Commit 4e7daed7 authored by Kieron Taylor's avatar Kieron Taylor 😠
Browse files

Removed use of SeqDumper and replaced it with our own FASTASerializer.

parent efb11cc5
......@@ -174,10 +174,12 @@ sub print_Seq {
$there = $end if($there > $end);
my $seq = $slice->subseq($here, $there);
$seq =~ s/(.{1,$width})/$1\n/g;
print $fh $seq;
print $fh $seq or die "Error writing to file handle";
$here = $there + 1;
}
if ($slice->length > 0) {$self->{'achieved_something'} = 1;}
}
=head2 line_width
......
......@@ -101,20 +101,6 @@ sub print_main_header {
warning("No writer for headers in this format. Nothing done" );
}
=head2 print_sequence
Arg [1] : Bio::EnsEMBL::Slice
Description: By default, prints a block of FASTA format sequence from the given slice
DEPRECATED - This feature is becoming FASTASerializer
=cut
#TODO : Remove in release 66
sub print_sequence {
my $self = shift;
my $slice = shift;
my $fh = $self->{'filehandle'};
Bio::EnsEMBL::Utils::SeqDumper->dump_fasta( $slice, $fh);
$self->{'achieved_something'} = 1;
}
=head2 printed_something
Description: Check if serializer has printed any useful data. Not accurate with FASTA
due to non-reporting dumper.
......
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