[med-svn] [roary] 01/05: Imported Upstream version 3.5.8+dfsg
Sascha Steinbiss
sascha at steinbiss.name
Sun Feb 7 11:46:37 UTC 2016
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sascha-guest pushed a commit to branch master
in repository roary.
commit 0901b109b185b80dd1564d2a56db11781262a820
Author: Sascha Steinbiss <sascha at steinbiss.name>
Date: Sun Feb 7 10:55:58 2016 +0000
Imported Upstream version 3.5.8+dfsg
---
bin/pan_genome_assembly_statistics | 4 +--
dist.ini | 2 +-
install_dependencies.sh | 2 +-
lib/Bio/Roary/AccessoryBinaryFasta.pm | 44 ++++++++-----------------
lib/Bio/Roary/AssemblyStatistics.pm | 4 +--
lib/Bio/Roary/CommandLine/AssemblyStatistics.pm | 4 +--
lib/Bio/Roary/SplitGroups.pm | 4 +--
t/Bio/Roary/AccessoryBinaryFasta.t | 25 --------------
8 files changed, 23 insertions(+), 66 deletions(-)
diff --git a/bin/pan_genome_assembly_statistics b/bin/pan_genome_assembly_statistics
index 5960b3e..54e1a17 100755
--- a/bin/pan_genome_assembly_statistics
+++ b/bin/pan_genome_assembly_statistics
@@ -2,12 +2,12 @@
package Bio::Roary::Main::AssemblyStatistics;
-# ABSTRACT: Given a spreadsheet of gene presence and absense calculate some statistics
+# ABSTRACT: Given a spreadsheet of gene presence and absence calculate some statistics
# PODNAME: pan_genome_assembly_statistics
=head1 SYNOPSIS
-Given a spreadsheet of gene presence and absense calculate some statistics
+Given a spreadsheet of gene presence and absence calculate some statistics
=cut
diff --git a/dist.ini b/dist.ini
index e1942c2..ececa65 100644
--- a/dist.ini
+++ b/dist.ini
@@ -1,5 +1,5 @@
name = Bio-Roary
-version = 3.5.7
+version = 3.5.8
author = Andrew J. Page <ap13 at sanger.ac.uk>
license = GPL_3
copyright_holder = Wellcome Trust Sanger Institute
diff --git a/install_dependencies.sh b/install_dependencies.sh
index 1dc2914..e53cf89 100755
--- a/install_dependencies.sh
+++ b/install_dependencies.sh
@@ -36,7 +36,7 @@ FASTTREE_VERSION="2.1.8"
FASTTREE_DOWNLOAD_FILENAME="FastTree-${FASTTREE_VERSION}.c"
FASTTREE_URL="http://microbesonline.org/fasttree/FastTree-${FASTTREE_VERSION}.c"
-MAFFT_VERSION="7.221"
+MAFFT_VERSION="7.271"
MAFFT_DOWNLOAD_FILENAME="mafft-${MAFFT_VERSION}-without-extensions-src.tgz"
MAFFT_URL="http://mafft.cbrc.jp/alignment/software/${MAFFT_DOWNLOAD_FILENAME}"
diff --git a/lib/Bio/Roary/AccessoryBinaryFasta.pm b/lib/Bio/Roary/AccessoryBinaryFasta.pm
index b398878..9f7fd16 100644
--- a/lib/Bio/Roary/AccessoryBinaryFasta.pm
+++ b/lib/Bio/Roary/AccessoryBinaryFasta.pm
@@ -20,16 +20,13 @@ use Bio::Roary::Exceptions;
use Bio::SeqIO;
use File::Basename;
-has 'input_files' => ( is => 'ro', isa => 'ArrayRef', required => 1 );
-has 'annotate_groups_obj' => ( is => 'ro', isa => 'Bio::Roary::AnnotateGroups', required => 1 );
-has 'analyse_groups_obj' => ( is => 'ro', isa => 'Bio::Roary::AnalyseGroups', required => 1 );
-has 'output_filename' => ( is => 'ro', isa => 'Str', default => 'accessory_binary_genes.fa' );
-has 'lower_bound_percentage' => ( is => 'ro', isa => 'Int', default => 5 );
-has 'upper_bound_percentage' => ( is => 'ro', isa => 'Int', default => 5 );
