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

💖 NAME 💖

Bio::Tools::Run::Profile — it's the wrapper module for the pfscan program, bestie. That's the whole vibe. 🦋

Also hi, this page lives in the User Contributed Perl Documentation section, so you know it's coming to you straight from the community. 💅

---

✨ SYNOPSIS ✨

Okay so first you gotta build a Profile factory. No cap:

Build a Profile factory
# $paramfile is the full path to the seg binary file

my @params = ('DB',$dbfile,'PROGRAM',$paramfile);
my $factory = Bio::Tools::Run::Profile->new($param);

Then you hand that factory a Bio::PrimarySeqI object, and @feats comes back as an array of Bio::SeqFeature::Generic objects:

# Pass the factory a Bio::PrimarySeqI object
# @feats is an array of Bio::SeqFeature::Generic objects
my @feats = $factory->run($seq);

Slay. That's the whole flow. 🌸

---

🎀 DESCRIPTION 🎀

It's a wrapper module for the pfscan program. That's it, that's the description. Short and iconic. 👑

---

💌 FEEDBACK 💌

Mailing Lists 📬

User feedback is an integral part of the evolution of this and other Bioperl modules — like, literally, it's giving community. 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. The way that many experienced and reponsive experts will be able look at the problem and quickly address it?? Obsessed. 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:

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

---

👑 AUTHOR - Balamurugan Kumarasamy 👑

Email: fugui@worf.fugu-sg.org

---

🌈 APPENDIX 🌈

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ — iykyk, that underscore is the "do not touch unless you know what you're doing" marker. 💀

---

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 :

new 🌟

• Title : new
• Usage : my $factory= Bio::Tools::Run::Profile->new($param);
• Function: creates a new Profile factory
• Returns: Bio::Tools::Run::Profile
• Args :

predict_protein_features 🧬

• Title : predict_protein_features
• Usage : DEPRECATED. Use $factory->run($seq) instead.
• Function: Runs Profile and creates an array of featrues
• Returns : An array of L<Bio::SeqFeature::FeaturePair> objects
• Args : A Bio::PrimarySeqI

Bestie, this one is DEPRECATED — the manpage literally says so. Use $factory->run($seq) instead, fr fr. 🙈

run 🏃♀️

• Title : run
• Usage : my @feats = $factory->run($seq)
• Function: Runs Profile
• Returns : An array of L<Bio::SeqFeature::FeaturePair> objects
• Args : A Bio::PrimarySeqI

_input 📥

• Title : _input
• Usage : $factory->_input($seqFile)
• Function: get/set for input file
• Returns :
• Args :

_run ⚙️

• Title : _run
• Usage : $factory->_run()
• Function: Makes a system call and runs pfscan
• Returns : An array of L<Bio::SeqFeature::FeaturePair> objects
• Args :

_writeSeqFile 📝

• Title : _writeSeqFile
• Usage : $factory->_writeSeqFile($seq)
• Function: Creates a file from the given seq object
• Returns : A string(filename)
• Args : Bio::PrimarySeqI

---

And that's the whole page, bestie!! This one's running on perl v5.36.0 and it was last touched on 2023-01-22, so go forth and wrap that pfscan with main character energy. Mwah. 💜✨🎀