Bio::DB::Fasta(3) User Contributed Perl Documentation Bio::DB::Fasta(3)NAMEBio::DB::Fasta-- Fast indexed access to a directory of fasta files
SYNOPSIS
use Bio::DB::Fasta;
# create database from directory of fasta files
my $db = Bio::DB::Fasta->new('/path/to/fasta/files');
# simple access (for those without Bioperl)
my $seq = $db->seq('CHROMOSOME_I',4_000_000 => 4_100_000);
my $revseq = $db->seq('CHROMOSOME_I',4_100_000 => 4_000_000);
my @ids = $db->ids;
my $length = $db->length('CHROMOSOME_I');
my $alphabet = $db->alphabet('CHROMOSOME_I');
my $header = $db->header('CHROMOSOME_I');
# Bioperl-style access
my $db = Bio::DB::Fasta->new('/path/to/fasta/files');
my $obj = $db->get_Seq_by_id('CHROMOSOME_I');
my $seq = $obj->seq; # sequence string
my $subseq = $obj->subseq(4_000_000 => 4_100_000); # string
my $trunc = $obj->trunc(4_000_000 => 4_100_000); # seq object
my $length = $obj->length;
# (etc)
# Bio::SeqIO-style access
my $stream = Bio::DB::Fasta->new('/path/to/files')->get_PrimarySeq_stream;
while (my $seq = $stream->next_seq) {
# Bio::PrimarySeqI stuff
}
my $fh = Bio::DB::Fasta->newFh('/path/to/fasta/files');
while (my $seq = <$fh>) {
# Bio::PrimarySeqI stuff
}
# tied hash access
tie %sequences,'Bio::DB::Fasta','/path/to/fasta/files';
print $sequences{'CHROMOSOME_I:1,20000'};
DESCRIPTIONBio::DB::Fasta provides indexed access to one or more Fasta files. It
provides random access to each sequence entry, and to subsequences
within each entry, allowing you to retrieve portions of very large
sequences without bringing the entire sequence into memory.
When you initialize the module, you point it at a single fasta file or
a directory of multiple such files. The first time it is run, the
module generates an index of the contents of the file or directory
using the AnyDBM module (Berkeley DB* preferred, followed by GDBM_File,
NDBM_File, and SDBM_File). Thereafter it uses the index file to find
the file and offset for any requested sequence. If one of the source
fasta files is updated, the module reindexes just that one file. (You
can also force reindexing manually). For improved performance, the
module keeps a cache of open filehandles, closing less-recently used
ones when the cache is full.
The fasta files may contain any combination of nucleotide and protein
sequences; during indexing the module guesses the molecular type.
Entries may have any line length up to 65,536 characters, and different
line lengths are allowed in the same file. However, within a sequence
entry, all lines must be the same length except for the last.
An error will be thrown if this is not the case.
The module uses /^>(\S+)/ to extract the primary ID of each sequence
from the Fasta header. During indexing, you may pass a callback
routine to modify this primary ID. For example, you may wish to
extract a portion of the gi|gb|abc|xyz nonsense that GenBank Fasta
files use. The original header line can be recovered later.
This module was developed for use with the C. elegans and human
genomes, and has been tested with sequence segments as large as 20
megabases. Indexing the C. elegans genome (100 megabases of genomic
sequence plus 100,000 ESTs) takes ~5 minutes on my 300 MHz pentium
laptop. On the same system, average access time for any 200-mer within
the C. elegans genome was <0.02s.
*Berkeley DB can be obtained free from www.sleepycat.com. After it is
installed you will need to install the BerkeleyDB Perl module.
DATABASE CREATION AND INDEXING
The two constructors for this class are new() and newFh(). The former
creates a Bio::DB::Fasta object which is accessed via method calls.
The latter creates a tied filehandle which can be used Bio::SeqIO style
to fetch sequence objects in a stream fashion. There is also a tied
hash interface.
$db = Bio::DB::Fasta->new($fasta_path [,%options])
Create a new Bio::DB::Fasta object from the Fasta file or files
indicated by $fasta_path. Indexing will be performed automatically
if needed. If successful, new() will return the database accessor
object. Otherwise it will return undef.
$fasta_path may be an individual Fasta file, or may refer to a
directory containing one or more of such files. Following the path,
you may pass a series of name=>value options or a hash with these
same name=>value pairs. Valid options are:
Option Name Description Default
----------- ----------- -------
-glob Glob expression to use *.{fa,fasta,fast,FA,FASTA,FAST,dna}
for searching for Fasta
files in directories.
-makeid A code subroutine for None
transforming Fasta IDs.
-maxopen Maximum size of 32
filehandle cache.
-debug Turn on status 0
messages.
-reindex Force the index to be 0
rebuilt.
-dbmargs Additional arguments none
to pass to the DBM
routines when tied
(scalar or array ref).
