Bio::PrimarySeqI(3pm)

📦
version 1.7.8 · 3 versions
, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble

💖 Bio::PrimarySeqI(3pm) 💖

User Contributed Perl Documentation · Bio::PrimarySeqI(3pm)

okay bestie, welcome to the manual page for Bio::PrimarySeqI — yes the (3pm) is part of the whole name-vibe, it's a Perl module thing, iykyk 🎀

✨ NAME ✨

Bio::PrimarySeqI — the interface definition for a Bio::PrimarySeq, fr fr.

🌸 SYNOPSIS 🌸

# Bio::PrimarySeqI is the interface class for sequences.
# If you are a newcomer to bioperl, you might want to start with
# Bio::Seq documentation.

# Test if this is a seq object
$obj->isa("Bio::PrimarySeqI") ||
  $obj->throw("$obj does not implement the Bio::PrimarySeqI interface");

# Accessors
$string    = $obj->seq();
$substring = $obj->subseq(12,50);
$display   = $obj->display_id();       # for human display
$id        = $obj->primary_id();       # unique id for this object,
                                       # implementation defined
$unique_key= $obj->accession_number(); # unique biological id

# Object manipulation
eval {
   $rev = $obj->revcom();
};
if( $@ ) {
   $obj->throw( "Could not reverse complement. ".
                "Probably not DNA. Actual exception\n$@\n" );
}

$trunc = $obj->trunc(12,50);
# $rev and $trunc are Bio::PrimarySeqI compliant objects

that's the whole vibe check right there 💅

🦋 DESCRIPTION 🦋

So. This object defines an abstract interface to basic sequence info — and for most users of the package, the docs (and methods) in this class are not useful. It's a developers-only class, periodt. What it does is define what methods have to be implemented by other Perl objects to comply to the Bio::PrimarySeqI interface. If you're here like "I just want my sequences", go run perldoc Bio::Seq or man Bio::Seq for the real tea on the main class for sequences. ☕

PrimarySeq is an object just for the sequence and its name(s), nothing more, no cap. Seq is the larger object, complete with features. There's a pure perl implementation of this in Bio::PrimarySeq — so if you just want to use Bio::PrimarySeq objects, please read that module first, bestie. 💖 This module defines the interface, and it's of more interest to people who want to wrap their own Perl Objects/RDBs/FileSystems etc in a way that they "are" bioperl sequence objects, even though it is not using Perl to store the sequence etc.

This interface defines what bioperl considers necessary to "be" a sequence. It doesn't provide an implementation of this — an implementation is provided in Bio::PrimarySeq. If you want to provide a Bio::PrimarySeq-compliant object which in fact wraps another object/database/out-of-perl experience, then this is the correct thing to wrap. Generally by providing a wrapper class which would inherit from your object and this Bio::PrimarySeqI interface. The wrapper class then would have methods lists in the "Implementation Specific Functions" which would provide these methods for your object. 🫶

💌 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. (yes really, they want to hear from you 🌈)

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 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. (the more detail the better, they ate with that 💅)

🐛 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

👑 AUTHOR - Ewan Birney 👑

Email birney@ebi.ac.uk — main character energy, honestly.

📖 APPENDIX 📖

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ (the little secret ones 🙈).

🧚 Implementation-specific Functions 🧚

These functions are the ones that a specific implementation must define. no skipping, bestie, they're required.

🍓 seq

Title   : seq
Usage   : $string = $obj->seq()
Function: Returns the sequence as a string of letters. The
          case of the letters is left up to the implementer.
          Suggested cases are upper case for proteins and lower case for
          DNA sequence (IUPAC standard), but implementations are suggested to
          keep an open mind about case (some users... want mixed case!)
Returns : A scalar
Status  : Virtual

like, the case is your call, be free 🌈

🌸 subseq

Title   : subseq
Usage   : $substring = $obj->subseq(10,40);
Function: Returns the subseq from start to end, where the first base
          is 1 and the number is inclusive, i.e. 1-2 are the first two
          bases of the sequence.

          Start cannot be larger than end but can be equal.

Returns : A string
Args    :
Status  : Virtual
heads up: the first base is 1, and it's inclusive. start can't be bigger than end, but it can be equal. equal is fine, slay. ✨

💜 display_id

Title   : display_id
Usage   : $id_string = $obj->display_id();
Function: Returns the display id, also known as the common name of the Sequence
          object.

          The semantics of this is that it is the most likely string
          to be used as an identifier of the sequence, and likely to
          have "human" readability.  The id is equivalent to the ID
          field of the GenBank/EMBL databanks and the id field of the
          Swissprot/sptrembl database. In fasta format, the >(\S+) is
          presumed to be the id, though some people overload the id
          to embed other information. Bioperl does not use any
          embedded information in the ID field, and people are
          encouraged to use other mechanisms (accession field for
          example, or extending the sequence object) to solve this.

          Notice that $seq->id() maps to this function, mainly for
          legacy/convenience reasons.
Returns : A string
Args    : None
Status  : Virtual

tl;dr: it's the human-readable name. and yes, $seq->id() maps to this one, purely for legacy/convenience reasons 🎀

⭐ accession_number

Title   : accession_number
Usage   : $unique_biological_key = $obj->accession_number;
Function: Returns the unique biological id for a sequence, commonly
          called the accession_number. For sequences from established
          databases, the implementors should try to use the correct
          accession number. Notice that primary_id() provides the
          unique id for the implementation, allowing multiple objects
          to have the same accession number in a particular implementation.

          For sequences with no accession number, this method should return
          "unknown".
Returns : A string
Args    : None
Status  : Virtual
no accession number? return "unknown". that's the rule, periodt.

🌈 primary_id

Title   : primary_id
Usage   : $unique_implementation_key = $obj->primary_id;
Function: Returns the unique id for this object in this
          implementation. This allows implementations to manage their
          own object ids in a way the implementation can control
          clients can expect one id to map to one object.

          For sequences with no accession number, this method should
          return a stringified memory location.

Returns : A string
Args    : None
Status  : Virtual

🎀 can_call_new

Title   : can_call_new
Usage   : if( $obj->can_call_new ) {
            $newobj = $obj->new( %param );
        }
Function: Can_call_new returns 1 or 0 depending
          on whether an implementation allows new
          constructor to be called. If a new constructor
          is allowed, then it should take the followed hashed
          constructor list.

          $myobject->new( -seq => $sequence_as_string,
                          -display_id  => $id
                          -accession_number => $accession
                          -alphabet => 'dna',
                          );
Returns : 1 or 0
Args    :

returns 1 or 0 — it's giving boolean, bestie 💅

💀 alphabet

Title   : alphabet
Usage   : if( $obj->alphabet eq 'dna' ) { /Do Something/ }
Function: Returns the type of sequence being one of
          'dna', 'rna' or 'protein'. This is case sensitive.

          This is not called "type" because this would cause
          upgrade problems from the 0.5 and earlier Seq objects.

Returns : A string either 'dna','rna','protein'. NB - the object must
          make a call of the alphabet, if there is no alphabet specified it
          has to guess.
Args    : None
Status  : Virtual
case sensitive, ok?! and ngl the object must make a call of the alphabet, and if there's no alphabet specified it has to guess. the audacity 😭

🦋 moltype

Title   : moltype
Usage   : Deprecated. Use alphabet() instead.
deprecated, bestie!! use alphabet() instead. it's giving legacy, it's giving ick. 🚫

…and that's part 1, more coming so don't go anywhere 💖

✨ Implementation-optional Functions ✨

Okay bestie, so these ones are built on top of all the functions we just talked about. An implementing class does not have to provide them — this class will hand them to you anyway — but you're totally free to override them if you want to do your own thing. 💅

Here's the tea though 🫖: the revcom(), trunc(), and translate() methods create new sequence objects. They'll call new() on the class of the sequence object instance that got passed as an argument — unless can_call_new() returns FALSE. In that case, a Bio::PrimarySeq object gets created instead. So if you're an implementor who really wants to control how objects are born (think object persistence over a database, or objects living in a CORBA framework 👀), you are genuinely encouraged to override these methods.

🌀 revcom

  • Title: revcom
  • Usage: $rev = $seq->revcom()
  • Function: Produces a new Bio::PrimarySeqI implementing object that is the reversed complement of the sequence. For protein sequences this throws an exception of "Sequence is a protein. Cannot revcom".

The id is the same id as the original sequence, and the accession number is also identical. If someone wants to track that this sequence has been reversed, it needs to define its own extensions.

To do an inplace edit of an object you can go:

$seq = $seq->revcom();

This of course causes Perl to handle the garbage collection of the old object, but it is roughly speaking as efficient as an inplace edit.

  • Returns: A new (fresh) Bio::PrimarySeqI object
  • Args: None

✂️ trunc

  • Title: trunc
  • Usage: $subseq = $myseq->trunc(10,100);
  • Function: Provides a truncation of a sequence.
  • Returns: A fresh Bio::PrimarySeqI implementing object.
  • Args: Two integers denoting first and last base of the sub-sequence.

🧬 translate

  • Title: translate
  • Usage:
$protein_seq_obj = $dna_seq_obj->translate

Or if you expect a complete coding sequence (CDS) translation, with initiator at the beginning and terminator at the end:

$protein_seq_obj = $cds_seq_obj->translate(-complete => 1);

Or if you want translate() to find the first initiation codon and return the corresponding protein:

$protein_seq_obj = $cds_seq_obj->translate(-orf => 1);
  • Function: Provides the translation of the DNA sequence using full IUPAC ambiguities in DNA/RNA and amino acid codes.

The complete CDS translation is identical to EMBL/TREMBL database translation. Note that the trailing terminator character is removed before returning the translated protein object.

Note: if you set $dna_seq_obj->verbose(1) you will get a warning if the first codon is not a valid initiator.

  • Returns: A Bio::PrimarySeqI implementing object
  • Args:
    • -terminator — character for terminator, default '*'
    • -unknown — character for unknown, default 'X'
    • -frame — positive integer frame shift (in bases), default 0
    • -codontable_id — integer codon table id, default 1
    • -complete — boolean, if true, complete CDS is expected. default false
    • -complete_codons — boolean, if true, codons which are incomplete are translated if a suitable amino acid is found. For instance, if the incomplete codon is 'GG', the completed codon is 'GGN', which is glycine (G). Defaults to 'false'; setting '-complete' also makes this true.
    • -throw — boolean, throw exception if ORF not complete, default false
    • -orf — if 'longest', find longest ORF. other true value, find first ORF. default 0
    • -codontable — optional Bio::Tools::CodonTable object to use for translation
    • -start — optional three-character string to force as initiation codon (e.g. 'atg'). If unset, start codons are determined by the CodonTable. Case insensitive.
    • -offset — optional positive integer offset for fuzzy locations. if set, must be either 1, 2, or 3

📝 Notes

The -start argument only applies when -orf is set to 1. By default all initiation codons found in the given codon table are used, but when "start" is set to some codon this codon will be used exclusively as the initiation codon. Note that the default codon table (NCBI "Standard") has 3 initiation codons! 😳

By default translate() translates termination codons to the same character (default is *), both internal and trailing codons. Setting "-complete" to 1 tells translate() to remove the trailing character.

-offset is used for seqfeatures which contain the \codon_start tag and can be set to 1, 2, or 3. This is the offset by which the sequence translation starts relative to the first base of the feature.

For details on codon tables used by translate() see Bio::Tools::CodonTable.

Deprecated argument set (v. 1.5.1 and prior versions) where each argument is an element in an array:

  1. character for terminator (optional), defaults to '*'.
  2. character for unknown amino acid (optional), defaults to 'X'.
  3. frame (optional), valid values are 0, 1, 2, defaults to 0.
  4. codon table id (optional), defaults to 1.
  5. complete coding sequence expected, defaults to 0 (false).
  6. boolean, throw exception if not complete coding sequence (true), defaults to warning (false)
  7. codontable, a custom Bio::Tools::CodonTable object (optional).
⚠️ Heads up: that array-style argument list is deprecated, like it's giving "my old MySpace page". Use the named args, bestie. 🙈

🌸 transcribe()

  • Title: transcribe
  • Usage: $xseq = $seq->transcribe
  • Function: Convert base T to base U
  • Returns: PrimarySeqI object of alphabet 'rna' or undef if $seq->alphabet ne 'dna'
  • Args:

🌸 rev_transcribe()

  • Title: rev_transcribe
  • Usage: $rtseq = $seq->rev_transcribe
  • Function: Convert base U to base T
  • Returns: PrimarySeqI object of alphabet 'dna' or undef if $seq->alphabet ne 'rna'
  • Args:

🏷️ id

  • Title: id
  • Usage: $id = $seq->id()
  • Function: ID of the sequence. This should normally be (and actually is in the implementation provided here) just a synonym for display_id().
  • Returns: A string.
  • Args:

📏 length

  • Title: length
  • Usage: $len = $seq->length()
  • Function:
  • Returns: Integer representing the length of the sequence.
  • Args:

💬 desc

  • Title: desc
  • Usage:
$seq->desc($newval);
$description = $seq->desc();
  • Function: Get/set description text for a seq object
  • Returns: Value of desc
  • Args: newvalue (optional)

⭕ is_circular

  • Title: is_circular
  • Usage: if( $obj->is_circular) { # Do something }
  • Function: Returns true if the molecule is circular
  • Returns: Boolean value
  • Args: none

🔒 Private functions

These are some private functions for the PrimarySeqI interface. You do not need to implement these functions. No cap. 🫶

🔍 _find_orfs_nucleotide

  • Title: _find_orfs_nucleotide
  • Usage:
  • Function: Finds ORF starting at 1st initiation codon in nucleotide sequence. The ORF is not required to have a termination codon.
  • Example:
  • Returns: a list of string coordinates of ORF locations (0-based half-open), sorted descending by length (so that the longest is first) as: [ start, end, frame, length ], [ start, end, frame, length ], ...
  • Args: Nucleotide sequence, CodonTable object, (optional) alternative initiation codon (e.g. 'ATA'), (optional) boolean that, if true, stops after finding the first available ORF

🤫 _attempt_to_load_Seq

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

and that's the whole page, bestie!! 🎀✨ This was perl v5.32.1, dated 2021-08-15, from the Bio::PrimarySeqI(3pm) page in the User Contributed Perl Documentation. Go forth and translate some codons, you absolute icon 👑🦋💖

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