--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Roary/lib/Bio/Roary/PrepareInputFiles.pm	Fri May 14 20:27:06 2021 +0000
@@ -0,0 +1,149 @@
+package Bio::Roary::PrepareInputFiles;
+
+# ABSTRACT: Take in a mixture of FASTA and GFF input files and output FASTA proteomes only
+
+=head1 SYNOPSIS
+
+Take in a mixture of FASTA and GFF input files and output FASTA proteomes only
+   use Bio::Roary::PrepareInputFiles;
+   
+   my $obj = Bio::Roary::PrepareInputFiles->new(
+     input_files   => ['abc.gff','ddd.faa'],
+   );
+   $obj->fasta_files;
+
+=cut
+
+use Moose;
+use Bio::Roary::Exceptions;
+use Bio::Roary::ExtractProteomeFromGFFs;
+use Bio::Roary::FilterUnknownsFromFasta;
+use Cwd qw(getcwd);
+use File::Temp;
+use Log::Log4perl qw(:easy);
+
+has 'input_files'        => ( is => 'ro', isa => 'ArrayRef',        required => 1 );
+has 'job_runner'         => ( is => 'ro', isa => 'Str',             default  => 'Local' );
+has 'cpus'               => ( is => 'ro', isa => 'Int',             default  => 1 );
+has '_input_gff_files'   => ( is => 'ro', isa => 'Maybe[ArrayRef]', lazy     => 1, builder => '_build__input_gff_files' );
+has '_input_fasta_files' => ( is => 'ro', isa => 'Maybe[ArrayRef]', lazy     => 1, builder => '_build__input_fasta_files' );
+has '_input_fasta_files_filtered' => ( is => 'ro', isa => 'Maybe[ArrayRef]', lazy => 1, builder => '_build__input_fasta_files_filtered' );
+has '_input_fasta_files_filtered_obj' =>
+  ( is => 'ro', isa => 'Bio::Roary::FilterUnknownsFromFasta', lazy => 1, builder => '_build__input_fasta_files_filtered_obj' );
+
+has '_derived_fasta_files' => ( is => 'ro', isa => 'Maybe[ArrayRef]', lazy => 1, builder => '_build__derived_fasta_files' );
+has '_extract_proteome_obj' => (
+    is      => 'ro',
+    isa     => 'Bio::Roary::ExtractProteomeFromGFFs',
+    lazy    => 1,
+    builder => '_build__extract_proteome_obj'
+);
+has 'apply_unknowns_filter' => ( is => 'rw', isa => 'Bool',                               default => 1 );
+has 'translation_table'     => ( is => 'rw', isa => 'Int',                                default => 11 );
+has 'verbose'               => ( is => 'rw', isa => 'Bool',                               default => 0 );
+has '_fasta_filter_obj'     => ( is => 'ro', isa => 'Bio::Roary::FilterUnknowsFromFasta', lazy    => 1, builder => '_fasta_filter_obj' );
+has 'working_directory' => ( is => 'ro', isa => 'File::Temp::Dir', default => sub { File::Temp->newdir( DIR => getcwd, CLEANUP => 1 ); } );
+has 'logger' => ( is => 'ro', lazy => 1, builder => '_build_logger' );
+
+sub _build_logger {
+    my ($self) = @_;
+    Log::Log4perl->easy_init($ERROR);
+    my $logger = get_logger();
+    return $logger;
+}
+
+sub _build__input_gff_files {
+    my ($self) = @_;
+    my @gff_files = grep( /\.gff$/, @{ $self->input_files } );
+    return \@gff_files;
+}
+
+sub _build__input_fasta_files {
+    my ($self) = @_;
+    my @fasta_files = grep( !/\.gff$/, @{ $self->input_files } );
+
+    my @validated_fasta_files;
+
+    for my $fasta_file (@fasta_files) {
+        eval {
+            my $inseq = Bio::SeqIO->new(
+                -file     => $fasta_file,
+                -format   => 'fasta',
+                -alphabet => 'protein'
+            );
+            while ( my $seq = $inseq->next_seq ) {
+
+                # do something to force the reading.
+                $seq->seq;
+            }
+        };
+        if ($@) {
+            $self->logger->warn(
+                "Input file doesnt have a .gff extension and isnt a protein FASTA file so excluding it from further analysis: $fasta_file"
+            );
+        }
+        else {
+            push( @validated_fasta_files, $fasta_file );
+        }
+
+    }
+
+    return \@fasta_files;
+}
+
+sub _build__input_fasta_files_filtered_obj {
+    my ($self) = @_;
+    return Bio::Roary::FilterUnknownsFromFasta->new( fasta_files => $self->_input_fasta_files );
+}
+
+sub _build__input_fasta_files_filtered {
+    my ($self) = @_;
+    return undef if ( !defined( $self->_input_fasta_files ) );
+    return $self->_input_fasta_files_filtered_obj->filtered_fasta_files();
+}
+
+sub _build__extract_proteome_obj {
+    my ($self) = @_;
+    return Bio::Roary::ExtractProteomeFromGFFs->new(
+        gff_files             => $self->_input_gff_files,
+        job_runner            => $self->job_runner,
+        apply_unknowns_filter => $self->apply_unknowns_filter,
+        translation_table     => $self->translation_table,
+        cpus                  => $self->cpus,
+        verbose               => $self->verbose,
+        working_directory     => $self->working_directory,
+    );
+}
+
+sub _build__derived_fasta_files {
+    my ($self) = @_;
+    return undef if ( !defined( $self->_input_gff_files ) );
+    return $self->_extract_proteome_obj->fasta_files();
+}
+
+sub fasta_files {
+    my ($self) = @_;
+    my @output_fasta_files = ( @{ $self->_input_fasta_files_filtered }, @{ $self->_derived_fasta_files } );
+    return \@output_fasta_files;
+}
+
+sub lookup_fasta_files_from_unknown_input_files {
+    my ( $self, $input_files ) = @_;
+    $self->fasta_files;
+
+    my @output_fasta_files;
+    for my $input_file ( @{$input_files} ) {
+        if ( defined( $self->_extract_proteome_obj->fasta_files_to_gff_files->{$input_file} ) ) {
+            push( @output_fasta_files, $self->_extract_proteome_obj->fasta_files_to_gff_files->{$input_file} );
+        }
+        else {
+            push( @output_fasta_files, $self->_input_fasta_files_filtered_obj->input_fasta_to_output_fasta->{$input_file} );
+        }
+    }
+    return \@output_fasta_files;
+}
+
+no Moose;
+__PACKAGE__->meta->make_immutable;
+
+1;