Filename | /Users/ap13/pathogens/Roary/lib/Bio/Roary/PostAnalysis.pm |
Statements | Executed 95 statements in 95.6ms |
Calls | P | F | Exclusive Time |
Inclusive Time |
Subroutine |
---|---|---|---|---|---|
1 | 1 | 1 | 91.5ms | 6.59s | _create_embl_files | Bio::Roary::PostAnalysis::
1 | 1 | 1 | 2.43ms | 5.81ms | BEGIN@12 | Bio::Roary::PostAnalysis::
1 | 1 | 1 | 2.24ms | 178ms | BEGIN@16 | Bio::Roary::PostAnalysis::
1 | 1 | 1 | 2.24ms | 167ms | BEGIN@20 | Bio::Roary::PostAnalysis::
1 | 1 | 1 | 2.06ms | 49.9ms | BEGIN@22 | Bio::Roary::PostAnalysis::
1 | 1 | 1 | 1.65ms | 36.8ms | BEGIN@21 | Bio::Roary::PostAnalysis::
1 | 1 | 1 | 1.50ms | 53.4ms | BEGIN@17 | Bio::Roary::PostAnalysis::
1 | 1 | 1 | 976µs | 36.4ms | BEGIN@19 | Bio::Roary::PostAnalysis::
1 | 1 | 1 | 971µs | 30.5ms | BEGIN@14 | Bio::Roary::PostAnalysis::
1 | 1 | 1 | 731µs | 61.5ms | BEGIN@13 | Bio::Roary::PostAnalysis::
1 | 1 | 1 | 664µs | 63.4ms | BEGIN@18 | Bio::Roary::PostAnalysis::
1 | 1 | 1 | 543µs | 17.2ms | BEGIN@15 | Bio::Roary::PostAnalysis::
1 | 1 | 1 | 262µs | 56.5s | run | Bio::Roary::PostAnalysis::
1 | 1 | 1 | 96µs | 12.4s | _build__group_statistics_obj | Bio::Roary::PostAnalysis::
1 | 1 | 1 | 60µs | 1.83s | _build__annotate_groups_obj | Bio::Roary::PostAnalysis::
1 | 1 | 1 | 54µs | 2.71s | _build__analyse_groups_obj | Bio::Roary::PostAnalysis::
1 | 1 | 1 | 47µs | 146µs | _build__group_labels_obj | Bio::Roary::PostAnalysis::
1 | 1 | 1 | 46µs | 284µs | _build__number_of_groups_obj | Bio::Roary::PostAnalysis::
1 | 1 | 1 | 40µs | 115µs | _build__inflate_clusters_obj | Bio::Roary::PostAnalysis::
1 | 1 | 1 | 37µs | 220µs | _build__order_genes_obj | Bio::Roary::PostAnalysis::
1 | 1 | 1 | 36µs | 4.67ms | BEGIN@11 | Bio::Roary::PostAnalysis::
1 | 1 | 1 | 32µs | 736µs | _build__split_groups_obj | Bio::Roary::PostAnalysis::
1 | 1 | 1 | 12µs | 21µs | _delete_intermediate_files | Bio::Roary::PostAnalysis::
1 | 1 | 1 | 11µs | 131µs | BEGIN@225 | Bio::Roary::PostAnalysis::
0 | 0 | 0 | 0s | 0s | _build__groups_multifastas_nuc_obj | Bio::Roary::PostAnalysis::
Line | State ments |
Time on line |
Calls | Time in subs |
Code |
---|---|---|---|---|---|
1 | package Bio::Roary::PostAnalysis; | ||||
2 | |||||
3 | # ABSTRACT: Post analysis of pan genomes | ||||
4 | |||||
5 | =head1 SYNOPSIS | ||||
6 | |||||
7 | Create a pan genome | ||||
8 | |||||
9 | =cut | ||||
10 | |||||
11 | 2 | 67µs | 2 | 9.30ms | # 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 # spent 4.67ms making 1 call to Bio::Roary::PostAnalysis::BEGIN@11
# spent 4.63ms making 1 call to Moose::import |
12 | 2 | 265µs | 2 | 5.86ms | # 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 # spent 5.81ms making 1 call to Bio::Roary::PostAnalysis::BEGIN@12
# spent 43µs making 1 call to Exporter::import |
13 | 2 | 159µs | 1 | 61.5ms | # 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 # spent 61.5ms making 1 call to Bio::Roary::PostAnalysis::BEGIN@13 |
14 | 2 | 180µs | 1 | 30.5ms | # 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 # spent 30.5ms making 1 call to Bio::Roary::PostAnalysis::BEGIN@14 |
15 | 2 | 183µs | 1 | 17.2ms | # 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 # spent 17.2ms making 1 call to Bio::Roary::PostAnalysis::BEGIN@15 |