-has 'max_accessory_to_include' => ( is => 'ro', isa => 'Int', default => 4000 );
-has 'groups_to_files' => ( is => 'ro', isa => 'HashRef', lazy => 1, builder => '_build__groups_to_files' );
-has '_lower_bound_value' => ( is => 'ro', isa => 'Int', lazy => 1, builder => '_build__lower_bound_value' );
-has '_upper_bound_value' => ( is => 'ro', isa => 'Int', lazy => 1, builder => '_build__upper_bound_value' );
+has 'input_files' => ( is => 'ro', isa => 'ArrayRef', required => 1 );
+has 'annotate_groups_obj' => ( is => 'ro', isa => 'Bio::Roary::AnnotateGroups', required => 1 );
+has 'analyse_groups_obj' => ( is => 'ro', isa => 'Bio::Roary::AnalyseGroups', required => 1 );
+has 'output_filename' => ( is => 'ro', isa => 'Str', default => 'accessory_binary_genes.fa' );
+has 'groups_to_files' => ( is => 'ro', isa => 'HashRef', lazy => 1, builder => '_build__groups_to_files' );
+has '_lower_bound_value' => ( is => 'ro', isa => 'Int', lazy => 1, builder => '_build__lower_bound_value' );
+has '_upper_bound_value' => ( is => 'ro', isa => 'Int', lazy => 1, builder => '_build__upper_bound_value' );
sub _build__groups_to_files {
my ($self) = @_;
@@ -47,37 +44,22 @@ sub _build__groups_to_files {
return \%groups_to_files;
}
-sub _build__lower_bound_value {
- my ($self) = @_;
- my $num_files = @{ $self->input_files };
- return ceil( $num_files * ( $self->lower_bound_percentage / 100 ) );
-}
-
-sub _build__upper_bound_value {
- my ($self) = @_;
- my $num_files = @{ $self->input_files };
- return $num_files - ceil( $num_files * ( $self->upper_bound_percentage / 100 ) );
-}
-
sub create_accessory_binary_fasta {
my ($self) = @_;
my $out_seq_io = Bio::SeqIO->new( -file => ">" . $self->output_filename, -format => 'Fasta' );
for my $full_filename ( @{ $self->input_files } ) {
- my($filename, $dirs, $suffix) = fileparse($full_filename);
-
+ my ( $filename, $dirs, $suffix ) = fileparse($full_filename);
+
my $output_sequence = '';
my $sample_name = $filename;
$sample_name =~ s!\.gff\.proteome\.faa!!;
- my $gene_count = 0;
+ my $gene_count = 0;
for my $group ( sort keys %{ $self->groups_to_files } ) {
- last if($gene_count > $self->max_accessory_to_include);
my @files = keys %{ $self->groups_to_files->{$group} };
- next if ( @files <= $self->_lower_bound_value || @files > $self->_upper_bound_value );
-
my $group_to_file_genes = $self->groups_to_files->{$group}->{$full_filename};
if ( defined($group_to_file_genes) && @{$group_to_file_genes} > 0 ) {
$output_sequence .= 'A';
@@ -85,10 +67,10 @@ sub create_accessory_binary_fasta {
else {
$output_sequence .= 'C';
}
- $gene_count++;
-
+ $gene_count++;
+
}
- next if($output_sequence eq '');
+ next if ( $output_sequence eq '' );
$out_seq_io->write_seq( Bio::Seq->new( -display_id => $sample_name, -seq => $output_sequence ) );
}
return 1;
diff --git a/lib/Bio/Roary/AssemblyStatistics.pm b/lib/Bio/Roary/AssemblyStatistics.pm
index cc0b32a..ccda667 100644
--- a/lib/Bio/Roary/AssemblyStatistics.pm
+++ b/lib/Bio/Roary/AssemblyStatistics.pm
@@ -1,10 +1,10 @@
package Bio::Roary::AssemblyStatistics;
