as a
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):
......