NAME

Bio::ASN1::Sequence - Regular expression-based Perl Parser for ASN.1-formatted NCBI Sequences.

VERSION

version 1.73

SYNOPSIS

  use Bio::ASN1::Sequence;

  my $parser = Bio::ASN1::Sequence->new('file' => "downloaded.asn1");
  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 sequence id:
  use Bio::ASN1::Sequence::Indexer;
  my $inx = Bio::ASN1::Sequence::Indexer->new(-filename => 'seq.idx');
  my $seq = $inx->fetch_hash('AF093062');

  # for creation of .idx index files please refer to
  # Bio::ASN1::Sequence::Indexer perldoc

DESCRIPTION

Bio::ASN1::Sequence is a regular expression-based Perl Parser for ASN.1-formatted NCBI sequences. It parses an ASN.1-formatted sequence record and returns a data structure that contains all data items from the sequence record.

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

The sequence parser is basically a modified version of the high-performance Bio::ASN1::EntrezGene parser. However, I created a standalone module for sequence since it is more efficient to keep Sequence-specific code out of EntrezGene.pm.

In fact 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 works well).

Since demand for parsing NCBI ASN.1-formatted sequences is much lower than EntrezGene, this module is more like a beta version that works on the examples I checked, but I did not check all available records or data definitions. The error-reporting function of this module has to be useful sometimes. :)

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 Sequence record(s)
  Example:    $parser->input_file($filename);
  Function:   Takes in name of a file containing Sequence 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::Sequence->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 Sequence 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 Sequence record, parses
                the record and returns a data structure.
  Returns:    A data structure containing all data items from the sequence
                record.
  Notes:      DEPRECATED as external function!!! Do not call this function
                directly!  Call next_seq() instead
              $string should not contain 'Seq-entry ::= set' 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 sequence
                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 possible
                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::Sequence::parse.
              The acceptable values for $trimopt include:
                1 - trim as much as possible
                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)
              This function is duplicate to EntrezGene.pm's and code should
                be compressed in the future (using util module & subclass).

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 sequence data file that was just parsed
  Returns:    a string containing the ASN1-formatted sequence 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::Sequence is part of the Bio::ASN1::EntrezGene package. Bio::ASN1::EntrezGene package can be installed & tested as follows:

  perl Makefile.PL
  make
  make test
  make install

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/Support.html    - 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://github.com/bioperl/bio-asn1-entrezgene/issues

AUTHOR

Dr. Mingyi Liu <mingyiliu@gmail.com>

COPYRIGHT

This software is available under the same terms as the perl 5 programming language system itself.