Merge pull request #244 from andrewjpage/prefix_commands_with_roary

prefix commands with roary

.gitignore

@@ -33,4 +33,3 @@ set_difference_unique_set_two_reannotated
 extras/
 bin/shred_assemblies
 Bio-Roary-*
-Roary-*

bin/roary-create_pan_genome_plots.R

@@ -0,0 +1,59 @@
+#!/usr/bin/env Rscript
+# ABSTRACT: Create R plots
+# PODNAME: create_plots.R
+# Take the output files from the pan genome pipeline and create nice plots.
+library(ggplot2)
+
+
+mydata = read.table("number_of_new_genes.Rtab")
+boxplot(mydata, data=mydata, main="Number of new genes",
+         xlab="No. of genomes", ylab="No. of genes",varwidth=TRUE, ylim=c(0,max(mydata)), outline=FALSE)
+
+mydata = read.table("number_of_conserved_genes.Rtab")
+boxplot(mydata, data=mydata, main="Number of conserved genes",
+          xlab="No. of genomes", ylab="No. of genes",varwidth=TRUE, ylim=c(0,max(mydata)), outline=FALSE)
+
+mydata = read.table("number_of_genes_in_pan_genome.Rtab")
+boxplot(mydata, data=mydata, main="No. of genes in the pan-genome",
+          xlab="No. of genomes", ylab="No. of genes",varwidth=TRUE, ylim=c(0,max(mydata)), outline=FALSE)
+
+mydata = read.table("number_of_unique_genes.Rtab")
+boxplot(mydata, data=mydata, main="Number of unique genes",
+         xlab="No. of genomes", ylab="No. of genes",varwidth=TRUE, ylim=c(0,max(mydata)), outline=FALSE)
+
+mydata = read.table("blast_identity_frequency.Rtab")
+plot(mydata,main="Number of blastp hits with different percentage identity",  xlab="Blast percentage identity", ylab="No. blast results")
+
+
+library(ggplot2)
+conserved = colMeans(read.table("number_of_conserved_genes.Rtab"))
+total = colMeans(read.table("number_of_genes_in_pan_genome.Rtab"))
+
+genes = data.frame( genes_to_genomes = c(conserved,total),
+                    genomes = c(c(1:length(conserved)),c(1:length(conserved))),
+                    Key = c(rep("Conserved genes",length(conserved)), rep("Total genes",length(total))) )
+
+ggplot(data = genes, aes(x = genomes, y = genes_to_genomes, group = Key, linetype=Key)) +geom_line()+
+theme_classic() +
+ylim(c(1,max(total)))+
+xlim(c(1,length(total)))+
+xlab("No. of genomes") +
+ylab("No. of genes")+ theme_bw(base_size = 16) +  theme(legend.justification=c(0,1),legend.position=c(0,1))+
+ggsave(filename="conserved_vs_total_genes.png", scale=1)
+
+######################
+
+unique_genes = colMeans(read.table("number_of_unique_genes.Rtab"))
+new_genes = colMeans(read.table("number_of_new_genes.Rtab"))
+
+genes = data.frame( genes_to_genomes = c(unique_genes,new_genes),
+                    genomes = c(c(1:length(unique_genes)),c(1:length(unique_genes))),
+                    Key = c(rep("Unique genes",length(unique_genes)), rep("New genes",length(new_genes))) )
+
+ggplot(data = genes, aes(x = genomes, y = genes_to_genomes, group = Key, linetype=Key)) +geom_line()+
+theme_classic() +
+ylim(c(1,max(unique_genes)))+
+xlim(c(1,length(unique_genes)))+
+xlab("No. of genomes") +
+ylab("No. of genes")+ theme_bw(base_size = 16) +  theme(legend.justification=c(1,1),legend.position=c(1,1))+
+ggsave(filename="unique_vs_new_genes.png", scale=1)

bin/roary-pan_genome_reorder_spreadsheet

@@ -0,0 +1,19 @@
+#!/usr/bin/env perl
+
+package Bio::Roary::Main::RoaryReorderSpreadsheet;
+
+# ABSTRACT: Take in a tree and a spreadsheet and output a reordered spreadsheet
+# PODNAME: pan_genome_reorder_spreadsheet
+
+=head1 SYNOPSIS
+
+Take in a tree and a spreadsheet and output a reordered spreadsheet
+
+=cut
+
+use Cwd qw(abs_path); 
+BEGIN { unshift( @INC, abs_path('./lib') ) }
+BEGIN { unshift( @INC, abs_path('./t/lib') ) }
+use Bio::Roary::CommandLine::RoaryReorderSpreadsheet;
+
+Bio::Roary::CommandLine::RoaryReorderSpreadsheet->new(args => \@ARGV, script_name => $0)->run;

bin/roary-query_pan_genome

@@ -0,0 +1,19 @@
+#!/usr/bin/env perl
+
+package Bio::Roary::Main::QueryRoary;
+
+# ABSTRACT: Take in a groups file and the protein fasta files and output selected data
+# PODNAME: query_pan_genome
+
+=head1 SYNOPSIS
+
+Take in a groups file and the protein fasta files and output selected data
+
+=cut
+
+use Cwd qw(abs_path); 
+BEGIN { unshift( @INC, abs_path('./lib') ) }
+BEGIN { unshift( @INC, abs_path('./t/lib') ) }
+use Bio::Roary::CommandLine::QueryRoary;
+
+Bio::Roary::CommandLine::QueryRoary->new(args => \@ARGV, script_name => $0)->run;

dist.ini

@@ -1,5 +1,5 @@
 name    = Bio-Roary
-version = 3.6.0
+version = 3.6.1
 author  = Andrew J. Page <[email protected]>
 license = GPL_3
 copyright_holder = Wellcome Trust Sanger Institute