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For bin/pan_genome_post_analysis
  Run on Fri Mar 27 11:43:32 2015
Reported on Fri Mar 27 11:45:41 2015

Filename/Users/ap13/pathogens/Roary/lib/Bio/Roary/PostAnalysis.pm
StatementsExecuted 95 statements in 95.6ms
Subroutines
Calls P F Exclusive
Time
Inclusive
Time
Subroutine
11191.5ms6.59sBio::Roary::PostAnalysis::::_create_embl_filesBio::Roary::PostAnalysis::_create_embl_files
1112.43ms5.81msBio::Roary::PostAnalysis::::BEGIN@12Bio::Roary::PostAnalysis::BEGIN@12
1112.24ms178msBio::Roary::PostAnalysis::::BEGIN@16Bio::Roary::PostAnalysis::BEGIN@16
1112.24ms167msBio::Roary::PostAnalysis::::BEGIN@20Bio::Roary::PostAnalysis::BEGIN@20
1112.06ms49.9msBio::Roary::PostAnalysis::::BEGIN@22Bio::Roary::PostAnalysis::BEGIN@22
1111.65ms36.8msBio::Roary::PostAnalysis::::BEGIN@21Bio::Roary::PostAnalysis::BEGIN@21
1111.50ms53.4msBio::Roary::PostAnalysis::::BEGIN@17Bio::Roary::PostAnalysis::BEGIN@17
111976µs36.4msBio::Roary::PostAnalysis::::BEGIN@19Bio::Roary::PostAnalysis::BEGIN@19
111971µs30.5msBio::Roary::PostAnalysis::::BEGIN@14Bio::Roary::PostAnalysis::BEGIN@14
111731µs61.5msBio::Roary::PostAnalysis::::BEGIN@13Bio::Roary::PostAnalysis::BEGIN@13
111664µs63.4msBio::Roary::PostAnalysis::::BEGIN@18Bio::Roary::PostAnalysis::BEGIN@18
111543µs17.2msBio::Roary::PostAnalysis::::BEGIN@15Bio::Roary::PostAnalysis::BEGIN@15
111262µs56.5sBio::Roary::PostAnalysis::::runBio::Roary::PostAnalysis::run
11196µs12.4sBio::Roary::PostAnalysis::::_build__group_statistics_objBio::Roary::PostAnalysis::_build__group_statistics_obj
11160µs1.83sBio::Roary::PostAnalysis::::_build__annotate_groups_objBio::Roary::PostAnalysis::_build__annotate_groups_obj
11154µs2.71sBio::Roary::PostAnalysis::::_build__analyse_groups_objBio::Roary::PostAnalysis::_build__analyse_groups_obj
11147µs146µsBio::Roary::PostAnalysis::::_build__group_labels_objBio::Roary::PostAnalysis::_build__group_labels_obj
11146µs284µsBio::Roary::PostAnalysis::::_build__number_of_groups_objBio::Roary::PostAnalysis::_build__number_of_groups_obj
11140µs115µsBio::Roary::PostAnalysis::::_build__inflate_clusters_objBio::Roary::PostAnalysis::_build__inflate_clusters_obj
11137µs220µsBio::Roary::PostAnalysis::::_build__order_genes_objBio::Roary::PostAnalysis::_build__order_genes_obj
11136µs4.67msBio::Roary::PostAnalysis::::BEGIN@11Bio::Roary::PostAnalysis::BEGIN@11
11132µs736µsBio::Roary::PostAnalysis::::_build__split_groups_objBio::Roary::PostAnalysis::_build__split_groups_obj
11112µs21µsBio::Roary::PostAnalysis::::_delete_intermediate_filesBio::Roary::PostAnalysis::_delete_intermediate_files
11111µs131µsBio::Roary::PostAnalysis::::BEGIN@225Bio::Roary::PostAnalysis::BEGIN@225
0000s0sBio::Roary::PostAnalysis::::_build__groups_multifastas_nuc_objBio::Roary::PostAnalysis::_build__groups_multifastas_nuc_obj
Call graph for these subroutines as a Graphviz dot language file.
