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

okay bestie, pull up a chair, hydrate, and put your phone on do-not-disturb, because today we're reading Bio::T...:ERPIN(3pm) together and it is a journey 💖 it's the manual page for the Perl wrapper around the ERPIN suite, and i'm gonna walk you through literally every single method, arg, URL and email in here. no skips. no summarising. we eat the whole plate 🍓

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🌸 NAME 🌸

Bio::Tools::Run::ERPIN — a wrapper for local execution of the ERPIN suite of programs. it's giving "middle management for your bioinformatics tools" and honestly? iconic 🫶

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✨ SYNOPSIS ✨

okay so here's the whole vibe in one code block, bestie. read it slow, it slaps:

#run

my @params = (
            trset => 'BL.erpin',
            region => [1, 10],
            # Set up search strategy this way...
            strategy => [ 'umask'   => [1, 2],
                          'umask'   => [1, 2, 3, 4],
                          'umask'   => [1, 2, 3, 4, 5, 6],
                          'nomask',
                          'cutoff'  => [0, 10, 15, 20]
                          ]
            # or use a simple string...
            #strategy => '-umask 4 -add 5 -nomask -cutoff 0 10 15',
            pcw => 100
           );

my $factory = Bio::Tools::Run::ERPIN->new(-program =>'erpin',
                                              @params);

# Pass the factory a Bio::Seq object or a file name
# Returns a Bio::SearchIO object

#my $search = $factory->run("B_sub.fas");
my $search = $factory->run($seq);
my @feat;
while (my $result = $searchio->next_result){
 while(my $hit = $result->next_hit){
  while (my $hsp = $hit->next_hsp){
          print join("\t", ( $r->query_name,
                             $hit->name,
                             $hsp->hit->start,
                             $hsp->hit->end,
                             $hsp->meta,
                             $hsp->score,
                             )), "\n";
  }
 }
}

so you build your @params, you spin up a Bio::Tools::Run::ERPIN->new(...) factory with -program =>'erpin', you hand it either a Bio::Seq object or a file name, and it hands you back a Bio::SearchIO object that you can loop over. and then you nest three whiles deep because that's just the life we chose 💅

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🌈 DESCRIPTION 🌈

bestie. it's empty. there is literally nothing here. the heading said "we're gonna describe it" and then it said nothing. main character silence. i respect it, honestly 🙈

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💌 FEEDBACK 💌

📬 Mailing Lists

user feedback is an integral part of the evolution of this module and all the other Bioperl modules, so like… say something, babe, they want to hear it 💜 send your comments and suggestions preferably to one of the Bioperl mailing lists. your participation is much appreciated and that's not just a polite line, they mean it.

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

🫶 Support

okay so if you have a usage question or a support issue, please direct it to the mailing list:

bioperl-l@bioperl.org

and not straight to the module maintainer. there are tons of experienced and responsive experts on there who can look at your problem and address it quickly, which is genuinely the dream 🌸

please include a thorough description of the problem along with code and data examples if at all possible. help them help you, bestie 🫶

🐛 Reporting Bugs

found a bug? report it to the Bioperl bug tracking system so they can keep track of the bugs and their resolution — closed loop, very organised, we love that for them. bug reports can be submitted via the web:

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

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👑 AUTHOR - Chris Fields 👑

Email: cjfields-at-uiuc-dot-edu

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💜 CONTRIBUTORS 💜

cjfields-at-uiuc-dot-edu

(the contributor list is one person and that person is also the author. solo run. main character energy. no notes ✨)

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📖 APPENDIX 📖

the rest of the documentation details each of the object methods, and heads up — internal methods are usually preceded with a _, so if you see an underscore just know that's the private lore iykyk 🔥

🎀 new

• Title: new
• Usage: my $wrapper = Bio::Tools::Run::RNAMotif->new(@params)
• Function: creates a new RNAMotif factory
• Returns: Bio::Tools::Run::RNAMotif
• Args: list of parameters
  • -tempfile => set tempfile flag (default 0)
  • -outfile_name => set file to send output to (default none)

not me reading "RNAMotif" in an ERPIN page 💀 i am simply the messenger, i do not edit the lore, the lore edits me

🎀 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: $v = $prog->version();
• Function: Determine the version number of the program
• Example:
• Returns: float or undef
• Args: none

🎀 run

• Title: run
• Usage: $obj->run($seqFile)
• Function: Runs ERPIN programs and returns Bio::SearchIO
• Returns:
• Args: Must pass Bio::PrimarySeqI's or file names

🎀 tempfile

• Title: tempfile
• Usage: $obj->tempfile(1)
• Function: Set tempfile flag. When set, writes output to a tempfile; this is overridden by outfile_name() if set
• Returns: Boolean setting (or undef if not set)
• Args: [OPTIONAL] Boolean

so like… if you set outfile_name(), that one wins. the tempfile is getting benched. know your power dynamics 💅

🎀 _run

• Title: _run
• Usage: $obj->_run()
• Function: Internal(not to be used directly)
• Returns:
• Args:

🎀 _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:

🎀 _writeSeqFile

• Title: _writeSeqFile
• Usage: obj->_writeSeqFile($seq)
• Function: Internal(not to be used directly)
• Returns: writes passed Seq objects to tempfile, to be used as input for program
• Args:

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and that's the whole page, bestie, you made it to the end and i'm so proud of you 🦋 this was perl v5.36.0, dated 2023-01-22, and it lives under the name Bio::T...:ERPIN(3pm) — go forth, run your ERPIN programs, and remember: internal methods are internal, don't touch the _ ones, that's the rules 💖✨🎀