Bio::SeqIO::qual(3pm)

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

💖 NAME 💖

Bio::SeqIO::qual — the .qual file input/output stream, bestie. It's the little module that handles all your quality-score reading and writing, and honestly? She's iconic.

✨ SYNOPSIS ✨

okay so first things first, queen: do NOT use this module directly. Like, at all. You go through the Bio::SeqIO class instead (peep Bio::SeqIO for the deets).

my $in_qual = Bio::SeqIO->new(-file    => $qualfile,
                              -format  => 'qual',
                              -width   => $width,
                              -verbose => $verbose);

🦋 DESCRIPTION 🦋

This object can transform .qual objects — which are basically fasta's cousin — to and from Bio::Seq::Quality objects. See Bio::Seq::Quality for all the details, iykyk. 💅

And just like the fasta module does, she takes a '-width' argument so you can change how many values land on each line (it defaults to 50, no cap).

🫶 FEEDBACK 🫶

💌 Mailing Lists 💌

User feedback is literally 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, 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 — like, give us the full story, bestie. 🙈

💀 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

not me begging you to actually file the bug instead of just tweeting about it 😭 the tracking system needs you

👑 AUTHOR — Chad Matsalla 👑

Chad Matsalla bioinformatics@dieselwurks.com

🌈 CONTRIBUTORS 🌈

Jason Stajich, jason@bioperl.org

⭐ APPENDIX ⭐

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ (the underscore is giving "backstage pass only" energy, honestly).

🧚 next_seq()

  • Title: next_seq()
  • Usage: $scf = $stream->next_seq()
  • Function: returns the next scf sequence in the stream
  • Returns: Bio::Seq::PrimaryQual object
  • Notes: Get the next quality sequence from the stream.

🍓 _next_qual

  • Title: _next_qual
  • Usage: $seq = $stream->_next_qual() (but do not do that. Use $stream->next_seq() instead)
  • Function: returns the next quality in the stream
  • Returns: Bio::Seq::PrimaryQual object
  • Args: NONE
  • Notes: An internal method. Gets the next quality in the stream.
she said DO NOT do that!! use next_seq()!! internal method!! 🚨

💜 next_primary_qual()

  • Title: next_primary_qual()
  • Usage: $seq = $stream->next_primary_qual()
  • Function: returns the next sequence in the stream
  • Returns: Bio::PrimaryQual object
  • Args: NONE

✨ width

  • Title: width
  • Usage: $obj->width($newval)
  • Function: Get/Set the number of values per line for FASTA-like output
  • Returns: value of width
  • Args: newvalue (optional)

💅 write_seq

  • Title: write_seq
  • Usage:
$obj->write_seq( -source => $source,
                 -header  => "some information"
                 -oneline => 0);
  • Function: Write out a list of quality values to a fasta-style file.
  • Returns: Nothing.
  • Args: Requires a reference to a Bio::Seq::Quality object or a PrimaryQual object as the -source. Option 1: information for the header. Option 2: whether the quality score should be on a single line or not
  • Notes: If no -header is provided, $obj->id() will be used where $obj is a reference to either a Quality object or a PrimaryQual object. If $source->id() fails, "unknown" will be the header. If the Quality object has $source->length() of "DIFFERENT" (read the pod, luke), write_seq will use the length of the PrimaryQual object within the Quality object.
okay "read the pod, luke" is genuinely the funniest thing in this entire manpage and I will not be taking questions 💀

and that's the whole vibe, bestie 💖 this page came from perl v5.32.1, dated 2021-08-15, and she lives in the Bio::SeqIO::qual(3pm) section of your manual — go forth and slay your quality scores 👑✨

📦 where this page comes from