Line State
ments
Time
on line
Calls Time
in subs
Code
1package Bio::Roary::PostAnalysis;
2
3# ABSTRACT: Post analysis of pan genomes
4
5=head1 SYNOPSIS
6
7Create a pan genome
8
9=cut
10
11267µs29.30ms
# spent 4.67ms (36µs+4.63) within Bio::Roary::PostAnalysis::BEGIN@11 which was called: # once (36µs+4.63ms) by Bio::Roary::CommandLine::RoaryPostAnalysis::BEGIN@13 at line 11
use Moose;
# spent 4.67ms making 1 call to Bio::Roary::PostAnalysis::BEGIN@11 # spent 4.63ms making 1 call to Moose::import
122265µs25.86ms
# spent 5.81ms (2.43+3.39) within Bio::Roary::PostAnalysis::BEGIN@12 which was called: # once (2.43ms+3.39ms) by Bio::Roary::CommandLine::RoaryPostAnalysis::BEGIN@13 at line 12
use File::Copy;
# spent 5.81ms making 1 call to Bio::Roary::PostAnalysis::BEGIN@12 # spent 43µs making 1 call to Exporter::import
132159µs161.5ms
# spent 61.5ms (731µs+60.8) within Bio::Roary::PostAnalysis::BEGIN@13 which was called: # once (731µs+60.8ms) by Bio::Roary::CommandLine::RoaryPostAnalysis::BEGIN@13 at line 13
use Bio::Roary::InflateClusters;
# spent 61.5ms making 1 call to Bio::Roary::PostAnalysis::BEGIN@13
142180µs130.5ms
# spent 30.5ms (971µs+29.6) within Bio::Roary::PostAnalysis::BEGIN@14 which was called: # once (971µs+29.6ms) by Bio::Roary::CommandLine::RoaryPostAnalysis::BEGIN@13 at line 14
use Bio::Roary::AnalyseGroups;
# spent 30.5ms making 1 call to Bio::Roary::PostAnalysis::BEGIN@14
152183µs117.2ms
# spent 17.2ms (543µs+16.6) within Bio::Roary::PostAnalysis::BEGIN@15 which was called: # once (543µs+16.6ms) by Bio::Roary::CommandLine::RoaryPostAnalysis::BEGIN@13 at line 15
use Bio::Roary::GroupLabels;
# spent 17.2ms making 1 call to Bio::Roary::PostAnalysis::BEGIN@15
162220µs1178ms
# spent 178ms (2.24+176) within Bio::Roary::PostAnalysis::BEGIN@16 which was called: # once (2.24ms+176ms) by Bio::Roary::CommandLine::RoaryPostAnalysis::BEGIN@13 at line 16
use Bio::Roary::AnnotateGroups;
# spent 178ms making 1 call to Bio::Roary::PostAnalysis::BEGIN@16
172194µs153.4ms
# spent 53.4ms (1.50+51.9) within Bio::Roary::PostAnalysis::BEGIN@17 which was called: # once (1.50ms+51.9ms) by Bio::Roary::CommandLine::RoaryPostAnalysis::BEGIN@13 at line 17
use Bio::Roary::GroupStatistics;
# spent 53.4ms making 1 call to Bio::Roary::PostAnalysis::BEGIN@17
182228µs163.4ms
# spent 63.4ms (664µs+62.7) within Bio::Roary::PostAnalysis::BEGIN@18 which was called: # once (664µs+62.7ms) by Bio::Roary::CommandLine::RoaryPostAnalysis::BEGIN@13 at line 18
use Bio::Roary::Output::GroupsMultifastasNucleotide;
# spent 63.4ms making 1 call to Bio::Roary::PostAnalysis::BEGIN@18
192210µs136.4ms
# spent 36.4ms (976µs+35.5) within Bio::Roary::PostAnalysis::BEGIN@19 which was called: # once (976µs+35.5ms) by Bio::Roary::CommandLine::RoaryPostAnalysis::BEGIN@13 at line 19
use Bio::Roary::Output::NumberOfGroups;
# spent 36.4ms making 1 call to Bio::Roary::PostAnalysis::BEGIN@19
202239µs1167ms
# spent 167ms (2.24+165) within Bio::Roary::PostAnalysis::BEGIN@20 which was called: # once (2.24ms+165ms) by Bio::Roary::CommandLine::RoaryPostAnalysis::BEGIN@13 at line 20
use Bio::Roary::OrderGenes;
