Bio::T...udowise(3pm)

📦
version 1.7.3 · 3 versions
, in debian bookworm, ubuntu noble

💖 Bio::T...udowise(3pm) 💖

okay bestie, this one's from the User Contributed Perl Documentation collection, and it's a whole mood. it's a Perl module, it's giving bioinformatics, it's giving pseudogene vibes. let's get into it 🧬✨

🌸 NAME

Bio::Tools::Run::Pseudowise — it's literally an object for predicting pseudogenes in a given sequence, when you hand it a protein sequence and a cdna sequence. periodt. 💅

🎀 SYNOPSIS

the vibe check, in code:

# Build a pseudowise alignment factory
my $factory = Bio::Tools::Run::Pseudowise->new();

# Pass the factory 3 Bio:SeqI objects (in the order of query
# peptide and cdna and target_genomic)
# @genes is an array of GenericSeqFeature objects
my @genes = $factory->run($seq1, $seq2, $seq3);

so you build the factory, you feed it 3 Bio:SeqI objects — and the order matters, bestie: query peptide, then cdna, then target_genomic — and @genes comes back as an array of GenericSeqFeature objects. iconic. 🌈

🦋 DESCRIPTION

Pseudowise is a pseudogene predition program developed by Ewan Birney — here's the link if you wanna go be nosy: http://www.sanger.ac.uk/software/wise2.

💜 FEEDBACK

💌 Mailing Lists

user feedback is an integral part of the evolution of this and other Bioperl modules, fr fr. send your comments and suggestions preferably to one of the Bioperl mailing lists — your participation is much appreciated, no cap 🫶

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. lowkey the whole point is that 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 — that's the difference between "help" and "help me help you" 😭

🐛 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:

http://redmine.open-bio.org/projects/bioperl/

👑 AUTHOR - Kiran

Email kiran@fugu-sg.org

✨ APPENDIX

the rest of the documentation details each of the object methods. internal methods are usually preceded with a _ (iykyk, don't touch those unless you know what you're doing 🙈)

🌟 program_name

  • Title: program_name
  • Usage: $factory>program_name()
  • Function: holds the program name
  • Returns: string
  • Args: None

🌟 program_dir

  • Title: program_dir
  • Usage: $factory->program_dir(@params)
  • Function: returns the program directory, obtained from ENV variable.
  • Returns: string
  • Args:

🌟 version

  • Title: version
  • Usage: exit if $prog->version() < 1.8
  • Function: Determine the version number of the program
  • Example:
  • Returns: float or undef
  • Args: none

🌟 predict_genes

  • Title: predict_genes
  • Usage: DEPRECATED. Use $factory->run instead
  • Function: Predict pseudogenes
  • Returns: An array of Bio::Seqfeature::Generic objects
  • Args: Name of a file containing a set of 3 fasta sequences in the order of peptide, cdna and genomic sequences or else 3 Bio::Seq objects.
okay so heads up: this one is DEPRECATED, bestie — go use $factory->run instead 💀

Throws an exception if argument is not either a string (eg a filename) or 3 Bio::Seq objects. If arguments are strings, throws exception if file corresponding to string name can not be found.

🌟 run

  • Title: run
  • Usage: my @feats = $factory->run($seq1, $seq2, $seq3);
  • Function: Executes pseudogene binary
  • Returns: An array of Bio::Seqfeature::Generic objects
  • Args: Name of a file containing a set of 3 fasta sequences in the order of peptide, cdna and genomic sequences or else 3 Bio::Seq objects.

Throws an exception if argument is not either a string (eg a filename) or 3 Bio::Seq objects. If arguments are strings, throws exception if file corresponding to string name can not be found.

🌟 _run

  • Title: _run
  • Usage: Internal function, not to be called directly
  • Function: makes actual system call to a pseudowise program
  • Example:
  • Returns: nothing; pseudowise output is written to a temporary file $TMPOUTFILE
  • Args: Name of a files containing 3 sequences in the order of peptide, cdna and genomic

🌟 _parse_results

  • Title: __parse_results
  • Usage: Internal function, not to be called directly
  • Function: Parses pseudowise output
  • Example:
  • Returns: an reference to an array of Seqfeatures
  • Args: the name of the output file

🌟 _setinput()

  • Title: _setinput
  • Usage: Internal function, not to be called directly
  • Function: Create input files for pseudowise program
  • Example:
  • Returns: name of file containing dba data input
  • Args: Seq objects in the order of query protein and cdna and target genomic sequence

🌟 _query_pep_seq()

  • Title: _query_pep_seq
  • Usage: Internal function, not to be called directly
  • Function: get/set for the query sequence
  • Example:
  • Returns:
  • Args:

🌟 _query_cdna_seq()

  • Title: _query_cdna_seq
  • Usage: Internal function, not to be called directly
  • Function: get/set for the query sequence
  • Example:
  • Returns:
  • Args:

🌟 _subject_dna_seq()

  • Title: _subject_dna_seq
  • Usage: Internal function, not to be called directly
  • Function: get/set for the subject sequence
  • Example:
  • Returns:
  • Args:

and that's the whole page, bestie!! 🫶 this one came from perl v5.36.0, dated 2023-01-22, and yes it's Bio::T...udowise(3pm) — go predict some pseudogenes, you absolute main character 💅✨

📦 where this page comes from