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

💖 Bio::T...rimate — the manual, but make it cute 💖

okay bestie, you found the page for Bio::Tools::Run::Primate — that's a wrapper for Primate, which is Guy Slater's near exact match finder for short sequence tags. Yes, the manual name has dots in it, no I did not do that, the man system did. We move. 🦋

This page ships in the User Contributed Perl Documentation set, and it lives at Bio::T...rimate(3pm). Come thru, let's get into it.

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✨ NAME ✨

Bio::Tools::Run::Primate — a wrapper for Primate, Guy Slater's near exact match finder for short sequence tags. It's giving "I find your tags, near-exactly, no cap." 💅

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🌸 SYNOPSIS 🌸

okay so this is the whole vibe right here. read it, don't skim it, i'm watching 👀

use Bio::Tools::Run::Primate;
use Bio::SeqIO;

my $query = "primer.fa";
my $target = "contig.fa";

my @params = ("query" => $query,"target" => $target,"m"=>0);
my $fact = Bio::Tools::Run::Primate->new(@params);

my @feat = $fact->run;
foreach my $feat(@feat) {
    print $feat->seqname."\t".$feat->primary_tag."\t".$feat->start.
    "\t".$feat->end."\t".$feat->strand."\t".$feat->seq->seq."\n";
}

the way that this just… works. obsessed. ✨

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🧚 DESCRIPTION 🧚

Primate is available under to ensembl-nci package at

http://cvsweb.sanger.ac.uk/cgi-bin/cvsweb.cgi/ensembl-nci/?cvsroot=Ensembl

(that's the link, verbatim, go click it bestie) 🔗

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🫶 FEEDBACK 🫶

💌 Mailing Lists 💌

User feedback is 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, they want to hear from you.

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. (yes the typo "reponsive" is theirs, we keep it, no edits 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:

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

ngl, filing a bug report is main character energy. do it. 🔥

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👑 AUTHOR - Shawn Hoon 👑

Email shawnh@fugu-sg.org

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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 it starts with an underscore, that's a backstage method — iykyk 💀)

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 $obj = Bio::Tools::Run::Primate->new()
Function: Builds a new Bio::Tools::Run::Primate objet
Returns : Bio::Tools::Run::Primate
Args    : query => the L<Bio::PrimarySeqI> object or a file path
          target => the L<Bio::PrimarySeqI> object or a file path
          m  => the number of mismatches allowed, default 1(integer)
          b  => [TRUE|FALSE] find best match, default FALSE
          executable=>where the program sits

so the args, one by one, because you deserve clarity ✨

• query — the L<Bio::PrimarySeqI> object or a file path
• target — the L<Bio::PrimarySeqI> object or a file path
• m — the number of mismatches allowed, default 1 (integer)
• b — [TRUE|FALSE] find best match, default FALSE
• executable — where the program sits

version

Title   : version
Usage   : $primate->version
Function: Determine the version number of the program
Returns : float or undef
Args    : none

search

Title   : search
Usage   : DEPRECATED. Use $factory->run() instead
Function: Perform a primate search
Returns : Array of L<Bio::SeqFeature::Generic>
Args    :

DEPRECATED bestie. she's retired. use $factory->run() instead, periodt. 💅

run

Title   : run
Usage   : @feat = $factory->run();
Function: Perform a primate search
Returns : Array of L<Bio::SeqFeature::Generic>
Args    :

this is the one. the moment. the icon. 🔥

_run

Title   :  _run
Usage   : Internal function, not to be called directly
Function: makes actual system call to dba program
Returns : array of L<Bio::SeqFeature::Generic>
Args    : path to query and target file and parameter string

_parse_results

Title   :  _parse_results
Usage   :  Internal function, not to be called directly
Function:  Passes primate output
Returns : array of L<Bio::SeqFeature::Generic>
Args    : the name of the output file

_setinput()

Title   : _setinput
Usage   : Internal function, not to be called directly
Function: Create input files for primate
Returns : name of file containing query and target
Args    : query and target (either a filename or a L<Bio::PrimarySeqI>

_setparams()

Title   : _setparams
Usage   : Internal function, not to be called directly
Function: Create parameter inputs for primate program
Returns : parameter string to be passed to primate
Args    : the param array

_query_seq()

Title   :  _query_seq
Usage   :  Internal function, not to be called directly
Function:  get/set for the query sequence
Returns :  a hash of seq with key the query tag
Args    :  optional

_target_seq()

Title   : _target_seq
Usage   : Internal function, not to be called directly
Function: get/set for the target sequence
Returns : L<Bio::PrimarySeqI>
Args    : optional

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and that's the whole page, bestie, you made it to the end 🎉

every one of those underscore methods is internal — do not call them directly, i am literally begging 🙈

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that's a wrap, angel 💖 this one's from the User Contributed Perl Documentation set, built with perl v5.36.0, dated 2023-01-22, and it lives at Bio::T...rimate(3pm). go run your near exact match finder, you're gonna slay. 🦋✨👑