# spent 167ms making 1 call to Bio::Roary::PostAnalysis::BEGIN@20
212232µs136.8ms
# spent 36.8ms (1.65+35.1) within Bio::Roary::PostAnalysis::BEGIN@21 which was called: # once (1.65ms+35.1ms) by Bio::Roary::CommandLine::RoaryPostAnalysis::BEGIN@13 at line 21
use Bio::Roary::Output::EmblGroups;
# spent 36.8ms making 1 call to Bio::Roary::PostAnalysis::BEGIN@21
2221.06ms149.9ms
# spent 49.9ms (2.06+47.9) within Bio::Roary::PostAnalysis::BEGIN@22 which was called: # once (2.06ms+47.9ms) by Bio::Roary::CommandLine::RoaryPostAnalysis::BEGIN@13 at line 22
use Bio::Roary::SplitGroups;
# spent 49.9ms making 1 call to Bio::Roary::PostAnalysis::BEGIN@22
23
2412µs12.11mshas 'fasta_files' => ( is => 'rw', isa => 'ArrayRef', required => 1 );
# spent 2.11ms making 1 call to Moose::has
2512µs11.71mshas 'input_files' => ( is => 'rw', isa => 'ArrayRef', required => 1 );
# spent 1.71ms making 1 call to Moose::has
2612µs11.84mshas 'output_filename' => ( is => 'rw', isa => 'Str', default => 'clustered_proteins' );
# spent 1.84ms making 1 call to Moose::has
2712µs11.79mshas 'output_pan_geneome_filename' => ( is => 'rw', isa => 'Str', default => 'pan_genome.fa' );
# spent 1.79ms making 1 call to Moose::has
2812µs11.99mshas 'output_statistics_filename' => ( is => 'rw', isa => 'Str', default => 'gene_presence_absence.csv' );
# spent 1.99ms making 1 call to Moose::has
2913µs12.34mshas 'output_multifasta_files' => ( is => 'ro', isa => 'Bool', default => 0 );
# spent 2.34ms making 1 call to Moose::has
30
3112µs11.96mshas 'clusters_filename' => ( is => 'rw', isa => 'Str', required => 1 );
# spent 1.96ms making 1 call to Moose::has
3212µs11.46mshas 'dont_delete_files' => ( is => 'ro', isa => 'Bool', default => 0 );
# spent 1.46ms making 1 call to Moose::has
3312µs11.50mshas 'dont_split_groups' => ( is => 'ro', isa => 'Bool', default => 0 );
# spent 1.50ms making 1 call to Moose::has
3412µs11.75mshas 'dont_create_rplots' => ( is => 'rw', isa => 'Bool', default => 1 );
# spent 1.75ms making 1 call to Moose::has
3512µs11.92mshas 'group_limit' => ( is => 'rw', isa => 'Num', default => 50000 );
# spent 1.92ms making 1 call to Moose::has
36
3712µs12.12mshas '_output_mcl_filename' => ( is => 'ro', isa => 'Str', default => '_uninflated_mcl_groups' );
# spent 2.12ms making 1 call to Moose::has
3812µs11.90mshas '_output_inflate_unsplit_clusters_filename' => ( is => 'ro', isa => 'Str', default => '_inflated_unsplit_mcl_groups' );
# spent 1.90ms making 1 call to Moose::has
3912µs11.54mshas '_output_inflate_clusters_filename' => ( is => 'ro', isa => 'Str', default => '_inflated_mcl_groups' );
# spent 1.54ms making 1 call to Moose::has
4012µs11.48mshas '_output_group_labels_filename' => ( is => 'ro', isa => 'Str', default => '_labeled_mcl_groups' );
# spent 1.48ms making 1 call to Moose::has
4112µs11.63mshas '_output_combined_filename' => ( is => 'ro', isa => 'Str', default => '_combined_files' );
# spent 1.63ms making 1 call to Moose::has
4213µs11.57mshas '_input_cd_hit_groups_file' => ( is => 'ro', isa => 'Str', default => '_combined_files.groups' );
