NAME
Bio::ASN1::Sequence::Indexer - Indexes NCBI Sequence files.
VERSION
version 1.73
SYNOPSIS
use Bio::ASN1::Sequence::Indexer;
# creating & using the index is just a few lines
my $inx = Bio::ASN1::Sequence::Indexer->new(
-filename => 'seq.idx',
-write_flag => 'WRITE'); # needed for make_index call, but if opening
# existing index file, don't set write flag!
$inx->make_index('seq1.asn', 'seq2.asn');
my $seq = $inx->fetch('AF093062'); # Bio::Seq obj for Sequence (doesn't work yet)
# alternatively, if one prefers just a data structure instead of objects
$seq = $inx->fetch_hash('AF093062'); # a hash produced by Bio::ASN1::Sequence
# that contains all data in the Sequence recordDESCRIPTION
Bio::ASN1::Sequence::Indexer is a Perl Indexer for NCBI Sequence genome databases. It processes an ASN.1-formatted Sequence record and stores the file position for each record in a way compliant with Bioperl standard (in fact its a subclass of Bioperl's index objects).
Note that this module does not parse record, because it needs to run fast and grab only the gene ids. For parsing record, use Bio::ASN1::Sequence.
As with Bio::ASN1::Sequence, this module is best thought of as beta version - it works, but is not fully tested.
METHODS
fetch
Parameters: $geneid - id for the Sequence record to be retrieved
Example: my $hash = $indexer->fetch(10); # get Sequence #10
Function: fetch the data for the given Sequence id.
Returns: A Bio::Seq object produced by Bio::SeqIO::sequence
Notes: Bio::SeqIO::sequence does not exist and probably won't
exist for a while! So call fetch_hash insteadfetch_hash
Parameters: $seqid - id for the Sequence record to be retrieved
Example: my $hash = $indexer->fetch_hash('AF093062');
Function: fetch a hash produced by Bio::ASN1::Sequence for given id
Returns: A data structure containing all data items from the Sequence
record.
Notes: Alternative to fetch()INTERNAL METHODS
_version
_type_stamp
_index_file
_file_format
_file_handle
Title : _file_handle
Usage : $fh = $index->_file_handle( INT )
Function: Returns an open filehandle for the file
index INT. On opening a new filehandle it
caches it in the @{$index->_filehandle} array.
If the requested filehandle is already open,
it simply returns it from the array.
Example : $fist_file_indexed = $index->_file_handle( 0 );
Returns : ref to a filehandle
Args : INT
Notes : This function is copied from Bio::Index::Abstract. Once that module
changes file handle code like I do below to fit perl 5.005_03, this
sub would be removed from this modulePREREQUISITE
Bio::ASN1::Sequence, Bioperl and all dependencies therein.
INSTALLATION
Same as Bio::ASN1::EntrezGene
SEE ALSO
Please check out perldoc for Bio::ASN1::EntrezGene for more info.
CITATION
Liu, Mingyi, and Andrei Grigoriev. "Fast parsers for Entrez Gene." Bioinformatics 21, no. 14 (2005): 3189-3190.
OPERATION SYSTEMS SUPPORTED
Any OS that Perl & Bioperl run on.
FEEDBACK
Mailing lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/Support.html - About the mailing listsSupport
Please direct usage questions or support issues to the mailing list: bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.
Reporting bugs
Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:
https://github.com/bioperl/bio-asn1-entrezgene/issuesAUTHOR
Dr. Mingyi Liu <mingyiliu@gmail.com>
COPYRIGHT
This software is copyright (c) 2005 by Mingyi Liu, 2005 by GPC Biotech AG, and 2005 by Altana Research Institute.
This software is available under the same terms as the perl 5 programming language system itself.