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sascha-guest pushed a commit to branch master
in repository roary.
commit 3227e01b06e44138242e7ff10ea1ed353b7306a1
Author: Sascha Steinbiss <sas...@steinbiss.name>
Date: Sun Dec 20 13:40:29 2015 +0000
add patches for manpage generation and script rename
---
debian/patches/add_abstract.patch | 40 ++++++++++++++++++++++++++++++
debian/patches/rename_R_script.patch | 11 +++++++++
debian/patches/series | 3 +++
debian/patches/spelling.patch | 48 ++++++++++++++++++++++++++++++++++++
4 files changed, 102 insertions(+)
diff --git a/debian/patches/add_abstract.patch
b/debian/patches/add_abstract.patch
new file mode 100644
index 0000000..02a6afa
--- /dev/null
+++ b/debian/patches/add_abstract.patch
@@ -0,0 +1,40 @@
+--- 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
+
+@@ -52,7 +52,7 @@
+
+ sub _build__analyse_groups_obj {
+ my ( $self ) = @_;
+-
++
+ return Bio::Roary::AnalyseGroups->new(
+ fasta_files => $self->fasta_files,
+ groups_filename => $self->groupfile
+@@ -85,9 +85,9 @@
+ {
+ my ( $filename, $directories, $suffix ) = fileparse( $fasta_file,
qr/\.[^.]*/ );
+ system('grep \> '.$fasta_file.'| sed \'s/>//\'
>'.$self->_gene_files_temp_dir_obj."/".$filename.$suffix ) ;
+-
++
+ my @genes =
read_lines($self->_gene_files_temp_dir_obj."/".$filename.$suffix );
+-
++
+ for(my $i =0; $i< @genes; $i++)
+ {
+ for(my $offset = 1; $offset <= $self->_neighbourhood_size;
$offset++)
+@@ -111,7 +111,7 @@
+
+ # iteratively
+ for my $x ( 0..($self->iterations - 1) ){
+- my ( $in_groups, $out_groups ) =
$self->_get_files_for_iteration( $x );
++ my ( $in_groups, $out_groups ) =
$self->_get_files_for_iteration( $x );
+
+ # read in groups, check paralogs and split
+ my @newgroups;
diff --git a/debian/patches/rename_R_script.patch
b/debian/patches/rename_R_script.patch
new file mode 100644
index 0000000..4718f63
--- /dev/null
+++ b/debian/patches/rename_R_script.patch
@@ -0,0 +1,11 @@
+--- a/lib/Bio/Roary/PostAnalysis.pm
++++ b/lib/Bio/Roary/PostAnalysis.pm
+@@ -125,7 +125,7 @@
+ $self->logger->info("Creating tab files for R");
+ $self->_number_of_groups_obj->create_output_files;
+
+- system("create_pan_genome_plots.R") unless ( $self->dont_create_rplots ==
1 );
++ system("create_pan_genome_plots") unless ( $self->dont_create_rplots == 1
);
+
+ $self->logger->info("Create EMBL files");
+ $self->_create_embl_files;
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..51f63b5
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1,3 @@
+rename_R_script.patch
+add_abstract.patch
+spelling.patch
diff --git a/debian/patches/spelling.patch b/debian/patches/spelling.patch
new file mode 100644
index 0000000..4ce6e6d
--- /dev/null
+++ b/debian/patches/spelling.patch
@@ -0,0 +1,48 @@
+--- 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
+
+--- 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
+
+--- 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
+
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