# spent 1.57ms making 1 call to Moose::has
4312µs11.55mshas 'core_accessory_tab_output_filename' => ( is => 'ro', isa => 'Str', default => 'core_accessory.tab' );
# spent 1.55ms making 1 call to Moose::has
4412µs11.57mshas 'accessory_tab_output_filename' => ( is => 'ro', isa => 'Str', default => 'accessory.tab' );
# spent 1.57ms making 1 call to Moose::has
4512µs11.56mshas 'core_accessory_ordering_key' => ( is => 'ro', isa => 'Str', default => 'core_accessory_overall_order_filtered' );
# spent 1.56ms making 1 call to Moose::has
4612µs11.78mshas 'accessory_ordering_key' => ( is => 'ro', isa => 'Str', default => 'accessory_overall_order_filtered' );
# spent 1.78ms making 1 call to Moose::has
4712µs11.91mshas 'core_definition' => ( is => 'ro', isa => 'Num', default => 1.0 );
# spent 1.91ms making 1 call to Moose::has
48
4912µs12.08mshas '_inflate_clusters_obj' => ( is => 'ro', isa => 'Bio::Roary::InflateClusters', lazy => 1, builder => '_build__inflate_clusters_obj' );
# spent 2.08ms making 1 call to Moose::has
5012µs12.00mshas '_group_labels_obj' => ( is => 'ro', isa => 'Bio::Roary::GroupLabels', lazy => 1, builder => '_build__group_labels_obj' );
# spent 2.00ms making 1 call to Moose::has
5112µs12.00mshas '_annotate_groups_obj' => ( is => 'ro', isa => 'Bio::Roary::AnnotateGroups', lazy => 1, builder => '_build__annotate_groups_obj' );
# spent 2.00ms making 1 call to Moose::has
5212µs11.95mshas '_analyse_groups_obj' => ( is => 'ro', isa => 'Bio::Roary::AnalyseGroups', lazy => 1, builder => '_build__analyse_groups_obj' );
# spent 1.95ms making 1 call to Moose::has
5312µs12.20mshas '_order_genes_obj' => ( is => 'ro', isa => 'Bio::Roary::OrderGenes', lazy => 1, builder => '_build__order_genes_obj' );
# spent 2.20ms making 1 call to Moose::has
5412µs12.36mshas '_group_statistics_obj' => ( is => 'ro', isa => 'Bio::Roary::GroupStatistics', lazy => 1, builder => '_build__group_statistics_obj' );
# spent 2.36ms making 1 call to Moose::has
5512µs12.37mshas '_number_of_groups_obj' => ( is => 'ro', isa => 'Bio::Roary::Output::NumberOfGroups', lazy => 1, builder => '_build__number_of_groups_obj' );
# spent 2.37ms making 1 call to Moose::has
5612µs12.07mshas '_groups_multifastas_nuc_obj' => ( is => 'ro', isa => 'Bio::Roary::Output::GroupsMultifastasNucleotide', lazy => 1, builder => '_build__groups_multifastas_nuc_obj' );
# spent 2.07ms making 1 call to Moose::has
5713µs14.02mshas '_split_groups_obj' => ( is => 'ro', isa => 'Bio::Roary::SplitGroups', lazy_build => 1 );
# spent 4.02ms making 1 call to Moose::has
58
5912µs13.29mshas 'verbose_stats' => ( is => 'rw', isa => 'Bool', default => 0 );
# spent 3.29ms making 1 call to Moose::has
60
61
# spent 56.5s (262µs+56.5) within Bio::Roary::PostAnalysis::run which was called: # once (262µs+56.5s) by Bio::Roary::CommandLine::RoaryPostAnalysis::run at line 114 of lib/Bio/Roary/CommandLine/RoaryPostAnalysis.pm
sub run {
6211164µs my ($self) = @_;
63
642172ms $self->_inflate_clusters_obj->inflate();
