Bio::A...equence(3pm)

💖 Bio::ASN1::Sequence 💖

okay bestie, gather round, because this is the Bio::ASN1::Sequence page — a regular expression-based Perl parser for ASN.1-formatted NCBI sequences. yes it's a mouthful, yes it slays, we move. ✨

This doc is for version 1.73, no cap. 🫶

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✨ SYNOPSIS ✨

here's the vibe, copy-paste coded, do not deviate:

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

like, that's the whole assignment. 💅

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🌸 DESCRIPTION 🌸

so. 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 hands you back a data structure containing all data items from that sequence record. the whole thing. every crumb. 🍓

if your input data does not conform to the NCBI Sequence annotation file format, the parser will report an error and a line number. it's literally giving accountability.

real talk: the sequence parser is basically a modified version of the high-performance Bio::ASN1::EntrezGene parser. but a standalone module got created for sequence anyway, because it is more efficient to keep Sequence-specific code out of EntrezGene.pm. separation, boundaries, self-care. 🧚

and honestly? it is possible to provide reading of all of NCBI's ASN.1-formatted files through simple variations of the Entrez Gene parser. (more investigation is needed to be sure, but at least the sequence parser works well — that part we know, fr fr.)

lowkey important disclosure though: 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 that were checked. not all available records or data definitions were checked. 🙈 the error-reporting function of this module has to be useful sometimes. :)

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⭐ 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: (nothing here, it's giving minimalism)

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)

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👑 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!

okay so that note matters: seeking on the file handle = line numbers chaos. be careful babe. 😭

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!

bestie do NOT call parse directly. it is DEPRECATED as an external function. use next_seq(). periodt. 💀

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!

"use with care" is doing a LOT of heavy lifting in that sentence, ngl. 🫠

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)

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🔥 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.

(internal. not yours. don't touch. iykyk.)

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🎀 PREREQUISITE 🎀

None.

like, none. iconic. 💅

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🌈 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

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🦋 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.

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💜 CITATION 💜

Liu, Mingyi, and Andrei Grigoriev. "Fast parsers for Entrez Gene." Bioinformatics 21, no. 14 (2005): 3189-3190.

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⭐ OPERATION SYSTEMS SUPPORTED ⭐

Any OS that Perl runs on.

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🫶 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

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👑 AUTHOR 👑

Dr. Mingyi Liu <mingyiliu@gmail.com>

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🌸 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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and that's the whole page bestie, we ate and left no crumbs 🍽️✨ this was Bio::ASN1::Sequence from the Bio::A...equence(3pm) manual, perl v5.38.2, dated 2024-03-04 — go parse some sequences, you've got this 💖🦋🎀