diff Roary/lib/Bio/Roary/Output/BlastIdentityFrequency.pm @ 0:c47a5f61bc9f draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Roary/lib/Bio/Roary/Output/BlastIdentityFrequency.pm	Fri May 14 20:27:06 2021 +0000
@@ -0,0 +1,62 @@
+package Bio::Roary::Output::BlastIdentityFrequency;
+
+# ABSTRACT:  Take in blast results and find the percentage identity graph
+
+=head1 SYNOPSIS
+
+Take in blast results and find the percentage identity graph
+   use Bio::Roary::Output::BlastIdentityFrequency;
+   
+   my $obj = Bio::Roary::Output::BlastIdentityFrequency->new(
+       input_filename      => '_blast_results',
+       output_filename  => 'blast_identity_frequency.Rtab',
+     );
+   $obj->create_file();
+
+=cut
+
+use Moose;
+use Bio::SeqIO;
+use Bio::Roary::Exceptions;
+
+has 'input_filename'        => ( is => 'ro', isa => 'Str', default => '_blast_results' );
+has 'output_filename'       => ( is => 'ro', isa => 'Str', default => 'blast_identity_frequency.Rtab' );
+
+has '_output_fh'            => ( is => 'ro', lazy => 1, builder => '_build__output_fh' );
+has '_input_fh'             => ( is => 'ro', lazy => 1, builder => '_build__input_fh' );
+
+sub _build__output_fh
+{
+  my ($self) = @_;
+  open( my $fh, '>', $self->output_filename )
+    or Bio::Roary::Exceptions::CouldntWriteToFile->throw(
+      error => "Couldnt write output file:" . $self->output_filename );
+  return $fh;
+}
+
+sub _build__input_fh
+{
+  my ($self) = @_;
+  my $input_string  = 'awk \'{print $3}\' '.$self->input_filename.'  | awk \'BEGIN {FS="."}; {print $1}\'| sort | uniq -c | awk \'{print $2"\t"$1}\'';
+  
+  open( my $fh, '-|', $input_string ) or die "Couldnt open results file";
+  return $fh;
+}
+
+sub create_file
+{
+  my ($self) = @_;
+  
+  my $input_fh = $self->_input_fh;
+  while(<$input_fh>)
+  {
+    print {$self->_output_fh} $_;
+  }
+  close($self->_input_fh);
+  close($self->_output_fh);
+}
+
+no Moose;
+__PACKAGE__->meta->make_immutable;
+
+1;