Bio::ASN1::Sequence.3pm

Langue: en

Version: 2005-05-04 (mandriva - 01/05/08)

Section: 3 (Bibliothèques de fonctions)

NAME

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

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
 
 

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
 
 

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. :)

SEE ALSO

The parse_sequence_example.pl script included in this package (please see the Bio-ASN1-EntrezGene-x.xx/examples directory) shows the usage.

Please check out perldoc for Bio::ASN1::EntrezGene for more info.

AUTHOR

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

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 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!
 
 

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:      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 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 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::Sequence::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)
               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)