Bio::ASN1::EntrezGene(3pm)				User Contributed Perl Documentation				Bio::ASN1::EntrezGene(3pm)

NAME

       Bio::ASN1::EntrezGene - Regular expression-based Perl Parser for NCBI Entrez Gene.

SYNOPSIS

	 use Bio::ASN1::EntrezGene;

	 my $parser = Bio::ASN1::EntrezGene->new('file' => "Homo_sapiens");
	 while(my $result = $parser->next_seq)
	 {
	   # extract data from $result, or Dumpvalue->new->dumpValue($result);
	 }

	 # a new way to get the $result data hash for a particular gene id:
	 use Bio::ASN1::EntrezGene::Indexer;
	 my $inx = Bio::ASN1::EntrezGene::Indexer->new(-filename => 'entrezgene.idx');
	 my $seq = $inx->fetch_hash(10); # returns $result for Entrez Gene record
					 # with geneid 10
	 # note that the index file 'entrezgene.idx' can be created as follows
	 my $inx = Bio::ASN1::EntrezGene::Indexer->new(
	   -filename => 'entrezgene.idx',
	   -write_flag => 'WRITE');
	 $inx->make_index('Homo_sapiens', 'Mus_musculus'); # files come from NCBI download

	 # for more detail please refer to Bio::ASN1::EntrezGene::Indexer perldoc

PREREQUISITE

       None.

INSTALLATION

       Bio::ASN1::EntrezGene package can be installed & tested as follows:

	 perl Makefile.PL
	 make
	 make test
	 make install

DESCRIPTION

       Bio::ASN1::EntrezGene is a regular expression-based Perl Parser for NCBI Entrez Gene genome databases
       (<http://www.ncbi.nih.gov/entrez/query.fcgi?db=gene>).  It parses an ASN.1-formatted Entrez Gene record and returns a data structure that
       contains all data items from the gene record.

       The parser will report error & line number if input data does not conform to the NCBI Entrez Gene genome annotation file format.

       Note that it is possible to provide reading of all NCBI's ASN.1-formatted files through simple variations of the Entrez Gene parser (I need
       more investigation to be sure, but at least the sequence parser is a very simple variation on Entrez Gene parser and works well).

       It took the parser version 1.0 11 minutes to parse the human genome Entrez Gene file on one 2.4 GHz Intel Xeon processor.  The addition of
       validation and error reporting in 1.03 and handling of new Entrez Gene format slowed the parser down about 40%.

       Since V1.07, this package also included an indexer that runs pretty fast (it takes 21 seconds for the indexer to index the human genome on
       the same processor).  Therefore the combination of the modules would allow user to retrieve and parse arbitrary records.

SEE ALSO

       The parse_entrez_gene_example.pl script included in this package (please see the Bio-ASN1-EntrezGene-x.xx/examples directory) is a very
       important and near-complete demo on using this module to extract all data items from Entrez Gene records.  Do check it out because in fact,
       this script took me about 3-4 times more time to make for my project than the parser V1.0 itself. Note that the example script was edited
       to leave out stuff specific to my internal project.

       For details on various parsers I generated for Entrez Gene, example scripts that uses/benchmarks the modules, please see
       <http://sourceforge.net/projects/egparser/>.  Those other parsers etc. are included in V1.05 download.

AUTHOR

       Dr. Mingyi Liu <mingyi.liu@gpc-biotech.com>

COPYRIGHT

       The Bio::ASN1::EntrezGene module and its related modules and scripts are copyright (c) 2005 Mingyi Liu, GPC Biotech AG and Altana Research
       Institute. All rights reserved. I created these modules when working on a collaboration project between these two companies. Therefore a
       special thanks for the two companies to allow the release of the code into public domain.

       You may use and distribute them under the terms of the Perl itself or GPL (<http://www.gnu.org/copyleft/gpl.html>).

CITATION

       Liu, M and Grigoriev, A(2005) "Fast Parsers for Entrez Gene" Bioinformatics. In press

OPERATION SYSTEMS SUPPORTED

       Any OS that Perl runs on.

