Bio::S...genbank(3pm)

okay so bestie, welcome to Bio::S...genbank(3pm), straight out of the User Contributed Perl Documentation collection ✨ it's the GenBank input/output stream for BioPerl and honestly? iconic. let's get into it 💅

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🌸 NAME 🌸

Bio::SeqIO::genbank — GenBank sequence input/output stream 🧬

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🎀 SYNOPSIS 🎀

ngl, the docs are literally begging you: do NOT use this object directly, go through the SeqIO handler instead, iykyk:

$stream = Bio::SeqIO->new(-file   => $filename,
                          -format => 'GenBank');

while ( my $seq = $stream->next_seq ) {
    # do something with $seq
}

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🦋 DESCRIPTION 🦋

This object can transform Bio::Seq objects to and from GenBank flat file databases. slay 💖

Real talk though: there's some flexibility in here about how to write GenBank output that is not fully documented. so like… vibes-based, lowkey.

✨ Optional functions ✨

• _show_dna() — (output only) shows the dna or not 🧬
• _post_sort() — (output only) provides a sorting func which is applied to the FTHelpers before printing
• _id_generation_func() — this is the function which is called as

print "ID   ", $func($seq), "\n";

to generate the ID line. If it's not there, it generates a sensible ID line using a number of tools.

If you want to output annotations in Genbank format they need to be stored in a Bio::Annotation::Collection object which is accessible through the Bio::SeqI interface method annotation().

The following are the names of the keys which are pulled from a Bio::Annotation::Collection object:

reference       - Should contain Bio::Annotation::Reference objects
comment         - Should contain Bio::Annotation::Comment objects
dblink          - Should contain a Bio::Annotation::DBLink object
segment         - Should contain a Bio::Annotation::SimpleValue object
origin          - Should contain a Bio::Annotation::SimpleValue object
wgs             - Should contain a Bio::Annotation::SimpleValue object

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👑 Where does the data go? 👑

Data parsed in Bio::SeqIO::genbank is stored in a variety of data fields in the sequence object that is returned. Here is a partial list of fields. 🍓

Items listed as RichSeq or Seq or PrimarySeq and then NAME() tell you the top level object which defines a function called NAME() which stores this information.

Items listed as Annotation 'NAME' tell you the data is stored the associated Bio::AnnotationCollectionI object which is associated with Bio::Seq objects. If it is explicitly requested that no annotations should be stored when parsing a record of course they will not be available when you try and get them. If you are having this problem look at the type of SeqBuilder that is being used to construct your sequence object.

• Comments → Annotation 'comment'
• References → Annotation 'reference'
• Segment → Annotation 'segment'
• Origin → Annotation 'origin'
• Dbsource → Annotation 'dblink'
• Accessions → PrimarySeq accession_number()
• Secondary accessions → RichSeq get_secondary_accessions()
• GI number → PrimarySeq primary_id()
• LOCUS → PrimarySeq display_id()
• Keywords → RichSeq get_keywords()
• Dates → RichSeq get_dates()
• Molecule → RichSeq molecule()
• Seq Version → RichSeq seq_version()
• PID → RichSeq pid()
• Division → RichSeq division()
• Features → Seq get_SeqFeatures()
• Alphabet → PrimarySeq alphabet()
• Definition → PrimarySeq description() or desc()
• Version → PrimarySeq version()
• Sequence → PrimarySeq seq()

There is more information in the Feature-Annotation HOWTO about each field and how it is mapped to the Sequence object — http://bioperl.org/howtos/Features_and_Annotations_HOWTO.html 💜

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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 one of the Bioperl mailing lists. 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 responsive 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 the bugs and their resolution. Bug reports can be submitted via the web:

https://github.com/bioperl/bioperl-live/issues

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⭐ AUTHOR - Bioperl Project ⭐

bioperl-l at bioperl.org

Original author Elia Stupka, elia -at- tigem.it

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💖 CONTRIBUTORS 💖

• Ewan Birney birney at ebi.ac.uk
• Jason Stajich jason at bioperl.org
• Chris Mungall cjm at fruitfly.bdgp.berkeley.edu
• Lincoln Stein lstein at cshl.org
• Heikki Lehvaslaiho, heikki at ebi.ac.uk
• Hilmar Lapp, hlapp at gmx.net
• Donald G. Jackson, donald.jackson at bms.com
• James Wasmuth, james.wasmuth at ed.ac.uk
• Brian Osborne, bosborne at alum.mit.edu
• Chris Fields, cjfields at bioperl dot org

