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 perldocDESCRIPTION
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 installSEE 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.
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 listsSupport
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/issuesAUTHOR
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.