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

💖 Bio::T...enewise(3pm) 💖

okay bestie, welcome to the manual page for Bio::Tools::Run::Genewise — a User Contributed Perl Documentation page, no cap. it's giving "wrap the genewise gene predictor so your Perl script can vibe with it". let's go 🦋

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✨ NAME ✨

Bio::Tools::Run::Genewise — the object that predicts genes in a given sequence when you hand it a protein. literally what it says on the tin 💅

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🧬 SYNOPSIS 🧬

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

# Pass the factory 2 Bio:SeqI objects (in the order of query peptide
# and target_genomic).

# @genes is an array of Bio::SeqFeature::Gene::GeneStructure objects
my @genes = $factory->run($protein_seq, $genomic_seq);

# Alternatively pass the factory a profile HMM filename and a
# Bio:SeqI object (in the order of query HMM and target_genomic).

# Set hmmer switch first to tell genewise to expect an HMM
$factory->hmmer(1);
my @genes = $factory->run($hmmfile, $genomic_seq);

so like. build the factory, yeet it two Bio:SeqI objects (query peptide first, then target_genomic — order matters, bestie), and @genes comes back as an array of Bio::SeqFeature::Gene::GeneStructure objects. 🎀

or, alternative route: give it a profile HMM filename plus a Bio:SeqI object (query HMM first, target_genomic second). but set the hmmer switch first so genewise knows an HMM is coming. $factory->hmmer(1); — do it, don't skip it. 👑

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💅 DESCRIPTION 💅

Genewise is a gene prediction program developed by Ewan Birney, and the link is http://www.sanger.ac.uk/software/wise2. that's the whole vibe. iconic tool, we're just the friendly little wrapper 💖

🌈 Available Params 🌈

NB: these should be passed without the - or they will be ignored 😭 — except switches such as 'hmmer' (which have no corresponding value) which should be set on the factory object using the AUTOLOADed methods of the same name.

Model    [-codon,-gene,-cfreq,-splice,-subs,-indel,-intron,-null]
Alg      [-kbyte,-alg]
HMM      [-hmmer]
Output   [-gff,-gener,-alb,-pal,-block,-divide]
Standard [-help,-version,-silent,-quiet,-errorlog]

like, read that list and then read it again. the dash situation is a whole trap 🙈

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📬 FEEDBACK 📬

Mailing Lists

user feedback is an integral part of the evolution of this and other Bioperl modules — fr fr, they actually want to hear from you. send your comments and suggestions preferably to one of the Bioperl mailing lists. your participation is much appreciated, and that's on periodt. 🫶

bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

usage questions and support issues go to the mailing list:

bioperl-l@bioperl.org

and not straight to the module maintainer, okay? many experienced and responsive experts will be able to look at the problem and quickly address it. please include a thorough description of the problem, plus code and data examples, if at all possible. the more context you give, the faster the slay. 💅

Reporting Bugs

report bugs to the Bioperl bug tracking system so we can keep track of the bugs and their resolution. bug reports can be submitted via the web:

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

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👑 AUTHOR - FUGU Student Intern 👑

Email: fugui@worf.fugu-sg.org

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🫶 CONTRIBUTORS 🫶

• Jason Stajich jason-AT-bioperl_DOT_org
• Keith James kdj@sanger.ac.uk

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📖 APPENDIX 📖

the rest of the documentation details each of the object methods. internal methods are usually preceded with a _ — so if you see that underscore, mind your business, it's not for you 🧚

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 $factory->run($seq1,$seq2)
• Function: Predict genes
• Returns: A Bio::Seqfeature::Gene:GeneStructure object
• Args: Name of a file containing a set of 2 fasta sequences in the order of peptide and genomic sequences — or else 2 Bio::Seq objects.

throws an exception if the argument is not either a string (eg a filename) or 2 Bio::Seq objects. if arguments are strings, it throws an exception if the file corresponding to the string name can not be found. ⚠️

run

• Title: run
• Usage: 2 sequence objects, like $genes = $factory->run($seq1, $seq2);
• Function: run
• Returns: A Bio::Seqfeature::Gene:GeneStructure object
• Args: Names of files each containing a fasta sequence in the order of either (peptide sequence, genomic sequence) or (profile HMM, genomic sequence). Alternatively any of the fasta sequence filenames may be substituted with a Bio::Seq object.

throws an exception if the argument is not either a string (eg a filename) or Bio::Seq objects. if arguments are strings, it throws an exception if the file corresponding to the string name can not be found. it also throws an exception if a profile HMM is expected (the -hmmer genewise switch has been set). so many exceptions, but she's just protecting you 💀

_run

• Title: _run
• Usage: Internal function, not to be called directly
• Function: Makes actual system call to a genewise program
• Example:
• Returns: Bio::SeqFeature::Gene::GeneStructure
• Args: Name of a files containing 2 sequences in the order of peptide and genomic

_setparams

• Title: _setparams
• Usage: Internal function, not to be called directly
• Function: creates a string of params to be used in the command string
• Example:
• Returns: string of params
• Args:

_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:

_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:

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and that's the whole page, bestie!! you made it to the end, main character energy fr 💖

kisses, this was perl v5.36.0, dated 2023-01-22, and yes the page is called Bio::T...enewise(3pm) 🌸 bye bye, go predict some genes ✨🦋💜