From ed50c2d080eb8a787af98b93b174f6908ef86f39 Mon Sep 17 00:00:00 2001
From: Kieron Taylor <ktaylor@ebi.ac.uk>
Date: Mon, 16 Jan 2012 17:33:04 +0000
Subject: [PATCH] Minor nomenclature tweaks, and better support for Bio::Seq
objects
---
.../Bio/EnsEMBL/Utils/IO/FASTASerializer.pm | 42 ++++++++++---------
1 file changed, 23 insertions(+), 19 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Utils/IO/FASTASerializer.pm b/modules/Bio/EnsEMBL/Utils/IO/FASTASerializer.pm
index 576858a829..cf38728575 100644
--- a/modules/Bio/EnsEMBL/Utils/IO/FASTASerializer.pm
+++ b/modules/Bio/EnsEMBL/Utils/IO/FASTASerializer.pm
@@ -27,7 +27,7 @@ Bio::EnsEMBL::Utils::IO::FASTASerializer
my $serializer = Bio::EnsEMBL::Utils::IO::FASTASerializer->new($filehandle);
$serializer->chunk_factor(1000);
$serializer->line_width(60);
- $serializer->print_Slice($slice);
+ $serializer->print_Seq($slice);
$serializer = Bio::EnsEMBL::Utils::IO::FASTASerializer->new($filehandle,
sub {
@@ -35,8 +35,6 @@ Bio::EnsEMBL::Utils::IO::FASTASerializer
return ">Custom header";
}
);
- $serializer->print_metadata($slice);
- $serializer->print_Slice($slice,"no duplicate headers please");
=head1 DESCRIPTION
@@ -56,6 +54,7 @@ package Bio::EnsEMBL::Utils::IO::FASTASerializer;
use strict;
use warnings;
use Bio::EnsEMBL::Utils::Exception;
+use Bio::EnsEMBL::Utils::Scalar qw/assert_ref check_ref/;
use base qw(Bio::EnsEMBL::Utils::IO::Serializer);
@@ -93,13 +92,21 @@ sub new {
else {
$self->{'header_function'} = sub {
my $slice = shift;
- my $id = $slice->seq_region_name;
- my $seqtype = 'dna';
- my $idtype = $slice->coord_system->name;
- my $location = $slice->name;
- return ">$id $seqtype:$idtype $location\n";
- }
+ if(check_ref($slice, 'Bio::EnsEMBL::Slice')) {
+ my $id = $slice->seq_region_name;
+ my $seqtype = 'dna';
+ my $idtype = $slice->coord_system->name;
+ my $location = $slice->name;
+
+ return ">$id $seqtype:$idtype $location";
+ }
+ else {
+ # must be a Bio::Seq , or we're doomed
+
+ return ">".$slice->name;
+ }
+ };
}
@@ -118,31 +125,28 @@ sub print_metadata {
my $self = shift;
my $slice = shift;
my $fh = $self->{'filehandle'};
- my $metadata = &{$self->{'header_function'}}($slice);
- print $fh $metadata;
+ my $metadata = $self->{'header_function'}->($slice);
+ print $fh $metadata."\n";
}
-=head2 print_slice
+=head2 print_Seq
Arg [1] : Bio::EnsEMBL::Slice or other Bio::PrimarySeqI compliant object
- Arg [2] : Optional Boolean - override the default serialisation of a header
+
Description: Serializes the slice into FASTA format. Buffering is used
While other Bioperl PrimarySeqI implementations can be used,
a custom header function will be required to accommodate it.
- Add an override as second argument if more control is needed
- over when and how custom headers are written.
Returntype : None
=cut
-sub print_Slice {
+sub print_Seq {
my $self = shift;
my $slice = shift;
- my $override = shift;
my $fh = $self->{'filehandle'};
- # Default print header, override
- $self->print_metadata($slice) unless $override;
+
+ $self->print_metadata($slice);
# set buffer size
my $chunk_size = $self->{'chunk_factor'} * $self->{'line_width'};
--
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