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📖 APPENDIX 📖

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ 🔍

🌟 next_seq

• Title: next_seq
• Usage: $seq = $stream->next_seq()
• Function: returns the next sequence in the stream
• Returns: Bio::Seq object
• Args:

🌟 write_seq

• Title: write_seq
• Usage: $stream->write_seq($seq)
• Function: writes the $seq object (must be seq) to the stream
• Returns: 1 for success and 0 for error
• Args: array of 1 to n Bio::SeqI objects

🌟 _print_GenBank_FTHelper

• Title: _print_GenBank_FTHelper
• Usage:
• Function:
• Example:
• Returns:
• Args:

🌟 _read_GenBank_References

• Title: _read_GenBank_References
• Usage:
• Function: Reads references from GenBank format. Internal function really
• Returns:
• Args:

🌟 _add_ref_to_array

• Title: _add_ref_to_array
• Usage:
• Function: Adds a Reference object to an array of Reference objects, takes care of possible cleanups to be done (currently, only author and title will be chopped of trailing semicolons).
• Args: A reference to an array of Reference objects and the Reference object to be added
• Returns: nothing

🌟 _read_GenBank_Species

• Title: _read_GenBank_Species
• Usage:
• Function: Reads the GenBank Organism species and classification lines. Able to deal with unconvential Organism naming formats, and varietas in plants
• Example:

ORGANISM  unknown marine gamma proteobacterium NOR5
$genus = undef
$species = unknown marine gamma proteobacterium NOR5

ORGANISM  Drosophila sp. 'white tip scutellum'
$genus = Drosophila
$species = sp. 'white tip scutellum'
(yes, this really is a species and that is its name)
$subspecies = undef

ORGANISM  Ajellomyces capsulatus var. farciminosus
$genus = Ajellomyces
$species = capsulatus
$subspecies = var. farciminosus

ORGANISM  Hepatitis delta virus
$genus = undef (though this virus has a genus in its lineage, we
                cannot know that without a database lookup)
$species = Hepatitis delta virus

• Returns: A Bio::Species object
• Args: A reference to the current line buffer

🌟 _read_FTHelper_GenBank

• Title: _read_FTHelper_GenBank
• Usage: _read_FTHelper_GenBank($buffer)
• Function: reads the next FT key line
• Example:
• Returns: Bio::SeqIO::FTHelper object
• Args: filehandle and reference to a scalar

🌟 _write_line_GenBank

• Title: _write_line_GenBank
• Usage:
• Function: internal function
• Example:
• Returns:
• Args:

🌟 _write_line_GenBank_regex

• Title: _write_line_GenBank_regex
• Usage:
• Function: internal function for writing lines of specified length, with different first and the next line left hand headers and split at specific points in the text
• Example:
• Returns: nothing
• Args: file handle, first header, second header, text-line, regex for line breaks, total line length

🌟 _post_sort

• Title: _post_sort
• Usage: $obj->_post_sort($newval)
• Function:
• Returns: value of _post_sort
• Args: newvalue (optional)

🌟 _show_dna

• Title: _show_dna
• Usage: $obj->_show_dna($newval)
• Function:
• Returns: value of _show_dna
• Args: newvalue (optional)

🌟 _id_generation_func

• Title: _id_generation_func
• Usage: $obj->_id_generation_func($newval)
• Function:
• Returns: value of _id_generation_func
• Args: newvalue (optional)

🌟 _ac_generation_func

• Title: _ac_generation_func
• Usage: $obj->_ac_generation_func($newval)
• Function:
• Returns: value of _ac_generation_func
• Args: newvalue (optional)

🌟 _sv_generation_func

• Title: _sv_generation_func
• Usage: $obj->_sv_generation_func($newval)
• Function:
• Returns: value of _sv_generation_func
• Args: newvalue (optional)

🌟 _kw_generation_func

• Title: _kw_generation_func
• Usage: $obj->_kw_generation_func($newval)
• Function:
• Returns: value of _kw_generation_func
• Args: newvalue (optional)

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and that's the whole page bestie, no cap, we ate and left zero crumbs 💅✨ this masterpiece dropped as perl v5.32.1, dated 2021-08-15, under the User Contributed Perl Documentation banner for Bio::S...genbank(3pm) 🎀 go forth and parse some sequences, main character 🦋💖