Christopher Fields > Bio-ASN1-EntrezGene > Bio::ASN1::EntrezGene

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Module Version: 1.70   Source  

NAME ^

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

VERSION ^

version 1.70

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

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.

ATTRIBUTES ^

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:

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)

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!

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!

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)

INTERNAL METHODS ^

_parse

NCBI's Apr 05, 2005 format change forced much usage of lookahead, which would for sure slows parser down. But can't code efficiently without it.

PREREQUISITE ^

None.

INSTALLATION ^

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

  perl Makefile.PL
  make
  make test
  make install

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.

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 runs 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/wiki/Mailing_lists  - About the mailing lists

Support

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://redmine.open-bio.org/projects/bioperl/

AUTHOR ^

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.

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