16 | 2 | 220µs | 1 | 178ms | # 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 # spent 178ms making 1 call to Bio::Roary::PostAnalysis::BEGIN@16 |
17 | 2 | 194µs | 1 | 53.4ms | # 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 # spent 53.4ms making 1 call to Bio::Roary::PostAnalysis::BEGIN@17 |
18 | 2 | 228µs | 1 | 63.4ms | # 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 # spent 63.4ms making 1 call to Bio::Roary::PostAnalysis::BEGIN@18 |
19 | 2 | 210µs | 1 | 36.4ms | # 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 # spent 36.4ms making 1 call to Bio::Roary::PostAnalysis::BEGIN@19 |
20 | 2 | 239µs | 1 | 167ms | # 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 # spent 167ms making 1 call to Bio::Roary::PostAnalysis::BEGIN@20 |
21 | 2 | 232µs | 1 | 36.8ms | # 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 # spent 36.8ms making 1 call to Bio::Roary::PostAnalysis::BEGIN@21 |
22 | 2 | 1.06ms | 1 | 49.9ms | # 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 # spent 49.9ms making 1 call to Bio::Roary::PostAnalysis::BEGIN@22 |
23 | |||||
24 | 1 | 2µs | 1 | 2.11ms | has 'fasta_files' => ( is => 'rw', isa => 'ArrayRef', required => 1 ); # spent 2.11ms making 1 call to Moose::has |
25 | 1 | 2µs | 1 | 1.71ms | has 'input_files' => ( is => 'rw', isa => 'ArrayRef', required => 1 ); # spent 1.71ms making 1 call to Moose::has |
26 | 1 | 2µs | 1 | 1.84ms | has 'output_filename' => ( is => 'rw', isa => 'Str', default => 'clustered_proteins' ); # spent 1.84ms making 1 call to Moose::has |
27 | 1 | 2µs | 1 | 1.79ms | has 'output_pan_geneome_filename' => ( is => 'rw', isa => 'Str', default => 'pan_genome.fa' ); # spent 1.79ms making 1 call to Moose::has |
28 | 1 | 2µs | 1 | 1.99ms | has 'output_statistics_filename' => ( is => 'rw', isa => 'Str', default => 'gene_presence_absence.csv' ); # spent 1.99ms making 1 call to Moose::has |
29 | 1 | 3µs | 1 | 2.34ms | has 'output_multifasta_files' => ( is => 'ro', isa => 'Bool', default => 0 ); # spent 2.34ms making 1 call to Moose::has |
30 | |||||
31 | 1 | 2µs | 1 | 1.96ms | has 'clusters_filename' => ( is => 'rw', isa => 'Str', required => 1 ); # spent 1.96ms making 1 call to Moose::has |
32 | 1 | 2µs | 1 | 1.46ms | has 'dont_delete_files' => ( is => 'ro', isa => 'Bool', default => 0 ); # spent 1.46ms making 1 call to Moose::has |
33 | 1 | 2µs | 1 | 1.50ms | has 'dont_split_groups' => ( is => 'ro', isa => 'Bool', default => 0 ); # spent 1.50ms making 1 call to Moose::has |
34 | 1 | 2µs | 1 | 1.75ms | has 'dont_create_rplots' => ( is => 'rw', isa => 'Bool', default => 1 ); # spent 1.75ms making 1 call to Moose::has |
35 | 1 | 2µs | 1 | 1.92ms | has 'group_limit' => ( is => 'rw', isa => 'Num', default => 50000 ); # spent 1.92ms making 1 call to Moose::has |
36 | |||||
37 | 1 | 2µs | 1 | 2.12ms | has '_output_mcl_filename' => ( is => 'ro', isa => 'Str', default => '_uninflated_mcl_groups' ); # spent 2.12ms making 1 call to Moose::has |
38 | 1 | 2µs | 1 | 1.90ms | has '_output_inflate_unsplit_clusters_filename' => ( is => 'ro', isa => 'Str', default => '_inflated_unsplit_mcl_groups' ); # spent 1.90ms making 1 call to Moose::has |
39 | 1 | 2µs | 1 | 1.54ms | has '_output_inflate_clusters_filename' => ( is => 'ro', isa => 'Str', default => '_inflated_mcl_groups' ); # spent 1.54ms making 1 call to Moose::has |
40 | 1 | 2µs | 1 | 1.48ms | has '_output_group_labels_filename' => ( is => 'ro', isa => 'Str', default => '_labeled_mcl_groups' ); # spent 1.48ms making 1 call to Moose::has |
41 | 1 | 2µs | 1 | 1.63ms | has '_output_combined_filename' => ( is => 'ro', isa => 'Str', default => '_combined_files' ); # spent 1.63ms making 1 call to Moose::has |
42 | 1 | 3µs | 1 | 1.57ms | has '_input_cd_hit_groups_file' => ( is => 'ro', isa => 'Str', default => '_combined_files.groups' ); # spent 1.57ms making 1 call to Moose::has |
43 | 1 | 2µs | 1 | 1.55ms | has 'core_accessory_tab_output_filename' => ( is => 'ro', isa => 'Str', default => 'core_accessory.tab' ); # spent 1.55ms making 1 call to Moose::has |
44 | 1 | 2µs | 1 | 1.57ms | has 'accessory_tab_output_filename' => ( is => 'ro', isa => 'Str', default => 'accessory.tab' ); # spent 1.57ms making 1 call to Moose::has |
45 | 1 | 2µs | 1 | 1.56ms | has 'core_accessory_ordering_key' => ( is => 'ro', isa => 'Str', default => 'core_accessory_overall_order_filtered' ); # spent 1.56ms making 1 call to Moose::has |
46 | 1 | 2µs | 1 | 1.78ms | has 'accessory_ordering_key' => ( is => 'ro', isa => 'Str', default => 'accessory_overall_order_filtered' ); # spent 1.78ms making 1 call to Moose::has |
47 | 1 | 2µs | 1 | 1.91ms | has 'core_definition' => ( is => 'ro', isa => 'Num', default => 1.0 ); # spent 1.91ms making 1 call to Moose::has |
48 | |||||
49 | 1 | 2µs | 1 | 2.08ms | has '_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 |
50 | 1 | 2µs | 1 | 2.00ms | has '_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 |
51 | 1 | 2µs | 1 | 2.00ms | has '_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 |
52 | 1 | 2µs | 1 | 1.95ms | has '_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 |
53 | 1 | 2µs | 1 | 2.20ms | has '_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 |
54 | 1 | 2µs | 1 | 2.36ms | has '_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 |
55 | 1 | 2µs | 1 | 2.37ms | has '_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 |
56 | 1 | 2µs | 1 | 2.07ms | has '_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 |
57 | 1 | 3µs | 1 | 4.02ms | has '_split_groups_obj' => ( is => 'ro', isa => 'Bio::Roary::SplitGroups', lazy_build => 1 ); # spent 4.02ms making 1 call to Moose::has |
58 | |||||
59 | 1 | 2µs | 1 | 3.29ms | has '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 | ||||
62 | 12 | 171µs | my ($self) = @_; | ||
63 | |||||
64 | 2 | 172ms | $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 ## | ||||
67 | 1 | 5µs | 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 { | ||||
71 | 2 | 10.5s | $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 | |||||
74 | 2 | 220ms | $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 | ||
75 | 2 | 5.17s | $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 | ||
76 | 2 | 30.3s | $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 | ||
