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

💖 NAME 💖

Bio::Tools::Run::Alignment::Exonerate — it's the wrapper bestie for the exonerate alignment program. That's the whole vibe. 👑

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✨ SYNOPSIS ✨

okay so this is literally how you use it, no cap:

use Bio::Tools::Run::Alignment::Exonerate;
use Bio::SeqIO;

my $qio = Bio::SeqIO->new(-file=>$ARGV[0],-format=>'fasta');
my $query = $qio->next_seq();
my $tio = Bio::SeqIO->new(-file=>$ARGV[1],-format=>'fasta');
my $target = $sio->next_seq();

#exonerate parameters can all be passed via arguments parameter.
#parameters passed are not checked for validity

my $run = Bio::Tools::Run::Alignment::Exonerate->
    new(arguments=>'--model est2genome --bestn 10');
my $searchio_obj = $run->run($query,$target);

while(my $result = $searchio->next_result){
  while( my $hit = $result->next_hit ) {
    while( my $hsp = $hit->next_hsp ) {
      print $hsp->start."\t".$hsp->end."\n";
    }
  }
}

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🦋 DESCRIPTION 🦋

So it's a wrapper for the Exonerate alignment program. You can grab exonerate at http://www.ebi.ac.uk/~guy/exonerate/. 🫶

This wrapper is written without parameter checking. Like, it is not doing a vibe check on your args, it just trusts you. All parameters get passed through the arugment parameter that you hand to the constructor. See the SYNOPSIS above, bestie. 👀

Wanna know what exonerate params actually exist? Run exonerate --help for more details. Periodt.

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👑 PROGRAM VERSIONS 👑

The tests have been shown to pass with exonorate versions 2.0 - 2.2. slay.

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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. 🙏

🐛 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/

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🎀 AUTHOR - Shawn Hoon 🎀

Email shawnh-at-stanford.edu

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🌈 APPENDIX 🌈

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ (iykyk, that underscore means stay in your lane 🙈).

⭐ 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::Phrap->new();
• Function — creates a new Phrap factory
• Returns — Bio::Tools::Run::Phrap
• 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

⭐ run

• Title — run()
• Usage — my $feats = $factory->run($seq)
• Function — Runs Phrap
• Returns — An array of Bio::SeqFeature::Generic 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 Phrap
• Returns — An array of Bio::SeqFeature::Generic objects
• Args —

⭐ _writeInput

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

⭐ _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 —

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🫶 that's the whole page bestie, go align something iconic 💅

this masterpiece is brought to you by perl v5.36.0, dated 2023-01-22, and it lives in the Bio::T...onerate(3pm) section of your friendly neighborhood User Contributed Perl Documentation. mwah 💋✨