NAME

Bio::Index::Fasta - Interface for indexing (multiple) fasta files

SYNOPSIS

    # Complete code for making an index for several
    # fasta files
    use Bio::Index::Fasta;

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

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

    my $Index_File_Name = shift;
    my $inx = Bio::Index::Fasta->new($Index_File_Name);

    foreach my $id (@ARGV) {
        my $seq = $inx->fetch($id); # Returns Bio::Seq object
        print $seq->layout('GCG');
    }

    # or, alternatively

    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.

Bio::Index::Fasta supports the Bio::DB::BioSeqI interface, meaning it can be used a a Sequence database for other parts of bioperl

FEED_BACK

Mailing Lists

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.

  vsns-bcd-perl@lists.uni-bielefeld.de          - General discussion
  vsns-bcd-perl-guts@lists.uni-bielefeld.de     - Technically-oriented discussion
  http://bio.perl.org/MailList.html             - About the mailing lists

Reporting Bugs

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://bio.perl.org/bioperl-bugs/

AUTHOR - James Gilbert

Email - jgrg@sanger.ac.uk

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

_initialize

  Title   : _initialize
  Usage   : $index->_initialize
  Function: Calls $index->SUPER::_initialize(), and then adds
            the default id parser for fasta files.
  Example : 
  Returns : 
  Args    : 

_index_file

  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    : 

record_id

  Title   : record_id
  Usage   : $index->record_id( STRING );
  Function: Parses the ID for an entry from the string
            supplied, using the code in $index->{'_id_parser'}
  Example : 
  Returns : scalar or exception
  Args    : STRING

id_parser

  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.
  Example : $index->id_parser( \&my_id_parser )
  Returns : ref to CODE if called without arguments
  Args    : CODE

default_id_parser

  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.
  Example : 
  Returns : ID string
  Args    : a fasta header line string

fetch

  Title   : fetch
  Usage   : $index->fetch( $id )
  Function: Returns a Bio::Seq object from the index
  Example : $seq = $index->fetch( 'dJ67B12' )
  Returns : Bio::Seq object
  Args    : ID

get_Seq_by_id

 Title   : get_Seq_by_id
 Usage   : $seq = $db->get_Seq_by_id()
 Function: retrieves a sequence object, identically to
           ->fetch, but here behaving as a Bio::DB::BioSeqI
 Returns : new Bio::Seq object
 Args    : string represents the id

cpanm Bio::Seq

perl -MCPAN -e shell
install Bio::Seq