/
LoadHelper.pm
205 lines (164 loc) · 4.7 KB
/
LoadHelper.pm
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
package Bio::DB::SeqFeature::Store::LoadHelper;
=head1 NAME
Bio::DB::SeqFeature::Store::LoadHelper -- Internal utility for Bio::DB::SeqFeature::Store
=head1 SYNOPSIS
# For internal use only.
=head1 DESCRIPTION
For internal use only
=head1 SEE ALSO
L<bioperl>,
L<Bio::DB::SeqFeature::Store>,
L<Bio::DB::SeqFeature::Segment>,
L<Bio::DB::SeqFeature::NormalizedFeature>,
L<Bio::DB::SeqFeature::GFF2Loader>,
L<Bio::DB::SeqFeature::Store::DBI::mysql>,
L<Bio::DB::SeqFeature::Store::berkeleydb>
=head1 AUTHOR
Lincoln Stein E<lt>lstein@cshl.orgE<gt>.
Copyright (c) 2006 Cold Spring Harbor Laboratory.
This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself.
=cut
use strict;
use DB_File;
use File::Path 'rmtree';
use File::Temp 'tempdir';
use File::Spec;
use Fcntl qw(O_CREAT O_RDWR);
our $VERSION = '1.10';
my %DBHandles;
sub new {
my $class = shift;
my $tmpdir = shift;
my $template = 'SeqFeatureLoadHelper_XXXXXX';
my @tmpargs = $tmpdir ? ($template,DIR=>$tmpdir) : ($template);
my $tmppath = tempdir(@tmpargs,CLEANUP=>1);
my $self = $class->create_dbs($tmppath);
$self->{tmppath} = $tmppath;
return bless $self,$class;
}
sub DESTROY {
my $self = shift;
# Destroy all filehandle references
# before trying to delete files and folder
%DBHandles = ();
undef $self->{IndexIt};
undef $self->{TopLevel};
undef $self->{Local2Global};
undef $self->{Parent2Child};
rmtree $self->{tmppath};
# File::Temp::cleanup() unless $self->{keep};
}
sub create_dbs {
my $self = shift;
my $tmp = shift;
my %self;
# experiment with caching these handles in memory
my $hash_options = DB_File::HASHINFO->new();
# Each of these hashes allow only unique keys
for my $dbname (qw(IndexIt TopLevel Local2Global)) {
unless ($DBHandles{$dbname}) {
my %h;
tie(%h,'DB_File',File::Spec->catfile($tmp,$dbname),
O_CREAT|O_RDWR,0666,$hash_options);
$DBHandles{$dbname} = \%h;
}
$self{$dbname} = $DBHandles{$dbname};
%{$self{$dbname}} = ();
}
# The Parent2Child hash allows duplicate keys, so we
# create it with the R_DUP flag.
my $btree_options = DB_File::BTREEINFO->new();
$btree_options->{flags} = R_DUP;
unless ($DBHandles{'Parent2Child'}) {
my %h;
tie(%h,'DB_File',File::Spec->catfile($tmp,'Parent2Child'),
O_CREAT|O_RDWR,0666,$btree_options);
$DBHandles{'Parent2Child'} = \%h;
}
$self{Parent2Child} = $DBHandles{'Parent2Child'};
%{$self{Parent2Child}} = ();
return \%self;
}
sub indexit {
my $self = shift;
my $id = shift;
$self->{IndexIt}{$id} = shift if @_;
return $self->{IndexIt}{$id};
}
sub toplevel {
my $self = shift;
my $id = shift;
$self->{TopLevel}{$id} = shift if @_;
return $self->{TopLevel}{$id};
}
sub each_toplevel {
my $self = shift;
my ($id) = each %{$self->{TopLevel}};
$id;
}
sub local2global {
my $self = shift;
my $id = shift;
$self->{Local2Global}{$id} = shift if @_;
return $self->{Local2Global}{$id};
}
sub add_children {
my $self = shift;
my $parent_id = shift;
# (@children) = @_;
$self->{Parent2Child}{$parent_id} = shift while @_;
}
sub children {
my $self = shift;
my $parent_id = shift;
my @children;
my $db = tied(%{$self->{Parent2Child}});
my $key = $parent_id;
my $value = '';
for (my $status = $db->seq($key,$value,R_CURSOR);
$status == 0 && $key eq $parent_id;
$status = $db->seq($key,$value,R_NEXT)
) {
push @children,$value;
}
return wantarray ? @children: \@children;
}
# this acts like each() and returns each parent id and an array ref of children
sub each_family {
my $self = shift;
my $db = tied(%{$self->{Parent2Child}});
if ($self->{_cursordone}) {
undef $self->{_cursordone};
undef $self->{_parent};
undef $self->{_child};
return;
}
# do a slightly tricky cursor search
unless (defined $self->{_parent}) {
return unless $db->seq($self->{_parent},$self->{_child},R_FIRST) == 0;
}
my $parent = $self->{_parent};
my @children = $self->{_child};
my $status;
while (($status = $db->seq($self->{_parent},$self->{_child},R_NEXT)) == 0
&& $self->{_parent} eq $parent
) {
push @children,$self->{_child};
}
$self->{_cursordone}++ if $status != 0;
return ($parent,\@children);
}
sub local_ids {
my $self = shift;
my @ids = keys %{$self->{Local2Global}}
if $self->{Local2Global};
return \@ids;
}
sub loaded_ids {
my $self = shift;
my @ids = values %{$self->{Local2Global}}
if $self->{Local2Global};
return \@ids;
}
1;