Bio::Index Fasta
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Summary
Bio::Index::Fasta - Interface for indexing (multiple) fasta files
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
    # fasta files
    use Bio::Index::Fasta;
    use strict;

    my $Index_File_Name = shift;
    my $inx = Bio::Index::Fasta->new(
        '-filename' => $Index_File_Name,
        '-write_flag' => 1);
    $inx->make_index(@ARGV);

    # Print out several sequences present in the index
    # in Fasta format
    use Bio::Index::Fasta;
    use strict;

    my $Index_File_Name = shift;
    my $inx = Bio::Index::Fasta->new('-filename' => $Index_File_Name);
    my $out = Bio::SeqIO->new('-format' => 'Fasta','-fh' => \*STDOUT);

    foreach my $id (@ARGV) {
        my $seq = $inx->fetch($id); # Returns Bio::Seq object
	$out->write_seq($seq);
    }

    # or, alternatively
    my $id;
    my $seq = $inx->get_Seq_by_id($id); #identical to fetch
Description
Inherits functions for managing dbm files from Bio::Index::Abstract.pm,
and provides the basic funtionallity for indexing fasta files, and
retrieving the sequence from them. For best results 'use strict'.
Bio::Index::Fasta supports the Bio::DB::BioSeqI interface, meaning
it can be used as a Sequence database for other parts of bioperl
Details on configuration and additional example code are available in the
biodatabases.pod file, scripts/index/*PLS and in bptutorial.pl.
Note that by default the key for the sequence will be the first continuous
string after the '>' in the fasta header. If you want to use a specific
substring of the fasta header you must use the id_parser() method.
Methods
_version
No description
Code
_file_formatDescriptionCode
_index_fileDescriptionCode
id_parserDescriptionCode
default_id_parserDescriptionCode
Methods description
_file_formatcode    nextTop
 Title   : _file_format
 Function: The file format for this package, which is needed
           by the SeqIO system when reading the sequence.
 Returns : 'Fasta'
_index_filecodeprevnextTop
  Title   : _index_file
  Usage   : $index->_index_file( $file_name, $i )
  Function: Specialist function to index FASTA format files.
            Is provided with a filename and an integer
            by make_index in its SUPER class.
  Example : 
  Returns : 
  Args    :
id_parsercodeprevnextTop
  Title   : id_parser
  Usage   : $index->id_parser( CODE )
  Function: Stores or returns the code used by record_id to
            parse the ID for record from a string.  Useful
            for (for instance) specifying a different
            parser for different flavours of FASTA file. 
            Returns \&default_id_parser (see below) if not
            set. If you supply your own id_parser
            subroutine, then it should expect a fasta
            description line.  An entry will be added to
            the index for each string in the list returned.
  Example : $index->id_parser( \&my_id_parser )
  Returns : ref to CODE if called without arguments
  Args    : CODE
default_id_parsercodeprevnextTop
  Title   : default_id_parser
  Usage   : $id = default_id_parser( $header )
  Function: The default Fasta ID parser for Fasta.pm
            Returns $1 from applying the regexp /^>\s*(\S+)/
            to $header.
  Returns : ID string
  Args    : a fasta header line string
Methods code
_versiondescriptionprevnextTop
sub _version {
    return 0.2;
}
_file_formatdescriptionprevnextTop
sub _file_format {
    return 'Fasta';
}
_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.
); $begin = 0; my $id_parser = $self->id_parser; open FASTA, $file or $self->throw("Can't open file for read : $file"); # Main indexing loop
while (<FASTA>) { if (/^>/) { # $begin is the position of the first character after the '>'
my $begin = tell(FASTA) - length( $_ ) + 1; foreach my $id (&$id_parser($_)) { $self->add_record($id, $i, $begin); } } } close FASTA; return 1;
}
id_parserdescriptionprevnextTop
sub id_parser {
    my( $self, $code ) = @_;
    
    if ($code) {
        $self->{'_id_parser'} = $code;
    }
    return $self->{'_id_parser'} ||\& default_id_parser;
}
default_id_parserdescriptionprevnextTop
sub default_id_parser {
        if ($_[0] =~ /^>\s*(\S+)/) {
        return $1;
    } else {
        return;
    }
}
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 - James GilbertTop
Email - jgrg@sanger.ac.uk
APPENDIXTop
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _