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Merge pull request #6 from andrewjpage/master
speedup searching fastas
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,19 @@ | ||
| #!/usr/bin/env perl | ||
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| package Bio::PanGenome::Main::PlotPanGenomeGroups; | ||
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| # ABSTRACT: Take in the groups file and output some summary plots | ||
| # PODNAME: plot_pan_genome_groups | ||
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| =head1 SYNOPSIS | ||
| Take in the groups file and output some summary plots | ||
| =cut | ||
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| BEGIN { unshift( @INC, '../lib' ) } | ||
| BEGIN { unshift( @INC, './lib' ) } | ||
| BEGIN { unshift( @INC, '/software/pathogen/internal/prod/lib/' ) } | ||
| use Bio::PanGenome::CommandLine::PlotPanGenomeGroups; | ||
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| Bio::PanGenome::CommandLine::PlotPanGenomeGroups->new(args => \@ARGV, script_name => $0)->run; |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,19 @@ | ||
| #!/usr/bin/env perl | ||
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| package Bio::PanGenome::Main::QueryPanGenome; | ||
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| # ABSTRACT: Take in a groups file and the protein fasta files and output selected data | ||
| # PODNAME: query_pan_genome | ||
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| =head1 SYNOPSIS | ||
| Take in a groups file and the protein fasta files and output selected data | ||
| =cut | ||
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| BEGIN { unshift( @INC, '../lib' ) } | ||
| BEGIN { unshift( @INC, './lib' ) } | ||
| BEGIN { unshift( @INC, '/software/pathogen/internal/prod/lib/' ) } | ||
| use Bio::PanGenome::CommandLine::QueryPanGenome; | ||
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| Bio::PanGenome::CommandLine::QueryPanGenome->new(args => \@ARGV, script_name => $0)->run; |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,175 @@ | ||
| package Bio::PanGenome::AnalyseGroups; | ||
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| # ABSTRACT: Take in a groups file and the original FASTA files and create plots and stats | ||
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| =head1 SYNOPSIS | ||
| Take in a groups file and the original FASTA files and create plots and stats | ||
| use Bio::PanGenome::AnalyseGroups; | ||
| my $plot_groups_obj = Bio::PanGenome::AnalyseGroups->new( | ||
| fasta_files => $fasta_files, | ||
| groups_filename => $groups_filename, | ||
| output_filename => $output_filename | ||
| ); | ||
| $plot_groups_obj->create_plots(); | ||
| =cut | ||
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| use Moose; | ||
| use Bio::PanGenome::Exceptions; | ||
| use Bio::PanGenome::Plot::FreqOfGenes; | ||
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| has 'fasta_files' => ( is => 'ro', isa => 'ArrayRef', required => 1 ); | ||
| has 'groups_filename' => ( is => 'ro', isa => 'Str', required => 1 ); | ||
| has 'output_filename' => ( is => 'ro', isa => 'Str', default => 'summary_of_groups' ); | ||
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| has '_number_of_isolates' => ( is => 'ro', isa => 'Int', lazy => 1, builder => '_builder__number_of_isolates' ); | ||
| has '_number_of_genes_per_file' => | ||
| ( is => 'ro', isa => 'HashRef', lazy => 1, builder => '_builder__number_of_genes_per_file' ); | ||
| has '_genes_to_file' => ( is => 'ro', isa => 'HashRef', lazy => 1, builder => '_builder__genes_to_file' ); | ||
| has '_freq_groups_per_genome' => | ||
| ( is => 'ro', isa => 'ArrayRef', lazy => 1, builder => '_builder__freq_groups_per_genome' ); | ||
| has '_groups_to_genes' => ( is => 'ro', isa => 'HashRef', lazy => 1, builder => '_builder__groups_to_genes' ); | ||
| has '_genes_to_groups' => ( is => 'ro', isa => 'HashRef', lazy => 1, builder => '_builder__genes_to_groups' ); | ||
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| # Fixme: Same files opened multiple times | ||
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| sub _builder__number_of_isolates { | ||
| my ($self) = @_; | ||
| return @{ $self->fasta_files }; | ||
| } | ||
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| sub _builder__number_of_genes_per_file { | ||