77 | 2 | 3.58s | $self->_number_of_groups_obj->create_output_files; # spent 3.58s making 1 call to Bio::Roary::Output::NumberOfGroups::create_output_files
# spent 378µs making 1 call to Bio::Roary::PostAnalysis::_number_of_groups_obj | ||
78 | 1 | 15µs | system("create_pan_genome_plots.R") unless($self->dont_create_rplots == 1); # spent 15µs making 1 call to Bio::Roary::PostAnalysis::dont_create_rplots | ||
79 | 1 | 91.4ms | 3 | 6.59s | $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 | |||||
81 | 1 | 18µs | $self->_groups_multifastas_nuc_obj->create_files() if($self->output_multifasta_files); # spent 18µs making 1 call to Bio::Roary::PostAnalysis::output_multifasta_files | ||
82 | |||||
83 | 1 | 21µs | $self->_delete_intermediate_files; # spent 21µs making 1 call to Bio::Roary::PostAnalysis::_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] | ||||
87 | 2 | 23µs | my ( $self ) = @_; | ||
88 | 6 | 704µs | 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 => $self->dont_delete_files | ||||
94 | ); | ||||
95 | } | ||||
96 | |||||
97 | sub _build__number_of_groups_obj | ||||
98 | # spent 284µs (46+238) within Bio::Roary::PostAnalysis::_build__number_of_groups_obj which was called:
# once (46µs+238µs) by Bio::Roary::PostAnalysis::_number_of_groups_obj at line 12 of (eval 25)[Eval/Closure.pm:125] | ||||
99 | 2 | 60µs | my ($self) = @_; | ||
100 | 5 | 238µs | 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 => $self->_annotate_groups_obj, | ||||
104 | ); | ||||
105 | } | ||||
106 | |||||
107 | sub _build__group_statistics_obj | ||||
108 | # spent 12.4s (96µs+12.4) within Bio::Roary::PostAnalysis::_build__group_statistics_obj which was called:
# once (96µs+12.4s) by Bio::Roary::PostAnalysis::_group_statistics_obj at line 12 of (eval 25)[Eval/Closure.pm:125] | ||||
109 | 2 | 90µs | my ($self) = @_; | ||
110 | 7 | 12.4s | 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 => $self->verbose_stats, | ||||
116 | ); | ||||
117 | } | ||||
118 | |||||
119 | |||||
120 | sub _build__order_genes_obj | ||||
121 | # spent 220µs (37+183) within Bio::Roary::PostAnalysis::_build__order_genes_obj which was called:
# once (37µs+183µs) by Bio::Roary::PostAnalysis::_order_genes_obj at line 12 of (eval 25)[Eval/Closure.pm:125] | ||||
122 | 2 | 41µs | my ($self) = @_; | ||
123 | 3 | 183µs | 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 => $self->input_files, | ||||
126 | ); | ||||
127 | } | ||||
128 | |||||
- - | |||||
131 | sub _build__group_labels_obj | ||||
132 | # spent 146µs (47+100) within Bio::Roary::PostAnalysis::_build__group_labels_obj which was called:
# once (47µs+100µs) by Bio::Roary::PostAnalysis::_group_labels_obj at line 12 of (eval 25)[Eval/Closure.pm:125] | ||||
133 | 2 | 46µs | my ($self) = @_; | ||
134 | 3 | 100µs | 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 => $self->_output_group_labels_filename | ||||
137 | ); | ||||
138 | } | ||||
139 | |||||
140 | sub _build__annotate_groups_obj | ||||
141 | # spent 1.83s (60µs+1.83) within Bio::Roary::PostAnalysis::_build__annotate_groups_obj which was called:
# once (60µs+1.83s) by Bio::Roary::PostAnalysis::_annotate_groups_obj at line 12 of (eval 25)[Eval/Closure.pm:125] | ||||
142 | 2 | 62µs | my ($self) = @_; | ||
