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1 # $Id: EMBL.pm,v 1.21.2.1 2003/03/19 16:23:08 heikki Exp $
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2 #
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3 # BioPerl module for Bio::Index::EMBL
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4 #
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5 # Cared for by Ewan Birney <birney@sanger.ac.uk>
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6 #
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7 # You may distribute this module under the same terms as perl itself
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8
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9 # POD documentation - main docs before the code
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10
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11 =head1 NAME
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12
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13 Bio::Index::EMBL - Interface for indexing (multiple) EMBL/Swissprot
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14 .dat files (ie flat file embl/swissprot format).
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15
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16 =head1 SYNOPSIS
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17
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18 # Complete code for making an index for several
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19 # EMBL files
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20 use Bio::Index::EMBL;
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21 use strict;
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22
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23 my $Index_File_Name = shift;
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24 my $inx = Bio::Index::EMBL->new('-filename' => $Index_File_Name,
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25 '-write_flag' => 'WRITE');
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26 $inx->make_index(@ARGV);
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27
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28 # Print out several sequences present in the index
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29 # in Fasta format
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30 use Bio::Index::EMBL;
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31 use strict;
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32
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33 my $Index_File_Name = shift;
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34 my $inx = Bio::Index::EMBL->new('-filename' => $Index_File_Name);
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35 my $out = Bio::SeqIO->new('-format' => 'Fasta','-fh' => \*STDOUT);
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36
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37 foreach my $id (@ARGV) {
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38 my $seq = $inx->fetch($id); # Returns Bio::Seq object
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39 $out->write_seq($seq);
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40 }
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41
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42 # alternatively
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43
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44 my $seq1 = $inx->get_Seq_by_id($id);
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45 my $seq2 = $inx->get_Seq_by_acc($acc);
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46
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47 =head1 DESCRIPTION
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48
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49 Inherits functions for managing dbm files from Bio::Index::Abstract.pm,
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50 and provides the basic funtionallity for indexing EMBL files, and
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51 retrieving the sequence from them. Heavily snaffled from James Gilbert's
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52 Fasta system. Note: for best results 'use strict'.
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53
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54 =head1 FEED_BACK
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55
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56 =head2 Mailing Lists
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57
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58 User feedback is an integral part of the evolution of this and other
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59 Bioperl modules. Send your comments and suggestions preferably to one
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60 of the Bioperl mailing lists. Your participation is much appreciated.
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61
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62 bioperl-l@bioperl.org - General discussion
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63 http://bioperl.org/MailList.shtml - About the mailing lists
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64
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65
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66
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67 =head2 Reporting Bugs
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68
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69 Report bugs to the Bioperl bug tracking system to help us keep track
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70 the bugs and their resolution. Bug reports can be submitted via
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71 email or the web:
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72
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73 bioperl-bugs@bio.perl.org
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74 http://bugzilla.bioperl.org/
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75
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76 =head1 AUTHOR - Ewan Birney
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77
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78 Email - birney@sanger.ac.uk
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79
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80 =head1 APPENDIX
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81
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82 The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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83
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84 =cut
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85
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86
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87 # Let's begin the code...
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88
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89
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90 package Bio::Index::EMBL;
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91
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92 use vars qw($VERSION @ISA);
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93 use strict;
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94
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95 use Bio::Index::AbstractSeq;
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96 use Bio::Seq;
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97
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98 @ISA = qw(Bio::Index::AbstractSeq);
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99
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100 sub _type_stamp {
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101 return '__EMBL_FLAT__'; # What kind of index are we?
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102 }
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103
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104 #
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105 # Suggested fix by Michael G Schwern <schwern@pobox.com> to
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106 # get around a clash with CPAN shell...
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107 #
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108
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109 BEGIN {
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110 $VERSION = 0.1;
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111 }
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112
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113 sub _version {
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114 return $VERSION;
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115 }
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116
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117 =head2 _index_file
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118
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119 Title : _index_file
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120 Usage : $index->_index_file( $file_name, $i )
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121 Function: Specialist function to index EMBL format files.
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122 Is provided with a filename and an integer
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123 by make_index in its SUPER class.
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124 Example :
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125 Returns :
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126 Args :
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127
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128 =cut
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129
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130 sub _index_file {
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131 my( $self,
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132 $file, # File name
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133 $i # Index-number of file being indexed
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134 ) = @_;
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135
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136 my( $begin, # Offset from start of file of the start
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137 # of the last found record.
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138 $id, # ID of last found record.
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139 @accs, # accession of last record. Also put into the index
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140 );
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141
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142 $begin = 0;
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143
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144 open EMBL, $file or $self->throw("Can't open file for read : $file");
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145
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146 # Main indexing loop
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147 $id = undef;
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148 @accs = ();
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149 while (<EMBL>) {
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150 if( /^\/\// ) {
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151 if( ! defined $id ) {
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152 $self->throw("Got to a end of entry line for an EMBL flat file with no parsed ID. Considering this a problem!");
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153 next;
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154 }
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155 if( ! @accs ) {
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156 $self->warn("For id [$id] in embl flat file, got no accession number. Storing id index anyway");
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157 }
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158
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159 $self->add_record($id, $i, $begin);
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160
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161 foreach my $acc (@accs) {
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162 if( $acc ne $id ) {
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163 $self->add_record($acc, $i, $begin);
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164 }
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165 }
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166 } elsif (/^ID\s+(\S+)/) {
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167 $id = $1;
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168 # not sure if I like this. Assummes tell is in bytes.
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169 # we could tell before each line and save it.
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170 $begin = tell(EMBL) - length( $_ );
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171
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172 } elsif (/^AC\s+(.*)?/) {
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173 push @accs , split (/[; ]+/, $1);
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174 } else {
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175 # do nothing
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176 }
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177 }
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178
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179 close EMBL;
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180 return 1;
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181 }
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182
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183 =head2 _file_format
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184
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185 Title : _file_format
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186 Usage : Internal function for indexing system
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187 Function: Provides file format for this database
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188 Example :
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189 Returns :
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190 Args :
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191
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192
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193 =cut
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194
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195 sub _file_format{
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196 my ($self,@args) = @_;
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197
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198 return 'EMBL';
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199 }
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200
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201
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202
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203 1;
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