/usr/share/perl5/Bio/Roary/CombinedProteome.pm is in roary 3.8.0+dfsg-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 | package Bio::Roary::CombinedProteome;
$Bio::Roary::CombinedProteome::VERSION = '3.8.0';
# ABSTRACT: Take in multiple FASTA sequences containing proteomes and concat them together and output a FASTA file, filtering out more than 5% X's
use Moose;
use Bio::Roary::Exceptions;
has 'proteome_files' => ( is => 'ro', isa => 'ArrayRef', required => 1 );
has 'output_filename' => ( is => 'ro', isa => 'Str', default => 'combined_output.fa' );
sub BUILD {
my ($self) = @_;
for my $filename ( @{ $self->proteome_files } ) {
Bio::Roary::Exceptions::FileNotFound->throw( error => 'Cant open file: ' . $filename )
unless ( -e $filename );
}
}
sub create_combined_proteome_file {
my ($self) = @_;
unlink($self->output_filename);
for my $filename (@{$self->proteome_files })
{
system(join(' ', ("cat", $filename, ">>", $self->output_filename)));
}
1;
}
no Moose;
__PACKAGE__->meta->make_immutable;
1;
__END__
=pod
=encoding UTF-8
=head1 NAME
Bio::Roary::CombinedProteome - Take in multiple FASTA sequences containing proteomes and concat them together and output a FASTA file, filtering out more than 5% X's
=head1 VERSION
version 3.8.0
=head1 SYNOPSIS
Take in multiple FASTA sequences containing proteomes and concat them together and output a FASTA file, filtering out more than 5% X's
use Bio::Roary::CombinedProteome;
my $obj = Bio::Roary::CombinedProteome->new(
proteome_files => ['abc.fa','efg.fa'],
output_filename => 'example_output.fa',
maximum_percentage_of_unknowns => 5.0,
);
$obj->create_combined_proteome_file;
=head1 AUTHOR
Andrew J. Page <ap13@sanger.ac.uk>
=head1 COPYRIGHT AND LICENSE
This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute.
This is free software, licensed under:
The GNU General Public License, Version 3, June 2007
=cut
|