143 | 4 | 1.83s | 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 => $self->_output_group_labels_filename, | ||||
147 | ); | ||||
148 | } | ||||
149 | |||||
150 | sub _build__analyse_groups_obj | ||||
151 | # spent 2.71s (54µs+2.71) within Bio::Roary::PostAnalysis::_build__analyse_groups_obj which was called:
# once (54µs+2.71s) by Bio::Roary::PostAnalysis::_analyse_groups_obj at line 12 of (eval 25)[Eval/Closure.pm:125] | ||||
152 | 2 | 54µs | my ($self) = @_; | ||
153 | 3 | 2.71s | 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 => $self->output_filename | ||||
156 | ); | ||||
157 | } | ||||
158 | |||||
159 | sub _build__inflate_clusters_obj | ||||
160 | # spent 115µs (40+75) within Bio::Roary::PostAnalysis::_build__inflate_clusters_obj which was called:
# once (40µs+75µs) by Bio::Roary::PostAnalysis::_inflate_clusters_obj at line 12 of (eval 25)[Eval/Closure.pm:125] | ||||
161 | 2 | 27µs | my ($self) = @_; | ||
162 | 5 | 75µs | return Bio::Roary::InflateClusters->new( # spent 56µs making 1 call to Bio::Roary::InflateClusters::new
# spent 5µs making 1 call to Bio::Roary::PostAnalysis::_output_mcl_filename
# spent 5µs making 1 call to Bio::Roary::PostAnalysis::clusters_filename
# spent 4µs making 1 call to Bio::Roary::PostAnalysis::_input_cd_hit_groups_file
# spent 4µs making 1 call to Bio::Roary::PostAnalysis::_output_inflate_unsplit_clusters_filename | ||
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 => $self->_output_inflate_unsplit_clusters_filename | ||||
167 | ); | ||||
168 | } | ||||
169 | |||||
170 | |||||
171 | sub _build__groups_multifastas_nuc_obj | ||||
172 | { | ||||
173 | my ($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 => $self->group_limit | ||||
180 | ); | ||||
181 | } | ||||
182 | |||||
183 | sub _create_embl_files | ||||
184 | # spent 6.59s (91.5ms+6.50) within Bio::Roary::PostAnalysis::_create_embl_files which was called:
# once (91.5ms+6.50s) by Bio::Roary::PostAnalysis::run at line 79 | ||||
185 | 5 | 134µs | my ($self) = @_; | ||
186 | 7 | 145µs | 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 | ); | ||||
193 | 1 | 3.65s | $core_accessory_tab_obj->create_files; # spent 3.65s making 1 call to Bio::Roary::Output::EmblGroups::create_files | ||
194 | |||||
195 | 7 | 191µs | 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 | ); | ||||
202 | 1 | 2.85s | $accessory_tab_obj->create_files; # spent 2.85s making 1 call to Bio::Roary::Output::EmblGroups::create_files | ||
203 | } | ||||
204 | |||||
205 | sub _delete_intermediate_files | ||||
206 | # spent 21µs (12+9) within Bio::Roary::PostAnalysis::_delete_intermediate_files which was called:
# once (12µs+9µs) by Bio::Roary::PostAnalysis::run at line 83 | ||||
207 | 2 | 14µs | my ($self) = @_; | ||
208 | 1 | 9µs | 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 | |||||
225 | 2 | 64µs | 2 | 251µs | # 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 # spent 131µs making 1 call to Bio::Roary::PostAnalysis::BEGIN@225
# spent 120µs making 1 call to Moose::unimport |
226 | 1 | 11µs | 2 | 21.0ms | __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 | |||||
228 | 1 | 132µs | 1; |