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

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


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). 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:      Attemps 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)
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