Bio::M...mHeader(3pm)

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

💖 NAME 💖

okay so bestie, welcome to the Bio::M...mHeader(3pm) page 💅 — this one's all about Bio::Matrix::PSM::PsmHeader, which is the PSM mast parser implementation. yes ma'am, a whole parser. iconic.

✨ SYNOPSIS ✨

like, the actual usage lives elsewhere, so go look there:

# See Bio::Matrix::PSM::IO for detailed documentation on how to use
# PSM parsers

🦋 DESCRIPTION 🦋

So this is a parser for mast. And the way it's built, it's not like meme or transfac for example — this driver is dedicated more to PSM sequence matches. different flavor, same slay. 🍓

🌸 FEEDBACK 🌸

📬 Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules, fr fr — the glow-up of these modules literally runs on y'all's input. 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. This is the way — 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 the bugs and their resolution. Bug reports can be submitted via the web:

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

👑 AUTHOR - Stefan Kirov 👑

Email skirov@utk.edu — the main character who wrote this 💜

🎀 APPENDIX 🎀

🧬 new

  • Title: new
  • Usage:
my $header= Bio::Matrix::PSM::PsmHeader->new(-seq=>\%seq,
                                             -mid=>\%mid,
                                             -width=>\%width,
                                             -instances=>\%instances,
                                             -header=>\@header,
                                             -type=>'mast');
  • Function: Creates a new Bio::Matrix::PSM::PsmHeader object ✨
  • Throws: (nothin', bestie)
  • Example: (none)
  • Returns: Bio::Matrix::PSM::PsmHeader object
  • Args: hash

🧬 seq

  • Title: seq
  • Usage: my %seq= $header->seq();
  • Function: Returns the sequence data as a hash, indexed by a sequence ID (motif id or accession number). In case the input data is a motif it would return the consenus seq for each of them (mast).
  • Throws: (nothin')
  • Example: (none)
  • Returns: hash
  • Args: (none)

🧬 hid

  • Title: hid
  • Usage: my @hid= $header->hid();
  • Function: Returns array with the motif ids
  • Throws: (nothin')
  • Example: (none)
  • Returns: array
  • Args: (none)

🧬 length

  • Title: length
  • Usage: my %length= $header->length();
  • Function: Returns the length of the input sequence or motifs as a hash, indexed by a sequence ID (motif id or accession number)
  • Throws: (nothin')
  • Example: (none)
  • Returns: hash
  • Args: (none)

🧬 instances

  • Title: instances
  • Usage: my %instances= $header->instances();
  • Function: Returns the info about the input data, contained in the header
  • Throws: (nothin')
  • Example: (none)
  • Returns: hash
  • Args: (none)

🧬 weight

  • Title: weight
  • Usage: my %weights= $header->weight();
  • Function: Returns the weights of the input sequence as a hash, indexed by a sequence ID
  • Throws: (nothin')
  • Example: (none)
  • Returns: hash
  • Args: (none)

🧬 unstuctured

nope, that spelling is not a typo of mine — the method is literally named unstuctured and we respect it 🫡
  • Title: unstuctured
  • Usage: my @unstructured= $header->unstuctured();
  • Function: Returns the unstructured data in the header as an array, one line per array element, all control symbols are removed with \W
  • Throws: (nothin')
  • Example: (none)
  • Returns: array
  • Args: (none)

🧬 version

  • Title: version
  • Usage: my $version= $header->version;
  • Function: Returns the version of the file being parsed if such exists
  • Throws: (nothin')
  • Example: (none)
  • Returns: string
  • Args: (none)

🧬 release

  • Title: release
  • Usage: my $release= $header->release;
  • Function: Returns the release of the file being parsed if such exists
  • Throws: (nothin')
  • Example: (none)
  • Returns: string
  • Args: (none)

🧬 _check

  • Title: _check
  • Usage: if ($self->_check('weights') { #do something} else {return 0;}
  • Function: Checks if the method called is aplicable to the file format
  • Throws: (nothin')
  • Example: (none)
  • Returns: boolean
  • Args: string

and that's the whole page, bestie — no notes, ate and left no crumbs 💅✨

this one's served up fresh from perl v5.32.1, dated 2021-08-15, straight outta the User Contributed Perl Documentation — mwah 🎀💖

📦 where this page comes from