-dbmargs can be used to control the format of the index. For
example, you can pass $DB_BTREE to this argument so as to force the
IDs to be sorted and retrieved alphabetically. Note that you must
use the same arguments every time you open the index!
-reindex can be used to force the index to be recreated from scratch.
$fh = Bio::DB::Fasta->newFh($fasta_path [,%options])
Create a tied filehandle opened on a Bio::DB::Fasta object. Reading
from this filehandle with <> will return a stream of sequence
objects, Bio::SeqIO style.
The -makeid option gives you a chance to modify sequence IDs during
indexing. The option value should be a code reference that will take a
scalar argument and return a scalar result, like this:
$db = Bio::DB::Fasta->new("file.fa",-makeid=>\&make_my_id);
sub make_my_id {
my $description_line = shift;
# get a different id from the fasta header, e.g.
$description_line =~ /(\S+)$/;
return $1;
}
make_my_id() will be called with the full fasta id line (including the
">" symbol!). For example:
>A12345.3 Predicted C. elegans protein egl-2
By default, this module will use the regular expression /^>(\S+)/ to
extract "A12345.3" for use as the ID. If you pass a -makeid callback,
you can extract any portion of this, such as the "egl-2" symbol.
The -makeid option is ignored after the index is constructed.
OBJECT METHODS
The following object methods are provided.
$raw_seq = $db->seq($id [,$start, $stop])
Return the raw sequence (a string) given an ID and optionally
a start and stop position in the sequence. In the case of
DNA sequence, if $stop is less than $start, then the reverse
complement of the sequence is returned (this violates
Bio::Seq conventions).
For your convenience, subsequences can be indicated with any
of the following compound IDs:
$db->seq("$id:$start,$stop")
$db->seq("$id:$start..$stop")
$db->seq("$id:$start-$stop")
$length = $db->length($id)
Return the length of the indicated sequence.
$header = $db->header($id)
Return the header line for the ID, including the initial ">".
$type = $db->alphabet($id)
Return the molecular type of the indicated sequence. One of
"dna", "rna" or "protein".
$filename = $db->file($id)
Return the name of the file in which the indicated sequence
can be found.
$offset = $db->offset($id)
Return the offset of the indicated sequence from the
beginning of the file in which it is located. The offset
points to the beginning of the sequence, not the beginning of
the header line.
$header_length = $db->headerlen($id)
Return the length of the header line for the indicated
sequence.
$header_offset = $db->header_offset($id)
Return the offset of the header line for the indicated
sequence from the beginning of the file in which it is
located.
$index_name = $db->index_name
Return the path to the index file.
$path = $db->path
Return the path to the Fasta file(s).
For BioPerl-style access, the following methods are provided:
$seq = $db->get_Seq_by_id($id)
Return a Bio::PrimarySeq::Fasta object, which obeys the
Bio::PrimarySeqI conventions. For example, to recover the raw DNA
or protein sequence, call $seq->seq().
Note that get_Seq_by_id() does not bring the entire sequence into
memory until requested. Internally, the returned object uses the
accessor to generate subsequences as needed.
$seq = $db->get_Seq_by_acc($id)
$seq = $db->get_Seq_by_primary_id($id)
These methods all do the same thing as get_Seq_by_id().
$stream = $db->get_PrimarySeq_stream()
Return a Bio::DB::Fasta::Stream object, which supports a single
method next_seq(). Each call to next_seq() returns a new
Bio::PrimarySeq::Fasta object, until no more sequences remain.
See Bio::PrimarySeqI for methods provided by the sequence objects
returned from get_Seq_by_id() and get_PrimarySeq_stream().
TIED INTERFACES
This module provides two tied interfaces, one which allows you to treat
the sequence database as a hash, and the other which allows you to
treat the database as an I/O stream.
Creating a Tied Hash
The tied hash interface is very straightforward
$obj = tie %db,'Bio::DB::Fasta','/path/to/fasta/files' [,@args]
Tie %db to Bio::DB::Fasta using the indicated path to the Fasta files.
The optional @args list is the same set of named argument/value pairs
used by Bio::DB::Fasta->new().
If successful, tie() will return the tied object. Otherwise it will
return undef.
Once tied, you can use the hash to retrieve an individual sequence by
its ID, like this:
my $seq = $db{CHROMOSOME_I};
You may select a subsequence by appending the comma-separated range to
the sequence ID in the format "$id:$start,$stop". For example, here is
the first 1000 bp of the sequence with the ID "CHROMOSOME_I":
my $seq = $db{'CHROMOSOME_I:1,1000'};
(The regular expression used to parse this format allows sequence IDs
to contain colons.)
When selecting subsequences, if $start > stop, then the reverse
complement will be returned for DNA sequences.
