From 07b57d02148b3cd29569cccd9d6c8f5c99e7c910 Mon Sep 17 00:00:00 2001
From: Brian Osborne <briano@bioteam.net>
Date: Mon, 15 Sep 2014 11:48:30 -0400
Subject: [PATCH] Add ability to remove specific features, using primary_tag

---
 Bio/Seq.pm        | 36 +++++++++++++++++++++---------------
 t/SeqIO/genbank.t | 16 +++++++++++++++-
 2 files changed, 36 insertions(+), 16 deletions(-)

diff --git a/Bio/Seq.pm b/Bio/Seq.pm
index e83974103..92ed49a1b 100644
--- a/Bio/Seq.pm
+++ b/Bio/Seq.pm
@@ -1163,25 +1163,31 @@ sub add_SeqFeature {
 
  Title   : remove_SeqFeatures
  Usage   : $seq->remove_SeqFeatures();
- Function: Flushes all attached SeqFeatureI objects.
-
-           To remove individual feature objects, delete those from the returned
-           array and re-add the rest.
- Example :
- Returns : The array of Bio::SeqFeatureI objects removed from this seq.
- Args    : None
+ Function: Removes all attached SeqFeatureI objects or those with the 
+           specified primary tag
+ Example : my @gene_feats = $seq->remove_seqFeatures('gene') or
+           my @feats = $seq->remove_seqFeatures()
+ Returns : The array of Bio::SeqFeatureI objects removed from the sequence
+ Args    : None, or a feature primary tag
 
 =cut
 
 sub remove_SeqFeatures {
-    my $self = shift;
-
+    my ( $self, $type ) = @_;
     return () unless $self->{'_as_feat'};
-    my @feats = @{$self->{'_as_feat'}};
-    $self->{'_as_feat'} = [];
-    return @feats;
-}
 
+    if ( $type ) {
+        my @selected_feats   = grep { $_->primary_tag eq $type } @{ $self->{'_as_feat'} };
+        my @unselected_feats = grep { $_->primary_tag ne $type } @{ $self->{'_as_feat'} };
+        $self->{'_as_feat'} = \@unselected_feats;
+        return @selected_feats;
+    }
+    else {
+        my @all_feats = @{ $self->{'_as_feat'} };
+        $self->{'_as_feat'} = [];
+        return @all_feats;
+    }
+}
 
 =head1 Methods provided in the Bio::PrimarySeqI interface
 
@@ -1191,8 +1197,8 @@ or other information as expected. See L<Bio::PrimarySeq>
 for more information.
 
 Sequence Features are B<not> transferred to the new objects.
-This is possibly a mistake. Anyone who feels the urge in
-dealing with this is welcome to give it a go.
+To reverse complement and include the features use
+L<Bio::SeqUtils::revcom_with_features>.
 
 =head2 revcom
 
diff --git a/t/SeqIO/genbank.t b/t/SeqIO/genbank.t
index b9fa2ef37..3c37dfc62 100644
--- a/t/SeqIO/genbank.t
+++ b/t/SeqIO/genbank.t
@@ -6,7 +6,7 @@ use strict;
 BEGIN {
     use lib '.';
     use Bio::Root::Test;
-    test_begin(-tests => 292);
+    test_begin(-tests => 296);
     use_ok('Bio::SeqIO::genbank');
 }
 
@@ -679,3 +679,17 @@ is($anns[0]->value, 'join(WP_015639704.1:1..205)');
 is($seq->seq, 'MENRKFGYIRVSSKDQNEGRQLEAMRKIGITERDIYLDKQSGKNFERANYQLLKRIIRKGDI'
             . 'LYIHSLDRFGRNKEEILQEWNDLTKNIEADIVVLDMPLLDTTQYKDSMGTFIADLVLQILSWMAEEERERIRK'
             . 'RQREGIDLALQNGIQFGRSPVVVSDEFKEVYRKWKAKELTAVEAMQEAGVKKTSFYKLVKAHENSIKVNS');
+
+$seq = Bio::SeqIO->new(-format => 'genbank',
+                       -file   => test_input_file('YP_007988852.gp') )->next_seq;
+@features = $seq->remove_SeqFeatures;
+is $#features, 10, 'Got 11 features';
+
+$seq = Bio::SeqIO->new(-format => 'genbank',
+                       -file   => test_input_file('YP_007988852.gp') )->next_seq;
+@features = $seq->remove_SeqFeatures('CDS');
+is $#features, 0, 'Got 1 feature';
+is $features[0]->primary_tag, 'CDS', 'Correct primary tag for feature';
+@features = $seq->remove_SeqFeatures;
+is $#features, 9, 'Got 10 features';
+
-- 
2.11.4.GIT