Bio-AutomatedAnnotation

 view release on metacpan or  search on metacpan

lib/Bio/AutomatedAnnotation/CommandLine/AnnotateBacteria.pm  view on Meta::CPAN

package Bio::AutomatedAnnotation::CommandLine::AnnotateBacteria;
$Bio::AutomatedAnnotation::CommandLine::AnnotateBacteria::VERSION = '1.182770';
# ABSTRACT: provide a commandline interface to the annotation wrappers


use Moose;
use Getopt::Long qw(GetOptionsFromArray);
use Bio::AutomatedAnnotation;

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 );

has 'sample_name'       => ( is => 'rw', isa => 'Str'  );
has 'dbdir'             => ( is => 'rw', isa => 'Str', default => '/lustre/scratch118/infgen/pathogen/pathpipe/prokka'  );
has 'assembly_file'     => ( is => 'rw', isa => 'Str'  );
has 'annotation_tool'   => ( is => 'rw', isa => 'Str', default  => 'Prokka' );
has 'tmp_directory'     => ( is => 'rw', isa => 'Str', default  => '/tmp' );
has 'sequencing_centre' => ( is => 'rw', isa => 'Str', default  => 'SC' );
has 'accession_number'  => ( is => 'rw', isa => 'Maybe[Str]' );

lib/Bio/AutomatedAnnotation/CommandLine/GeneNameOccurances.pm  view on Meta::CPAN

package Bio::AutomatedAnnotation::CommandLine::GeneNameOccurances;
$Bio::AutomatedAnnotation::CommandLine::GeneNameOccurances::VERSION = '1.182770';
# ABSTRACT: Create a spreadsheet with gene name occurances


use Moose;
use Getopt::Long qw(GetOptionsFromArray);
use Bio::AutomatedAnnotation::SpreadsheetOfGeneOccurances;
use Bio::AutomatedAnnotation::GeneNameOccurances;

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 );

has 'gff_files'       => ( is => 'rw', isa => 'ArrayRef' );
has 'output_filename' => ( is => 'rw', isa => 'Str' );

has '_error_message' => ( is => 'rw', isa => 'Str' );

sub BUILD {
    my ($self) = @_;

lib/Bio/AutomatedAnnotation/CommandLine/ParseGenesFromGFFs.pm  view on Meta::CPAN

package Bio::AutomatedAnnotation::CommandLine::ParseGenesFromGFFs;
$Bio::AutomatedAnnotation::CommandLine::ParseGenesFromGFFs::VERSION = '1.182770';
# ABSTRACT: provide a commandline interface to pull out genes from multiple GFF files


use Moose;
use Getopt::Long qw(GetOptionsFromArray);
use Bio::AutomatedAnnotation::ParseGenesFromGFFs;

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 );

has 'amino_acids'       => ( is => 'rw', isa => 'Bool', default => 0);
has 'gff_files'         => ( is => 'rw', isa => 'ArrayRef' );
has 'search_query'      => ( is => 'rw', isa => 'Str' );
has 'search_qualifiers' => ( is => 'rw', isa => 'ArrayRef', default => sub { ['gene'] } );
has 'output_filename'   => ( is => 'rw', isa => 'Str' );

has '_error_message'    => ( is => 'rw', isa => 'Str' );

lib/Bio/AutomatedAnnotation/External/Cmscan.pm  view on Meta::CPAN

use Moose;
use Bio::SeqFeature::Generic;

has 'cmdb'       => ( is => 'ro', isa => 'Str', required => 1 );
has 'input_file' => ( is => 'ro', isa => 'Str', required => 1 );

has 'exec'     => ( is => 'ro', isa => 'Str',     default => 'cmscan' );
has 'version'  => ( is => 'ro', isa => 'Str',     default => '1.1' );
has 'cpus'     => ( is => 'ro', isa => 'Int',     default => 1 );
has 'evalue'   => ( is => 'ro', isa => 'Num',     default => 1E-6 );
has 'features' => ( is => 'ro', isa => 'HashRef', lazy    => 1, builder => '_build_features' );
has 'number_of_features'  => ( is => 'rw', isa => 'Int',  default => 0 );

has '_tool'        => ( is => 'ro', isa => 'Str', lazy => 1, builder => '_build__tool' );
has '_cpus'        => ( is => 'ro', isa => 'Int', lazy => 1, builder => '_build__cpus' );
has '_infernal_fh' => ( is => 'ro',  lazy => 1, builder => '_build__infernal_fh' );

sub _build__tool {
    my ($self) = @_;
    return "Infernal:" . $self->version;
}

lib/Bio/AutomatedAnnotation/GeneNameOccurances.pm  view on Meta::CPAN

package Bio::AutomatedAnnotation::GeneNameOccurances;
$Bio::AutomatedAnnotation::GeneNameOccurances::VERSION = '1.182770';
# ABSTRACT: Parse the gene names from multiple GFF files and provide a matrix of matches.