# spent 172ms making 1 call to Bio::Roary::InflateClusters::inflate # spent 164µs making 1 call to Bio::Roary::PostAnalysis::_inflate_clusters_obj
65
66 ## SPLIT GROUPS WITH PARALOGS ##
6717µs15µs if ( $self->dont_split_groups ){
# spent 5µs making 1 call to Bio::Roary::PostAnalysis::dont_split_groups
68 move( $self->_output_inflate_unsplit_clusters_filename, $self->_output_inflate_clusters_filename );
69 }
70 else {
71210.5s $self->_split_groups_obj->split_groups;
# spent 10.5s making 1 call to Bio::Roary::SplitGroups::split_groups # spent 768µs making 1 call to Bio::Roary::PostAnalysis::_split_groups_obj
72 }
73
742220ms $self->_group_labels_obj->add_labels();
# spent 220ms making 1 call to Bio::Roary::GroupLabels::add_labels # spent 216µs making 1 call to Bio::Roary::PostAnalysis::_group_labels_obj
7525.17s $self->_annotate_groups_obj->reannotate;
# spent 3.34s making 1 call to Bio::Roary::AnnotateGroups::reannotate # spent 1.83s making 1 call to Bio::Roary::PostAnalysis::_annotate_groups_obj
76230.3s $self->_group_statistics_obj->create_spreadsheet;
# spent 17.9s making 1 call to Bio::Roary::GroupStatistics::create_spreadsheet # spent 12.4s making 1 call to Bio::Roary::PostAnalysis::_group_statistics_obj
7723.58s $self->_number_of_groups_obj->create_output_files;
78115µs system("create_pan_genome_plots.R") unless($self->dont_create_rplots == 1);
# spent 15µs making 1 call to Bio::Roary::PostAnalysis::dont_create_rplots
79191.4ms36.59s $self->_create_embl_files;
# spent 6.59s making 1 call to Bio::Roary::PostAnalysis::_create_embl_files # spent 50µs making 2 calls to Bio::Roary::Output::EmblGroups::DESTROY, avg 25µs/call
80
81118µs $self->_groups_multifastas_nuc_obj->create_files() if($self->output_multifasta_files);
82
83121µs $self->_delete_intermediate_files;
84}
85
86
# spent 736µs (32+704) within Bio::Roary::PostAnalysis::_build__split_groups_obj which was called: # once (32µs+704µs) by Bio::Roary::PostAnalysis::_split_groups_obj at line 12 of (eval 25)[Eval/Closure.pm:125]
sub _build__split_groups_obj {
87223µs my ( $self ) = @_;
886704µs return Bio::Roary::SplitGroups->new(
# spent 689µs making 1 call to Bio::Roary::SplitGroups::new # spent 3µs making 1 call to Bio::Roary::PostAnalysis::_output_inflate_unsplit_clusters_filename # spent 3µs making 1 call to Bio::Roary::PostAnalysis::dont_delete_files # spent 3µs making 1 call to Bio::Roary::PostAnalysis::input_files # spent 3µs making 1 call to Bio::Roary::PostAnalysis::_output_inflate_clusters_filename # spent 3µs making 1 call to Bio::Roary::PostAnalysis::fasta_files
89 groupfile => $self->_output_inflate_unsplit_clusters_filename,
90 gff_files => $self->input_files,
91 fasta_files => $self->fasta_files,
92 outfile => $self->_output_inflate_clusters_filename,
93 dont_delete => $self->dont_delete_files
94 );
95}
96
97sub _build__number_of_groups_obj
98
# spent 284µs (46+238) within Bio::Roary::PostAnalysis::_build__number_of_groups_obj which was called: # once (46µs+238µs) by Bio::Roary::PostAnalysis::_number_of_groups_obj at line 12 of (eval 25)[Eval/Closure.pm:125]
{
99260µs my ($self) = @_;