The keys() and values() functions will return the sequence IDs and
their sequences, respectively. In addition, each() can be used to
iterate over the entire data set:
while (my ($id,$sequence) = each %db) {
print "$id => $sequence\n";
}
When dealing with very large sequences, you can avoid bringing them
into memory by calling each() in a scalar context. This returns the
key only. You can then use tied(%db) to recover the Bio::DB::Fasta
object and call its methods.
while (my $id = each %db) {
print "$id => $db{$sequence:1,100}\n";
print "$id => ",tied(%db)->length($id),"\n";
}
You may, in addition invoke Bio::DB::Fasta the FIRSTKEY and NEXTKEY
tied hash methods directly.
$id = $db->FIRSTKEY
Return the first ID in the database.
$id = $db->NEXTKEY($id)
Given an ID, return the next ID in sequence.
This allows you to write the following iterative loop using just the
object-oriented interface:
my $db = Bio::DB::Fasta->new('/path/to/fasta/files');
for (my $id=$db->FIRSTKEY; $id; $id=$db->NEXTKEY($id)) {
# do something with sequence
}
Creating a Tied Filehandle
The Bio::DB::Fasta->newFh() method creates a tied filehandle from which
you can read Bio::PrimarySeq::Fasta sequence objects sequentially. The
following bit of code will iterate sequentially over all sequences in
the database:
my $fh = Bio::DB::Fasta->newFh('/path/to/fasta/files');
while (my $seq = <$fh>) {
print $seq->id,' => ',$seq->length,"\n";
}
When no more sequences remain to be retrieved, the stream will return
undef.
BUGS
When a sequence is deleted from one of the Fasta files, this deletion
is not detected by the module and removed from the index. As a result,
a "ghost" entry will remain in the index and will return garbage
results if accessed.
Currently, the only way to accomodate deletions is to rebuild the
entire index, either by deleting it manually, or by passing -reindex=>1
to new() when initializing the module.
SEE ALSO
bioperl
AUTHOR
Lincoln Stein <lstein@cshl.org>.
Copyright (c) 2001 Cold Spring Harbor Laboratory.
This library is free software; you can redistribute it and/or modify it
under the same terms as Perl itself. See DISCLAIMER.txt for
disclaimers of warranty.
new
Title : new
Usage : my $db = Bio::DB::Fasta->new( $path, @options);
Function: initialize a new Bio::DB::Fasta object
Returns : new Bio::DB::Fasta object
Args : path to dir of fasta files or a single filename
These are optional arguments to pass in as well.
-glob Glob expression to use *.{fa,fasta,fast,FA,FASTA,FAST}
for searching for Fasta
files in directories.
-makeid A code subroutine for none
transforming Fasta IDs.
-maxopen Maximum size of 32
filehandle cache.
-debug Turn on status 0
messages.
-reindex Force the index to be 0
rebuilt.
-dbmargs Additional arguments none
to pass to the DBM
routines when tied
(scalar or array ref).
newFh
Title : newFh
Function: gets a new Fh for a file
Example : internal method
Returns : GLOB
Args :
index_dir
Title : index_dir
Usage : $db->index_dir($dir)
Function: set the index dir and load all files in the dir
Returns : hashref of seq offsets in each file
Args : dirname, boolean to force a reload of all files
get_Seq_by_id
Title : get_Seq_by_id
Usage : my $seq = $db->get_Seq_by_id($id)
Function: Bio::DB::RandomAccessI method implemented
Returns : Bio::PrimarySeqI object
Args : id
set_pack_method
Title : set_pack_method
Usage : $db->set_pack_method( @files )
Function: Determines whether data packing uses 32 or 64 bit integers
Returns :
Args : one or more file paths
index_file
Title : index_file
Usage : $db->index_file($filename)
Function: (re)loads a sequence file and indexes sequences offsets in the file
Returns : seq offsets in the file
Args : filename,
boolean to force reloading a file
dbmargs
Title : dbmargs
Usage : my @args = $db->dbmargs;
Function: gets stored dbm arguments
Returns : array
Args : none
index_name
Title : index_name
Usage : my $indexname = $db->index_name($path,$isdir);
Function: returns the name of the index for a specific path
Returns : string
Args : path to check,
boolean if it is a dir
calculate_offsets
Title : calculate_offsets
Usage : $db->calculate_offsets($filename,$offsets);
Function: calculates the sequence offsets in a file based on id
Returns : offset hash for each file
Args : file to process
$offsets - hashref of id to offset storage
get_all_ids
Title : get_all_ids
Usage : my @ids = $db->get_all_ids
Function: gets all the stored ids in all indexes
Returns : list of ids
Args : none
subseq
Title : subseq
Usage : $seqdb->subseq($id,$start,$stop);
Function: returns a subseq of a sequence in the db
Returns : subsequence data
Args : id of sequence, starting point, ending point
get_PrimarySeq_stream
Title : get_PrimarySeq_stream
Usage :
Function:
Example :
Returns :
Args :
perl v5.14.1 2011-07-22 Bio::DB::Fasta(3)
