NAME

FASTAid - index a FASTA sequence database for fast random-access sequence retrieval

VERSION

This document describes FASTAid version 0.0.3

SYNOPSIS

use FASTAid qw( create_index retrieve_entry );

my $FASTA_file = 'lots_of_seqs.fa';

# index the file of FASTA seqs
create_index($FASTA_file);

# retrieve one or more FASTA seqs from the file
my $seq_array_ref = retrieve_entry($FASTA_file, 'NM_00204', 'AA23456');

foreach my $seq ( @{$seq_array_ref} ) {

    ...do something with each FASTA sequence...
}

DESCRIPTION

FASTAid indexes files containing FASTA sequence records and allows quick random-access retrieval of one or more FASTA sequences.

FASTAid writes the index to a file with the suffix '.fec'.

DIAGNOSTICS

could not open FASTA file

A file could not be opened. Probably the path you supplied is incorrect or the permissions are incorrect.

There is already an entry ID

The same identifier appears more than once in the FASTA file you supplied. This is a fatal error because FASTAid uses the identifier to index the position of the sequence.

Cannot write FASTAid index

The index could not be written. This is a file system error, so probably you don't have permissions to write in the directory.

Must supply at least one ID

No identifiers were supplied as arguments to retrieve_entry. Since FASTAid uses the identifier as the lookup, it can't retrieve an entry without an identifier.

Entry ID = <id> not found!

An identifier could not be found in the index. This is a warning, not a fatal error, because if other identifiers are supplied to retrieve_entry, those sequences will be returned even if others fail.

There are two common causes for this error: either the index is out of date and the identifier doesn't exist in the index, or the identifier was misspelled when attempting the lookup.

DEPENDENCIES

version

INCOMPATIBILITIES

None reported.

BUGS AND LIMITATIONS

No bugs have been reported.

Please report any bugs or feature requests to bug-FASTAid@rt.cpan.org, or through the web interface at http://rt.cpan.org.

AUTHOR

Jarret Glasscock C<< <glasscock_cpan@mac.com> >>
Dave Messina C<< <dave-pause@davemessina.net> >>

ACKNOWLEDGMENTS

This software was developed at the Genome Sequencing Center at Washington
University, St. Louis, MO.

COPYRIGHT

Copyright (C) 2004-6 Glasscock, Messina. All Rights Reserved.

DISCLAIMER

This software is provided "as is" without warranty of any kind.

create_index

Usage : create_index(my_fasta_file) or die "index was not created"; Function : creates a byte index file representing positions of FASTA formatted entries. Returns : returns true upon success of index creation, false upon failure Args : a single argument, the path to a FASTA file

retrieve_entry

Usage : my $array_ref = retrieve_entry(FASTA_file_path, identifier1, identifier2, ..); Function : retrieves FASTA sequence given index and identifier(s). Returns : returns a reference to an array of FASTA entries Args : FASTA_file_path, identifier1, identifier2, ..