1005238µs return Bio::Roary::Output::NumberOfGroups->new(
# spent 200µs making 1 call to Bio::Roary::Output::NumberOfGroups::new # spent 11µs making 1 call to Bio::Roary::PostAnalysis::_annotate_groups_obj # spent 9µs making 1 call to Bio::Roary::PostAnalysis::_order_genes_obj # spent 9µs making 1 call to Bio::Roary::PostAnalysis::_group_statistics_obj # spent 8µs making 1 call to Bio::Roary::OrderGenes::groups_to_contigs
101 group_statistics_obj => $self->_group_statistics_obj,
102 groups_to_contigs => $self->_order_genes_obj->groups_to_contigs,
103 annotate_groups_obj => $self->_annotate_groups_obj,
104 );
105}
106
107sub _build__group_statistics_obj
108
# spent 12.4s (96µs+12.4) within Bio::Roary::PostAnalysis::_build__group_statistics_obj which was called: # once (96µs+12.4s) by Bio::Roary::PostAnalysis::_group_statistics_obj at line 12 of (eval 25)[Eval/Closure.pm:125]
{
109290µs my ($self) = @_;
110712.4s return Bio::Roary::GroupStatistics->new(
# spent 9.70s making 1 call to Bio::Roary::OrderGenes::groups_to_contigs # spent 2.71s making 1 call to Bio::Roary::PostAnalysis::_analyse_groups_obj # spent 265µs making 1 call to Bio::Roary::PostAnalysis::_order_genes_obj # spent 120µs making 1 call to Bio::Roary::GroupStatistics::new # spent 18µs making 1 call to Bio::Roary::PostAnalysis::verbose_stats # spent 11µs making 1 call to Bio::Roary::PostAnalysis::output_statistics_filename # spent 3µs making 1 call to Bio::Roary::PostAnalysis::_annotate_groups_obj
111 output_filename => $self->output_statistics_filename,
112 annotate_groups_obj => $self->_annotate_groups_obj,
113 analyse_groups_obj => $self->_analyse_groups_obj,
114 groups_to_contigs => $self->_order_genes_obj->groups_to_contigs,
115 _verbose => $self->verbose_stats,
116 );
117}
118
119
120sub _build__order_genes_obj
121
# spent 220µs (37+183) within Bio::Roary::PostAnalysis::_build__order_genes_obj which was called: # once (37µs+183µs) by Bio::Roary::PostAnalysis::_order_genes_obj at line 12 of (eval 25)[Eval/Closure.pm:125]
{
122241µs my ($self) = @_;
1233183µs return Bio::Roary::OrderGenes->new(
# spent 171µs making 1 call to Bio::Roary::OrderGenes::new # spent 10µs making 1 call to Bio::Roary::PostAnalysis::input_files # spent 3µs making 1 call to Bio::Roary::PostAnalysis::_analyse_groups_obj
124 analyse_groups_obj => $self->_analyse_groups_obj,
125 gff_files => $self->input_files,
126 );
127}
128
- -
131sub _build__group_labels_obj
132
# spent 146µs (47+100) within Bio::Roary::PostAnalysis::_build__group_labels_obj which was called: # once (47µs+100µs) by Bio::Roary::PostAnalysis::_group_labels_obj at line 12 of (eval 25)[Eval/Closure.pm:125]
{
133246µs my ($self) = @_;
1343100µs return Bio::Roary::GroupLabels->new(
# spent 83µs making 1 call to Bio::Roary::GroupLabels::new # spent 11µs making 1 call to Bio::Roary::PostAnalysis::_output_inflate_clusters_filename # spent 6µs making 1 call to Bio::Roary::PostAnalysis::_output_group_labels_filename
135 groups_filename => $self->_output_inflate_clusters_filename,
136 output_filename => $self->_output_group_labels_filename