METHODS

   new
	 Parameters: maxerrstr => 20 (optional) - maximum number of characters after
		       offending element, used by error reporting, default is 20
		     file or -file => $filename (optional) - name of the file to be
		       parsed. call next_seq to parse!
		     fh or -fh => $filehandle (optional) - handle of the file to be
		       parsed.
	 Example:    my $parser = Bio::ASN1::EntrezGene->new();
	 Function:   Instantiate a parser object
	 Returns:    Object reference
	 Notes:      Setting file or fh will reset line numbers etc. that are used
		       for error reporting purposes, and seeking on file handle would
		       mess up linenumbers!

   maxerrstr
	 Parameters: $maxerrstr (optional) - maximum number of characters after
		       offending element, used by error reporting, default is 20
	 Example:    $parser->maxerrstr(20);
	 Function:   get/set maxerrstr.
	 Returns:    maxerrstr.
	 Notes:

   parse
	 Parameters: $string that contains Entrez Gene record,
		     $trimopt (optional) that specifies how the data structure
		       returned should be trimmed. 2 is recommended and
		       default
		     $noreset (optional) that species that line number should not
		       be reset
		     DEPRECATED as external function!!! Do not call this function
		       directly!  Call next_seq() instead
	 Example:    my $value = $parser->parse($text); # DEPRECATED as
		       # external function!!! Do not call this function
		       # directly!  Call next_seq() instead
	 Function:   Takes in a string representing Entrez Gene record, parses
		       the record and returns a data structure.
	 Returns:    A data structure containing all data items from the Entrez
		       Gene record.
	 Notes:      DEPRECATED as external function!!! Do not call this function
		       directly!  Call next_seq() instead
		     $string should not contain 'EntrezGene ::=' at beginning!

   input_file
	 Parameters: $filename for file that contains Entrez Gene record(s)
	 Example:    $parser->input_file($filename);
	 Function:   Takes in name of a file containing Entrez Gene records.
		     opens the file and stores file handle
	 Returns:    none.
	 Notes:      Attempts to open file larger than 2 GB even on Perl that
		       does not support 2 GB file (accomplished by calling
		       "cat" and piping output. On OS that does not have "cat"
		       error message will be displayed)

   next_seq
	 Parameters: $trimopt (optional) that specifies how the data structure
		       returned should be trimmed. option 2 is recommended and
		       default
	 Example:    my $value = $parser->next_seq();
	 Function:   Use the file handle generated by input_file, parses the next
		       the record and returns a data structure.
	 Returns:    A data structure containing all data items from the Entrez
		       Gene record.
	 Notes:      Must pass in a filename through new() or input_file() first!
		     For details on how to use the $trimopt data trimming option
		       please see comment for the trimdata method. An option
		       of 2 is recommended and default
		     The acceptable values for $trimopt include:
		       1 - trim as much as possibile
		       2 (or 0, undef) - trim to an easy-to-use structure
		       3 - no trimming (in version 1.06, prior to version
			   1.06, 0 or undef means no trimming)

   trimdata
	 Parameters: $hashref or $arrayref
		     $trimflag (optional, see Notes)
	 Example:    trimdata($datahash); # using the default flag
	 Function:   recursively process all attributes of a hash/array
		     hybrid and get rid of any arrayref that points to
		     one-element arrays (trims data structure) depending on
		     the optional flag.
	 Returns:    none - trimming happenes in-place
	 Notes:      This function is useful to compact a data structure produced by
		       Bio::ASN1::EntrezGene::parse.
		     The acceptable values for $trimopt include:
		       1 - trim as much as possibile
		       2 (or 0, undef) - trim to an easy-to-use structure
		       3 - no trimming (in version 1.06, prior to version
			   1.06, 0 or undef means no trimming)

   fh
	 Parameters: $filehandle (optional)
	 Example:    trimdata($datahash); # using the default flag
	 Function:   getter/setter for file handle
	 Returns:    file handle for current file being parsed.
	 Notes:      Use with care!
		     Line number report would not be corresponding to file's line
		       number if seek operation is performed on the file handle!

   rawdata
	 Parameters: none
	 Example:    my $data = $parser->rawdata();
	 Function:   Get the entrez gene data file that was just parsed
	 Returns:    a string containing the ASN1-formatted Entrez Gene record
	 Notes:      Must first parse a record then call this function!
		     Could be useful in interpreting line number value in error
		       report (if user did a seek on file handle right before parsing
		       call)

perl v5.14.2							    2012-01-12						Bio::ASN1::EntrezGene(3pm)