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.IX Title "Bio::ASN1::Sequence::Indexer 3pm"
.TH Bio::ASN1::Sequence::Indexer 3pm "2021-03-04" "perl v5.32.1" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "NAME"
Bio::ASN1::Sequence::Indexer \- Indexes NCBI Sequence files.
.SH "VERSION"
.IX Header "VERSION"
version 1.73
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\&  use Bio::ASN1::Sequence::Indexer;
\&
\&  # creating & using the index is just a few lines
\&  my $inx = Bio::ASN1::Sequence::Indexer\->new(
\&    \-filename => \*(Aqseq.idx\*(Aq,
\&    \-write_flag => \*(AqWRITE\*(Aq); # needed for make_index call, but if opening
\&                             # existing index file, don\*(Aqt set write flag!
\&  $inx\->make_index(\*(Aqseq1.asn\*(Aq, \*(Aqseq2.asn\*(Aq);
\&  my $seq = $inx\->fetch(\*(AqAF093062\*(Aq); # Bio::Seq obj for Sequence (doesn\*(Aqt work yet)
\&  # alternatively, if one prefers just a data structure instead of objects
\&  $seq = $inx\->fetch_hash(\*(AqAF093062\*(Aq); # a hash produced by Bio::ASN1::Sequence
\&                            # that contains all data in the Sequence record
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
Bio::ASN1::Sequence::Indexer is a Perl Indexer for \s-1NCBI\s0 Sequence genome
databases. It processes an \s-1ASN\s0.1\-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).
.PP
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.
.PP
As with Bio::ASN1::Sequence, this module is best thought of as beta version \-
it works, but is not fully tested.
.SH "METHODS"
.IX Header "METHODS"
.SS "fetch"
.IX Subsection "fetch"
.Vb 6
\&  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\*(Aqt
\&                exist for a while!  So call fetch_hash instead
.Ve
.SS "fetch_hash"
.IX Subsection "fetch_hash"
.Vb 6
\&  Parameters: $seqid \- id for the Sequence record to be retrieved
\&  Example:    my $hash = $indexer\->fetch_hash(\*(AqAF093062\*(Aq);
\&  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()
.Ve
.SH "INTERNAL METHODS"
.IX Header "INTERNAL METHODS"
.SS "_version"
.IX Subsection "_version"
.SS "_type_stamp"
.IX Subsection "_type_stamp"
.SS "_index_file"
.IX Subsection "_index_file"
.SS "_file_format"
.IX Subsection "_file_format"
.SS "_file_handle"
.IX Subsection "_file_handle"
.Vb 10
\&  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 module
.Ve
.SH "PREREQUISITE"
.IX Header "PREREQUISITE"
Bio::ASN1::Sequence, Bioperl and all dependencies therein.
.SH "INSTALLATION"
.IX Header "INSTALLATION"
Same as Bio::ASN1::EntrezGene
.SH "SEE ALSO"
.IX Header "SEE ALSO"
Please check out perldoc for Bio::ASN1::EntrezGene for more info.
.SH "CITATION"
.IX Header "CITATION"
Liu, Mingyi, and Andrei Grigoriev. \*(L"Fast parsers for Entrez Gene.\*(R"
Bioinformatics 21, no. 14 (2005): 3189\-3190.
.SH "OPERATION SYSTEMS SUPPORTED"
.IX Header "OPERATION SYSTEMS SUPPORTED"
Any \s-1OS\s0 that Perl & Bioperl run on.
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org              \- General discussion
\&  http://bioperl.org/Support.html    \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  https://github.com/bioperl/bio\-asn1\-entrezgene/issues
.Ve
.SH "AUTHOR"
.IX Header "AUTHOR"
Dr. Mingyi Liu <mingyiliu@gmail.com>
.SH "COPYRIGHT"
.IX Header "COPYRIGHT"
This software is copyright (c) 2005 by Mingyi Liu, 2005 by \s-1GPC\s0 Biotech \s-1AG,\s0 and 2005 by Altana Research Institute.
.PP
This software is available under the same terms as the perl 5 programming language system itself.