137 );
138}
139
140sub _build__annotate_groups_obj
141
# spent 1.83s (60µs+1.83) within Bio::Roary::PostAnalysis::_build__annotate_groups_obj which was called: # once (60µs+1.83s) by Bio::Roary::PostAnalysis::_annotate_groups_obj at line 12 of (eval 25)[Eval/Closure.pm:125]
{
142262µs my ($self) = @_;
14341.83s return Bio::Roary::AnnotateGroups->new(
# spent 1.83s making 1 call to Bio::Roary::AnnotateGroups::new # spent 14µs making 1 call to Bio::Roary::PostAnalysis::input_files # spent 12µs making 1 call to Bio::Roary::PostAnalysis::output_filename # spent 4µs making 1 call to Bio::Roary::PostAnalysis::_output_group_labels_filename
144 gff_files => $self->input_files,
145 output_filename => $self->output_filename,
146 groups_filename => $self->_output_group_labels_filename,
147 );
148}
149
150sub _build__analyse_groups_obj
151
# spent 2.71s (54µs+2.71) within Bio::Roary::PostAnalysis::_build__analyse_groups_obj which was called: # once (54µs+2.71s) by Bio::Roary::PostAnalysis::_analyse_groups_obj at line 12 of (eval 25)[Eval/Closure.pm:125]
{
152254µs my ($self) = @_;
15332.71s return Bio::Roary::AnalyseGroups->new(
# spent 2.71s making 1 call to Bio::Roary::AnalyseGroups::new # spent 9µs making 1 call to Bio::Roary::PostAnalysis::fasta_files # spent 7µs making 1 call to Bio::Roary::PostAnalysis::output_filename
154 fasta_files => $self->fasta_files,
155 groups_filename => $self->output_filename
156 );
157}
158
159sub _build__inflate_clusters_obj
160
# spent 115µs (40+75) within Bio::Roary::PostAnalysis::_build__inflate_clusters_obj which was called: # once (40µs+75µs) by Bio::Roary::PostAnalysis::_inflate_clusters_obj at line 12 of (eval 25)[Eval/Closure.pm:125]
{
161227µs my ($self) = @_;
162575µs return Bio::Roary::InflateClusters->new(
163 clusters_filename => $self->clusters_filename,
164 cdhit_groups_filename => $self->_input_cd_hit_groups_file,
165 mcl_filename => $self->_output_mcl_filename,
166 output_file => $self->_output_inflate_unsplit_clusters_filename
167 );
168}
169
170
171sub _build__groups_multifastas_nuc_obj
172{
173 my ($self) = @_;
174 return Bio::Roary::Output::GroupsMultifastasNucleotide->new(
175 output_multifasta_files => $self->output_multifasta_files,
176 gff_files => $self->input_files,
177 annotate_groups => $self->_annotate_groups_obj,
178 group_names => $self->_analyse_groups_obj->_groups,
179 group_limit => $self->group_limit
180 );
181}
182
183sub _create_embl_files
184
# spent 6.59s (91.5ms+6.50) within Bio::Roary::PostAnalysis::_create_embl_files which was called: # once (91.5ms+6.50s) by Bio::Roary::PostAnalysis::run at line 79
{
1855134µs my ($self) = @_;
1867145µs my $core_accessory_tab_obj = Bio::Roary::Output::EmblGroups->new(
# spent 108µs making 1 call to Bio::Roary::Output::EmblGroups::new # spent 9µs making 1 call to Bio::Roary::PostAnalysis::core_accessory_tab_output_filename # spent 8µs making 1 call to Bio::Roary::PostAnalysis::_analyse_groups_obj # spent 7µs making 1 call to Bio::Roary::PostAnalysis::core_accessory_ordering_key # spent 5µs making 1 call to Bio::Roary::PostAnalysis::_annotate_groups_obj # spent 4µs making 1 call to Bio::Roary::PostAnalysis::_order_genes_obj # spent 4µs making 1 call to Bio::Roary::OrderGenes::groups_to_contigs
187 output_filename => $self->core_accessory_tab_output_filename,