use Moose;
use Bio::Tools::GFF;
use Bio::AutomatedAnnotation::Exceptions;
use Bio::AutomatedAnnotation::GeneNamesFromGFF;

has 'gff_files'         => ( is => 'ro', isa => 'ArrayRef', required => 1 );
has 'all_gene_names'    => ( is => 'ro', isa => 'HashRef',  lazy     => 1, builder => '_build_all_gene_names' );
has 'sorted_all_gene_names'    => ( is => 'ro', isa => 'ArrayRef',  lazy     => 1, builder => '_build_sorted_all_gene_names' );

has 'gene_name_hashes' => ( is => 'ro', isa => 'HashRef',  lazy     => 1, builder => '_build_gene_name_hashes' );
has 'number_of_files'   => ( is => 'ro', isa => 'Int',      lazy     => 1, builder => '_build_number_of_files' );

sub _build_sorted_all_gene_names
{
  my ($self) = @_;
  my %all_gene_names = %{$self->all_gene_names};
  
  my @sorted_gene_names = sort { $b cmp $a } keys %all_gene_names;
  return \@sorted_gene_names;
}

lib/Bio/AutomatedAnnotation/GeneNamesFromGFF.pm  view on Meta::CPAN

use Bio::Tools::GFF;

has 'gff_file' => ( is => 'ro', isa => 'Str', required => 1 );

has '_tags_to_filter' => ( is => 'ro', isa => 'Str',             default => 'CDS' );
has '_tags_to_ignore' => ( is => 'ro', isa => 'Str',             default => 'rRNA|tRNA|ncRNA|tmRNA' );
has '_gff_parser'     => ( is => 'ro', isa => 'Bio::Tools::GFF', lazy    => 1, builder => '_build__gff_parser' );
has '_awk_filter'     => ( is => 'ro', isa => 'Str',             lazy    => 1, builder => '_build__awk_filter' );
has '_remove_sequence_filter' => ( is => 'ro', isa => 'Str', lazy => 1, builder => '_build__remove_sequence_filter' );

has 'gene_names' => ( is => 'ro', isa => 'HashRef', lazy => 1, builder => '_build_gene_names' );

sub _build_gene_names {
    my ($self) = @_;
    my %gene_names;

    while ( my $raw_feature = $self->_gff_parser->next_feature() ) {
        last unless defined($raw_feature);    # No more features
        next if !( $raw_feature->primary_tag eq 'CDS' );

        if ( $raw_feature->has_tag('gene') ) {

lib/Bio/AutomatedAnnotation/ParseGenesFromGFF.pm  view on Meta::CPAN

use Bio::PrimarySeq;
use Bio::SeqIO;
use Bio::Perl;

has 'gff_file'     => ( is => 'ro', isa => 'Str', required => 1 );
has 'search_query' => ( is => 'ro', isa => 'Str', required => 1 );

has '_awk_filter' => ( is => 'ro', isa => 'Str',             lazy => 1, builder => '_build__awk_filter' );
has '_gff_parser' => ( is => 'ro', isa => 'Bio::Tools::GFF', lazy => 1, builder => '_build__gff_parser' );
has '_tags_to_filter'    => ( is => 'ro', isa => 'Str',      default => 'CDS' );
has '_matching_features' => ( is => 'ro', isa => 'ArrayRef', lazy    => 1, builder => '_build__matching_features' );
has '_bio_seq_objects'   => ( is => 'ro', isa => 'ArrayRef', lazy    => 1, builder => '_build__bio_seq_objects' );
has 'search_qualifiers' => ( is => 'ro', isa => 'ArrayRef', lazy    => 1, builder => '_build_search_qualifiers' );
has '_sequences'         => ( is => 'ro', isa => 'HashRef',  lazy    => 1, builder => '_build__sequences' );


sub _build_search_qualifiers
{
  my ($self) = @_;
  return [ 'gene', 'product' ];
}

sub _build__sequences {
    my ($self) = @_;

lib/Bio/AutomatedAnnotation/ParseGenesFromGFFs.pm  view on Meta::CPAN

package Bio::AutomatedAnnotation::ParseGenesFromGFFs;
$Bio::AutomatedAnnotation::ParseGenesFromGFFs::VERSION = '1.182770';
# ABSTRACT: Parse GFF files and efficiency extract the gene sequence.


use Moose;
use Bio::AutomatedAnnotation::ParseGenesFromGFF;
use Bio::SeqIO;

has 'gff_files'         => ( is => 'ro', isa => 'ArrayRef', required => 1 );
has 'search_query'      => ( is => 'ro', isa => 'Str',      required => 1 );
has 'search_qualifiers' => ( is => 'ro', isa => 'ArrayRef', required => 1 );
has 'codontable_id'     => ( is => 'ro', isa => 'Int',      default  => 11 );
has 'amino_acids'       => ( is => 'ro', isa => 'Bool',     default  => 0 );
has 'output_file'       => ( is => 'ro', isa => 'Str',      lazy     => 1, builder => '_build_output_file' );
has 'output_base'       => ( is => 'rw', isa => 'Str',      default  => 'output' );
has '_parser_objects'   => ( is => 'ro', isa => 'ArrayRef', lazy     => 1, builder => '_build__parser_objects' );

has 'files_with_hits'    => ( is => 'rw', isa => 'Int',     default  => 0 );
has 'files_without_hits' => ( is => 'rw', isa => 'Int',     default  => 0 );

sub _build_output_file {
    my ($self) = @_;
    my $file_suffix = $self->search_query;
    $file_suffix =~ s!\W!!gi;
    return join( '.', ( $self->output_base, $file_suffix, 'fa' ) );
}