| my ($self) = @_; | ||
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| my %gene_count; | ||
| for my $filename ( @{ $self->fasta_files } ) { | ||
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| # Count the number of sequence description lines | ||
| open( my $fh, '-|', 'grep \> ' . $filename . ' | wc -l' ); | ||
| my $count = <$fh>; | ||
| chomp($count); | ||
| $count =~ s/^\s*(.*?)\s*$/$1/; | ||
| $gene_count{$filename} = $count; | ||
| close($fh); | ||
| } | ||
| return \%gene_count; | ||
| } | ||
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| sub _freq_dist_of_genes { | ||
| my ($self) = @_; | ||
| my @gene_counts = values %{ $self->_number_of_genes_per_file }; | ||
| my %gene_freq; | ||
| for my $gene_count (@gene_counts) { | ||
| $gene_freq{$gene_count}++; | ||
| } | ||
| return \%gene_freq; | ||
| } | ||
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| sub _builder__genes_to_file { | ||
| my ($self) = @_; | ||
| my %genes_to_file; | ||
| for my $filename ( @{ $self->fasta_files } ) { | ||
| open(my $fh, '-|', 'grep \> '.$filename.' | awk \'{print $1}\' | sed \'s/>//\' '); | ||
| while(<$fh>) | ||
| { | ||
| chomp; | ||
| $genes_to_file{ $_ } = $filename; | ||
| } | ||
| close($fh); | ||
| } | ||
| return \%genes_to_file; | ||
| } | ||
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| sub _count_num_files_in_group { | ||
| my ( $self, $genes ) = @_; | ||
| my $count = 0; | ||
| my %filename_freq; | ||
| for my $gene ( @{$genes} ) { | ||
| next if ( $gene eq "" ); | ||
| if ( defined( $self->_genes_to_file->{$gene} ) ) { | ||
| $filename_freq{ $self->_genes_to_file->{$gene} }++; | ||
| } | ||
| } | ||
| my @uniq_filenames = keys %filename_freq; | ||
| return @uniq_filenames; | ||
| } | ||
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| sub _builder__genes_to_groups { | ||
| my ($self) = @_; | ||
| my %genes_to_groups; | ||
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| open( my $fh, $self->groups_filename ) | ||
| or Bio::PanGenome::Exceptions::FileNotFound->throw( error => "Group file not found:" . $self->groups_filename ); | ||
| while (<$fh>) { | ||
| chomp; | ||
| my $line = $_; | ||
| if ( $line =~ /^(.+): (.+)$/ ) { | ||
| my $group_name = $1; | ||
| my $genes = $2; | ||
| my @elements = split( /\s+/, $genes ); | ||
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| for my $gene (@elements) { | ||
| $genes_to_groups{$gene} = $group_name; | ||
| } | ||
| } | ||
| } | ||
| return \%genes_to_groups; | ||
| } | ||
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| sub _builder__groups_to_genes { | ||
| my ($self) = @_; | ||
| my %groups_to_genes; | ||
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| open( my $fh, $self->groups_filename ) | ||
| or Bio::PanGenome::Exceptions::FileNotFound->throw( error => "Group file not found:" . $self->groups_filename ); | ||
| while (<$fh>) { | ||
| chomp; | ||
| my $line = $_; | ||
| if ( $line =~ /^(.+): (.+)$/ ) { | ||
| my $group_name = $1; | ||
| my $genes = $2; | ||
| my @elements = split( /\s+/, $genes ); | ||
| $groups_to_genes{$group_name} = \@elements; | ||
| } | ||
| } | ||
| return \%groups_to_genes; | ||
| } | ||
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| sub _builder__freq_groups_per_genome { | ||
| my ($self) = @_; | ||
| my @group_count; | ||
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| open( my $fh, $self->groups_filename ) | ||
| or Bio::PanGenome::Exceptions::FileNotFound->throw( error => "Group file not found:" . $self->groups_filename ); | ||
| while (<$fh>) { | ||
| chomp; | ||
| my $line = $_; | ||
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| # Remove the group name | ||
| $line =~ s!^(.+: )?!!; | ||
| my @elements = split( /\s+/, $line ); | ||
| my $number_of_files_in_group = $self->_count_num_files_in_group( \@elements ); | ||
| $number_of_files_in_group = ( $number_of_files_in_group * 100 / $self->_number_of_isolates ); | ||
| push( @group_count, $number_of_files_in_group ); | ||
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| } | ||
| close($fh); | ||
| my @sorted_group_count = sort { $b <=> $a } @group_count; | ||
| return \@sorted_group_count; | ||
| } | ||
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| sub create_plots { | ||
| my ($self) = @_; | ||