188 annotate_groups_obj => $self->_annotate_groups_obj,
189 analyse_groups_obj => $self->_analyse_groups_obj,
190 ordering_key => $self->core_accessory_ordering_key,
191 groups_to_contigs => $self->_order_genes_obj->groups_to_contigs
192 );
19313.65s $core_accessory_tab_obj->create_files;
# spent 3.65s making 1 call to Bio::Roary::Output::EmblGroups::create_files
194
1957191µs my $accessory_tab_obj = Bio::Roary::Output::EmblGroups->new(
# spent 129µs making 1 call to Bio::Roary::Output::EmblGroups::new # spent 18µs making 1 call to Bio::Roary::PostAnalysis::accessory_tab_output_filename # spent 14µs making 1 call to Bio::Roary::PostAnalysis::accessory_ordering_key # spent 9µs making 1 call to Bio::Roary::OrderGenes::groups_to_contigs # spent 8µs making 1 call to Bio::Roary::PostAnalysis::_annotate_groups_obj # spent 7µs making 1 call to Bio::Roary::PostAnalysis::_order_genes_obj # spent 6µs making 1 call to Bio::Roary::PostAnalysis::_analyse_groups_obj
196 output_filename => $self->accessory_tab_output_filename,
197 annotate_groups_obj => $self->_annotate_groups_obj,
198 analyse_groups_obj => $self->_analyse_groups_obj,
199 ordering_key => $self->accessory_ordering_key,
200 groups_to_contigs => $self->_order_genes_obj->groups_to_contigs
201 );
20212.85s $accessory_tab_obj->create_files;
# spent 2.85s making 1 call to Bio::Roary::Output::EmblGroups::create_files
203}
204
205sub _delete_intermediate_files
206
# spent 21µs (12+9) within Bio::Roary::PostAnalysis::_delete_intermediate_files which was called: # once (12µs+9µs) by Bio::Roary::PostAnalysis::run at line 83
{
207214µs my ($self) = @_;
20819µs return if($self->dont_delete_files == 1);
# spent 9µs making 1 call to Bio::Roary::PostAnalysis::dont_delete_files
209
210 unlink($self->_output_mcl_filename) ;
211 unlink($self->_output_inflate_clusters_filename) ;
212 unlink($self->_output_group_labels_filename) ;
213 unlink($self->_output_combined_filename) ;
214 unlink($self->clusters_filename) ;
215 unlink($self->clusters_filename . '.clstr' ) ;
216 unlink($self->clusters_filename . '.bak.clstr' ) ;
217 unlink('_gff_files') ;
218 unlink('_fasta_files') ;
219 unlink('_clustered_filtered.fa') ;
220 unlink($self->_input_cd_hit_groups_file) ;
221 unlink('database_masking.asnb') ;
222 unlink('_clustered') ;
223}
224
225264µs2251µs
# spent 131µs (11+120) within Bio::Roary::PostAnalysis::BEGIN@225 which was called: # once (11µs+120µs) by Bio::Roary::CommandLine::RoaryPostAnalysis::BEGIN@13 at line 225
no Moose;
# spent 131µs making 1 call to Bio::Roary::PostAnalysis::BEGIN@225 # spent 120µs making 1 call to Moose::unimport
226111µs221.0ms__PACKAGE__->meta->make_immutable;
# spent 21.0ms making 1 call to Class::MOP::Class::make_immutable # spent 32µs making 1 call to Bio::Roary::PostAnalysis::meta
227
2281132µs1;