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2 # $Id: Ace.pm,v 1.10 2002/10/22 07:38:29 lapp Exp $
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3 #
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4 # BioPerl module for Bio::DB::Ace
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5 #
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6 # Cared for by Ewan Birney <birney@sanger.ac.uk>
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7 #
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8 # Copyright Ewan Birney
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9 #
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10 # You may distribute this module under the same terms as perl itself
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11
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12 # POD documentation - main docs before the code
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13
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14 =head1 NAME
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15
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16 Bio::DB::Ace - Database object interface to ACeDB servers
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17
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18 =head1 SYNOPSIS
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19
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20 $db = Bio::DB::Ace->new( -server => 'myace.server.com', port => '120000');
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21
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22 $seq = $db->get_Seq_by_id('MUSIGHBA1'); # Unique ID
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23
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24 # or ...
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25
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26 $seq = $db->get_Seq_by_acc('J00522'); # Accession Number
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27
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28 =head1 DESCRIPTION
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29
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30 This provides a standard BioPerl database access to Ace, using Lincoln Steins
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31 excellent AcePerl module. You need to download and install the aceperl module from
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32
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33 http://stein.cshl.org/AcePerl/
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34
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35 before this interface will work.
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36
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37 This interface is designed at the moment to work through a aceclient/aceserver
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38 type mechanism
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39
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40 =head1 INSTALLING ACEPERL
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41
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42 Download the latest aceperl tar file, gunzip/untar and cd into the directory.
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43 This is a standard CPAN-style directory, so if you go
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44
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45 Perl Makefile.PL
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46 make
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47 <become root>
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48 make install
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49
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50 Then you will have installed Aceperl. Use the PREFIX mechanism to install elsewhere.
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51
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52 =head1 FEEDBACK
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53
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54 =head2 Mailing Lists
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55
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56 User feedback is an integral part of the evolution of this
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57 and other Bioperl modules. Send your comments and suggestions preferably
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58 to one of the Bioperl mailing lists.
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59 Your participation is much appreciated.
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60
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61 bioperl-l@bioperl.org - General discussion
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62 http://bioperl.org/MailList.shtml - About the mailing lists
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63
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64 =head2 Reporting Bugs
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65
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66 Report bugs to the Bioperl bug tracking system to help us keep track
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67 the bugs and their resolution.
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68 Bug reports can be submitted via email or the web:
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69
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70 bioperl-bugs@bio.perl.org
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71 http://bugzilla.bioperl.org/
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72
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73 =head1 AUTHOR - Ewan Birney
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74
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75 Email birney@sanger.ac.uk
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76
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77 =head1 APPENDIX
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78
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79 The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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80
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81 =cut
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82
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83 # Let the code begin...
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84
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85 package Bio::DB::Ace;
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86 use vars qw(@ISA);
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87 use strict;
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88
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89 # Object preamble - inherits from Bio::DB::RandomAccessI
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90
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91 use Bio::DB::RandomAccessI;
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92 use Bio::Seq;
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93
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94 BEGIN {
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95 eval {
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96 require Ace;
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97 };
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98 if( $@) {
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99 print STDERR "You have not installed Ace.pm.\n Read the docs in Bio::DB::Ace for more information about how to do this.\n It is very easy\n\nError message $@";
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100 }
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101 }
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102
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103
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104 @ISA = qw(Bio::DB::RandomAccessI);
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105
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106 # new() is inherited from Bio::DB::Abstract
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107
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108 # _initialize is where the heavy stuff will happen when new is called
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109
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110 sub new {
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111 my($class,@args) = @_;
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112 my $self = $class->SUPER::new(@args);
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113 my ($host,$port) = $self->_rearrange([qw(
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114 HOST
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115 PORT
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116 )],
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117 @args,
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118 );
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119
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120 if( !$host || !$port ) {
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121 $self->throw("Must have a host and port for an acedb server to work");
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122 }
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123
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124 my $aceobj = Ace->connect(-host => $host,
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125 -port => $port) ||
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126 $self->throw("Could not make acedb object to $host:$port");
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127
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128 $self->_aceobj($aceobj);
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129
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130
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131 return $self;
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132 }
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133
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134 =head2 get_Seq_by_id
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135
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136 Title : get_Seq_by_id
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137 Usage : $seq = $db->get_Seq_by_id($uid);
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138 Function: Gets a Bio::Seq object by its unique identifier/name
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139 Returns : a Bio::Seq object
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140 Args : $id : the id (as a string) of the desired sequence entry
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141
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142 =cut
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143
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144 sub get_Seq_by_id {
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145 my $self = shift;
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146 my $id = shift or $self->throw("Must supply an identifier!\n");
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147 my $ace = $self->_aceobj();
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148 my ($seq,$dna,$out);
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149
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150 $seq = $ace->fetch( 'Sequence' , $id);
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151
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152 # get out the sequence somehow!
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153
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154 $dna = $seq->asDNA();
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155
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156 $dna =~ s/^>.*\n//;
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157 $dna =~ s/\n//g;
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158
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159 $out = Bio::Seq->new( -id => $id, -type => 'Dna', -seq => $dna, -name => "Sequence from Bio::DB::Ace $id");
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160 return $out;
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161
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162 }
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163
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164 =head2 get_Seq_by_acc
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165
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166 Title : get_Seq_by_acc
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167 Usage : $seq = $db->get_Seq_by_acc($acc);
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168 Function: Gets a Bio::Seq object by its accession number
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169 Returns : a Bio::Seq object
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170 Args : $acc : the accession number of the desired sequence entry
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171
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172
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173 =cut
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174
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175 sub get_Seq_by_acc {
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176
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177 my $self = shift;
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178 my $acc = shift or $self->throw("Must supply an accesion number!\n");
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179
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180 return $self->get_Seq_by_id($acc);
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181 }
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182
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183 =head2 _aceobj
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184
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185 Title : _aceobj
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186 Usage : $ace = $db->_aceobj();
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187 Function: Get/Set on the acedb object
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188 Returns : Ace object
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189 Args : New value of the ace object
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190
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191 =cut
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192
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193 sub _aceobj {
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194 my ($self,$arg) = @_;
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195
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196 if( $arg ) {
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197 $self->{'_aceobj'} = $arg;
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198 }
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199
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200 return $self->{'_aceobj'};
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201 }
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202
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203 1;
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204
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205
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