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| my $plot_groups_obj = | ||
| Bio::PanGenome::Plot::FreqOfGenes->new( freq_groups_per_genome => $self->_freq_groups_per_genome ); | ||
| $plot_groups_obj->create_plot(); | ||
| } | ||
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| no Moose; | ||
| __PACKAGE__->meta->make_immutable; | ||
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| 1; | ||
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|
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,99 @@ | ||
| package Bio::PanGenome::CommandLine::PlotPanGenomeGroups; | ||
|
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| # ABSTRACT: Take in the groups file and output some summary plots | ||
|
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| =head1 SYNOPSIS | ||
| Take in the groups file and output some summary plots | ||
| =cut | ||
|
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| use Moose; | ||
| use Getopt::Long qw(GetOptionsFromArray); | ||
| use Bio::PanGenome::AnalyseGroups; | ||
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| has 'args' => ( is => 'ro', isa => 'ArrayRef', required => 1 ); | ||
| has 'script_name' => ( is => 'ro', isa => 'Str', required => 1 ); | ||
| has 'help' => ( is => 'rw', isa => 'Bool', default => 0 ); | ||
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| has 'fasta_files' => ( is => 'rw', isa => 'ArrayRef' ); | ||
| has 'groups_filename' => ( is => 'rw', isa => 'Str' ); | ||
| has 'output_filename' => ( is => 'rw', isa => 'Str', default => 'clustered_proteins' ); | ||
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| has '_error_message' => ( is => 'rw', isa => 'Str' ); | ||
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| sub BUILD { | ||
| my ($self) = @_; | ||
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| my ( $fasta_files, $output_filename, $groups_filename, $help ); | ||
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| GetOptionsFromArray( | ||
| $self->args, | ||
| 'o|output=s' => \$output_filename, | ||
| 'g|groups_filename=s' => \$groups_filename, | ||
| 'h|help' => \$help, | ||
| ); | ||
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| if ( @{ $self->args } == 0 ) { | ||
| $self->_error_message("Error: You need to provide a FASTA file"); | ||
| } | ||
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| $self->output_filename($output_filename) if ( defined($output_filename) ); | ||
| if ( defined($groups_filename) && (-e $groups_filename)) | ||
| { | ||
| $self->groups_filename($groups_filename) ; | ||
| } | ||
| else | ||
| { | ||
| $self->_error_message("Error: Cant access the groups file $groups_filename"); | ||
| } | ||
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| for my $filename ( @{ $self->args } ) { | ||
| if ( !-e $filename ) { | ||
| $self->_error_message("Error: Cant access file $filename"); | ||
| last; | ||
| } | ||
| } | ||
| $self->fasta_files( $self->args ); | ||
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| } | ||
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| sub run { | ||
| my ($self) = @_; | ||
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| ( !$self->help ) or die $self->usage_text; | ||
| if ( defined( $self->_error_message ) ) { | ||
| print $self->_error_message . "\n"; | ||
| die $self->usage_text; | ||
| } | ||
|
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| my $plot_groups_obj = Bio::PanGenome::AnalyseGroups->new( | ||
| fasta_files => $self->fasta_files, | ||
| groups_filename => $self->groups_filename, | ||
| output_filename => $self->output_filename | ||
| ); | ||
| $plot_groups_obj->create_plots(); | ||
| } | ||
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| sub usage_text { | ||
| my ($self) = @_; | ||
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| return <<USAGE; | ||
| Usage: plot_pan_genome_groups [options] | ||
| Take in the groups file and output some summary plots | ||
| # Create summary plots | ||
| plot_pan_genome_groups -g groupfile example.faa | ||
| # Provide an output filename | ||
| plot_pan_genome_groups -g groupfile -o results *.faa | ||
| # This help message | ||
| plot_pan_genome_groups -h | ||
| USAGE | ||
| } | ||
|
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| __PACKAGE__->meta->make_immutable; | ||
| no Moose; | ||
| 1; |
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