-# ABSTRACT: Given a spreadsheet of gene presence and absense calculate some statistics
+# ABSTRACT: Given a spreadsheet of gene presence and absence calculate some statistics
=head1 SYNOPSIS
-Given a spreadsheet of gene presence and absense calculate some statistics
+Given a spreadsheet of gene presence and absence calculate some statistics
=cut
diff --git a/lib/Bio/Roary/CommandLine/AssemblyStatistics.pm b/lib/Bio/Roary/CommandLine/AssemblyStatistics.pm
index 5562c65..0d4754f 100644
--- a/lib/Bio/Roary/CommandLine/AssemblyStatistics.pm
+++ b/lib/Bio/Roary/CommandLine/AssemblyStatistics.pm
@@ -1,11 +1,11 @@
undef $VERSION;
package Bio::Roary::CommandLine::AssemblyStatistics;
-# ABSTRACT: Given a spreadsheet of gene presence and absense calculate some statistics
+# ABSTRACT: Given a spreadsheet of gene presence and absence calculate some statistics
=head1 SYNOPSIS
-Given a spreadsheet of gene presence and absense calculate some statistics
+Given a spreadsheet of gene presence and absence calculate some statistics
=cut
diff --git a/lib/Bio/Roary/SplitGroups.pm b/lib/Bio/Roary/SplitGroups.pm
index 0c2a991..590a835 100644
--- a/lib/Bio/Roary/SplitGroups.pm
+++ b/lib/Bio/Roary/SplitGroups.pm
@@ -1,6 +1,6 @@
package Bio::Roary::SplitGroups;
-# ABSTRACT:
+# ABSTRACT: split groups
=head1 SYNOPSIS
@@ -321,4 +321,4 @@ sub _parse_gene_neighbourhood {
no Moose;
__PACKAGE__->meta->make_immutable;
-1;
\ No newline at end of file
+1;
diff --git a/t/Bio/Roary/AccessoryBinaryFasta.t b/t/Bio/Roary/AccessoryBinaryFasta.t
index 435839b..1c0870e 100755
--- a/t/Bio/Roary/AccessoryBinaryFasta.t
+++ b/t/Bio/Roary/AccessoryBinaryFasta.t
@@ -33,8 +33,6 @@ ok(
group_3 => { 't/abc/aaa' => [1], 't/abc/bbb' => [2], 't/abc/ccc' => [3] },
group_4 => { 't/abc/aaa' => [1], 't/abc/bbb' => [2], 't/abc/ccc' => [3], 't/abc/ddd' => [4] },
},
- _lower_bound_value => 0,
- _upper_bound_value => 4,
annotate_groups_obj => $dummy_annotate_groups,
analyse_groups_obj => $dummy_analyse_groups
),
@@ -46,27 +44,4 @@ ok( $obj->create_accessory_binary_fasta(), 'create output file' );
compare_ok( 'accessory_binary_genes.fa', 't/data/expected_accessory_binary_genes.fa','binary accessory fasta file created');
-ok(
- $obj = Bio::Roary::AccessoryBinaryFasta->new(
- input_files => [ 'aaa', 'bbb', 'ccc', 'ddd' ],
- groups_to_files =>
- {
- group_1 => { 'aaa' => [1] },
- group_2 => { 'aaa' => [1], 'bbb' => [2] },
- group_3 => { 'aaa' => [1], 'bbb' => [2], 'ccc' => [3] },
- group_4 => { 'aaa' => [1], 'bbb' => [2], 'ccc' => [3], 'ddd' => [4] },
- },
- annotate_groups_obj => $dummy_annotate_groups,
- analyse_groups_obj => $dummy_analyse_groups
- ),
- 'initialise accessory binary fasta file bounded'
-);
-
-is($obj->_lower_bound_value, 1, 'lower bound value');
-is($obj->_upper_bound_value, 3, 'upper bound value');
-ok( $obj->create_accessory_binary_fasta(), 'create output file bounded' );
-
-compare_ok( 'accessory_binary_genes.fa', 't/data/expected_accessory_binary_genes_bounded.fa','binary accessory fasta file created bounded');
-
-
done_testing();
--
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