Bio::Index GenBank
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Summary
Bio::Index::GenBank - Interface for indexing (multiple) GenBank
.seq files (ie flat file GenBank format).
Package variables
No package variables defined.
Included modules
Bio::Index::AbstractSeq
Bio::Seq
Inherit
Bio::Index::AbstractSeq
Synopsis
    # Complete code for making an index for several
# GenBank files
use Bio::Index::GenBank;
use strict;
my $Index_File_Name = shift; my $inx = Bio::Index::GenBank->new('-filename' => $Index_File_Name, '-write_flag' => 'WRITE'); $inx->make_index(@ARGV); # Print out several sequences present in the index # in gcg format use Bio::Index::GenBank; use Bio::SeqIO; use strict; my $Index_File_Name = shift; my $inx = Bio::Index::GenBank->new('-filename' => $Index_File_Name); my $seqio = new Bio::SeqIO(-format => 'gcg'); foreach my $id (@ARGV) { my $seq = $inx->fetch($id); # Returns Bio::Seq object $seqio->write_seq($seq); } # alternatively my $seq1 = $inx->get_Seq_by_id($id); my $seq2 = $inx->get_Seq_by_acc($acc);
Description
Inherits functions for managing dbm files from Bio::Index::Abstract.pm,
and provides the basic funtionallity for indexing GenBank files, and
retrieving the sequence from them. Heavily snaffled from James Gilbert's
Fasta system. Note: for best results 'use strict'.
Methods
_file_formatDescriptionCode
_index_fileDescriptionCode
_type_stamp
No description
Code
_version
No description
Code
Methods description
_file_formatcode    nextTop
 Title   : _file_format
Usage : Internal function for indexing system
Function: Provides file format for this database
Example :
Returns :
Args :
_index_filecodeprevnextTop
  Title   : _index_file
Usage : $index->_index_file( $file_name, $i )
Function: Specialist function to index GenBank format files.
Is provided with a filename and an integer
by make_index in its SUPER class.
Example :
Returns :
Args :
Methods code
_file_formatdescriptionprevnextTop
sub _file_format {
   my ($self,@args) = @_;

   return 'GenBank';
}

1;
}
_index_filedescriptionprevnextTop
sub _index_file {
    my( $self,
        $file, # File name
$i # Index-number of file being indexed
) = @_; my( $begin, # Offset from start of file of the start
# of the last found record.
$id, # ID of last found record.
@accs, # accession of last record. Also put into the index
); $begin = 0; open GenBank, $file or $self->throw("Can't open file for read : $file"); # Main indexing loop
$id = undef; @accs = (); while (<GenBank>) { if( /^\/\// ) { if( ! defined $id ) { $self->throw("Got to a end of entry line for an GenBank flat file with no parsed ID. Considering this a problem!"); next; } if( ! @accs ) { $self->warn("For id [$id] in GenBank flat file, got no accession number. Storing id index anyway"); } $self->add_record($id, $i, $begin); foreach my $acc (@accs) { if( $acc ne $id ) { $self->add_record($acc, $i, $begin); } } @accs = (); } elsif (/^LOCUS\s+(\S+)/) { $id = $1; # not sure if I like this. Assummes tell is in bytes.
# we could tell before each line and save it.
$begin = tell(GenBank) - length( $_ ); } elsif (/^ACCESSION(.*)/) { # ignore ? if there.
@accs = ($1 =~ /\s*(\S+)/g); } elsif( /^VERSION(.*)/) { my $a = $1; $a =~ s/^\s+//; $a =~ s/\s+$//; $a =~ s/GI\://; push @accs, split(/\s+/,$a); } else { # do nothing
} } close GenBank; return 1;
}
_type_stampdescriptionprevnextTop
sub _type_stamp {
    return '__GenBank_FLAT__'; # What kind of index are we?
} #
# Suggested fix by Michael G Schwern <schwern@pobox.com> to
# get around a clash with CPAN shell...
#
BEGIN { $VERSION = 0.1;
}
_versiondescriptionprevnextTop
sub _version {
    return $VERSION;
}
General documentation
FEED_BACKTop
Mailing ListsTop
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
  bioperl-l@bioperl.org             - General discussion
http://bioperl.org/MailList.shtml - About the mailing lists
Reporting BugsTop
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via
email or the web:
  bioperl-bugs@bio.perl.org
http://bugzilla.bioperl.org/
AUTHOR - Ewan BirneyTop
Email - birney@ebi.ac.uk
APPENDIXTop
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _