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

💖 Bio::S...ableSeq(3pm) 💖

okay bestie, welcome to the manual page for Bio::Seq::LargeLocatableSeq — from the User Contributed Perl Documentation collection, no less. pull up a chair, grab a strawberry 🍓, we're doing this.

---

✨ NAME ✨

Bio::Seq::LargeLocatableSeq — a LocatableSeq object that stores its sequence as files in the tempdir. yes literally. it's giving "my brain is in a folder" energy 🧠📁

---

🌸 SYNOPSIS 🌸

normal primary seq usage, but make it file-based:

  # normal primary seq usage
    use Bio::Seq::LargeLocatableSeq;
    my $seq = Bio::Seq::LargeLocatableSeq->new(-seq => "CAGT-GGT",
                                              -id  => "seq1",
                                              -start => 1,
                                              -end   => 7);

that's it, that's the whole vibe check. 💅

---

🦋 DESCRIPTION 🦋

Bio::Seq::LargeLocatableSeq — an object with start/end points on it that can be projected into a MSA or have coordinates relative to another seq. main character coordinates energy, we love to see it. 👑

this object, unlike Bio::LocatableSeq, stores a sequence as a series of files in a temporary directory. the whole point? letting you store very large sequences (eg, > 100MBases) on a file system without running out of memory (eg, on a 64 MB real memory machine!). it's iconic, honestly. 🔥

of course, to actually make use of this functionality, the programs which use this object must not call $primary_seq->seq — otherwise the entire sequence will come out into memory and probably crash your machine. 😭💀 no cap. however, calls like $primary_seq->subseq(10,100) will cause only 90 characters to be brought into real memory. slay, restrained queen. ✨

---

🫶 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. fr fr. 🥹

  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. give them the tea, bestie, all of it. ☕✨

🐛 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/bioperl-live/issues

go off, tell them everything. we're tracking every single one. 👀

---

👑 AUTHOR - Albert Vilella 👑

Email avilella-AT-gmail-DOT-com — icon behavior. 📧

---

📚 APPENDIX 📚

the rest of the documentation details each of the object methods. internal methods are usually preceded with a _. (iykyk 🫢)

🌟 new

Title   : new
Usage   : my $obj = Bio::Seq::LargeLocatableSeq->new();
Function: Builds a new Bio::Seq::LargeLocatableSeq object
Returns : an instance of Bio::Seq::LargeLocatableSeq
Args    :

🌟 length

Title   : length
Usage   :
Function:
Example :
Returns :
Args    :

🌟 seq

Title   : seq
Usage   :
Function:
Example :
Returns :
Args    :

🌟 subseq

Title   : subseq
Usage   :
Function:
Example :
Returns :
Args    :

🌟 add_sequence_as_string

Title   : add_sequence_as_string
Usage   : $seq->add_sequence_as_string("CATGAT");
Function: Appends additional residues to an existing LargeLocatableSeq object.
          This allows one to build up a large sequence without storing
          entire object in memory.
Returns : Current length of sequence
Args    : string to append

building up a giant sequence bit by bit without hoarding it all in memory?? that's the dream, bestie. no notes. 💜

🌟 _filename

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

(internal method, hence the lil _ — you already knew that tho 🧚)

🌟 alphabet

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

---

okay that's the whole page, you absolutely ate that reading session. 💅✨

one last thing before you go: this beauty lives at Bio::S...ableSeq(3pm) and it was generated by perl v5.32.1 on 2021-08-15. stay slay, stay file-backed, and don't you dare call $primary_seq->seq on a huge sequence. mwah. 💖🎀🌈